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Array-feature-overlap-05.html
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Array-feature-overlap-05.html
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<!DOCTYPE html>
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<title>Array-feature-overlap-05</title>
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</div></div></div><div class="cell text_cell rendered unselected" tabindex="2"><div class="prompt input_prompt"></div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-default CodeMirror-wrap"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 5.59375px; left: 5.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="bottom: 0px; min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true" style=""><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; padding-right: 0px; padding-bottom: 0px; margin-bottom: 0px; border-right-width: 30px; min-height: 45px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors"><div class="CodeMirror-cursor" style="left: 0px; top: 0px; height: 16.5px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;">Based on notebook 04 - but separating out to see if there is difference between hypo and hyper methylated.</span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 45px;"></div><div class="CodeMirror-gutters" style="display: none; height: 75px;"></div></div></div></div><div class="text_cell_render rendered_html" tabindex="-1"><p>Based on notebook 04 - but separating out to see if there is difference between hypo and hyper methylated.</p>
</div></div></div><div class="cell text_cell rendered unselected" tabindex="2"><div class="prompt input_prompt"></div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-default CodeMirror-wrap"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 5.59375px; left: 5.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="bottom: 0px; min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true" style=""><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; padding-right: 0px; padding-bottom: 0px; margin-bottom: 0px; border-right-width: 30px; min-height: 62px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors"><div class="CodeMirror-cursor" style="left: 0px; top: 0px; height: 16.5px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-tag cm-bracket"><</span><span class="cm-tag">img</span> <span class="cm-attribute">src</span>=<span class="cm-string">"</span><span class="cm-string cm-link">http://eagle.fish.washington.edu/cnidarian/skitch/half-shell___Lab_notebook_of_Steven_Roberts_1ACECD10.png</span><span class="cm-string">"</span> <span class="cm-attribute">alt</span>=<span class="cm-string">"half-shell___Lab_notebook_of_Steven_Roberts_1ACECD10.png"</span><span class="cm-tag cm-bracket">/></span></span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 62px;"></div><div class="CodeMirror-gutters" style="display: none; height: 92px;"></div></div></div></div><div class="text_cell_render rendered_html" tabindex="-1"><p><img src="./Array-feature-overlap-05_files/half-shell___Lab_notebook_of_Steven_Roberts_1ACECD10.png" alt="half-shell___Lab_notebook_of_Steven_Roberts_1ACECD10.png"></p>
</div></div></div><div class="cell code_cell unselected rendered" tabindex="2"><div class="input"><div class="prompt input_prompt">In [2]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 5.59375px; left: 5.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true" style=""><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 45px; margin-bottom: 0px; border-right-width: 30px; min-height: 28px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"><span><span></span>x</span></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors"><div class="CodeMirror-cursor" style="left: 0px; top: 0px; height: 17px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">date</span></span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 28px;"></div><div class="CodeMirror-gutters" style="display: none; height: 58px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to expand output; double click to hide output" style=""></div><div class="output" style=""><div class="output_area"><div class="prompt"></div><div class="output_subarea output_text output_stream output_stdout"><pre>Fri Apr 3 06:28:54 PDT 2015
</pre></div></div></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell code_cell rendered unselected" tabindex="2"><div class="input"><div class="prompt input_prompt">In [20]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 22.59375px; left: 173.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true" style=""><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 229.828125px; margin-bottom: 0px; border-right-width: 30px; min-height: 45px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors" style="visibility: hidden;"><div class="CodeMirror-cursor" style="left: 168px; top: 17px; height: 17px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">%</span><span class="cm-variable">pylab</span> <span class="cm-variable">inline</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-keyword">import</span> <span class="cm-variable">scipy</span>.<span class="cm-variable">stats</span> <span class="cm-keyword">as</span> <span class="cm-variable">stats</span></span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 45px;"></div><div class="CodeMirror-gutters" style="display: none; height: 75px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to scroll output; double click to hide" style=""></div><div class="output" style=""><div class="output_area"><div class="prompt"></div><div class="output_subarea output_text output_stream output_stdout"><pre>Populating the interactive namespace from numpy and matplotlib
</pre></div></div></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell text_cell rendered unselected" tabindex="2"><div class="prompt input_prompt"></div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-default CodeMirror-wrap"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 5.59375px; left: 5.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="bottom: 0px; min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true" style=""><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; padding-right: 0px; padding-bottom: 0px; margin-bottom: 0px; border-right-width: 30px; min-height: 232px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors"><div class="CodeMirror-cursor" style="left: 0px; top: 0px; height: 17px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;">Feature (from nb -03)<span class="cm-trailing-space-a"> </span><span class="cm-trailing-space-b"> </span><span class="cm-trailing-space-a"> </span><span class="cm-trailing-space-new-line"> </span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span></span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-strong">**tldr**</span> 4 "new" tracks</span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-tag cm-bracket"><</span><span class="cm-tag">img</span> <span class="cm-attribute">src</span>=<span class="cm-string">"</span><span class="cm-string cm-link">http://eagle.fish.washington.edu/cnidarian/skitch/IGV_and_Directory_Listing_of__halfshell_2015-02-hs-bedgraph__1AA51F1B.png</span><span class="cm-string">"</span> <span class="cm-attribute">width</span> =<span class="cm-string">100%</span> <span class="cm-attribute">alt</span>=<span class="cm-string">"IGV_and_Directory_Listing_of__halfshell_2015-02-hs-bedgraph__1AA51F1B.png"</span><span class="cm-tag cm-bracket">/></span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-comment">```</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-comment">/Users/sr320/data-genomic/tentacle/Cuffdiff_geneexp.sig.gtf</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-comment">/Users/sr320/data-genomic/tentacle/rebuilt.gtf</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-comment">/Users/sr320/data-genomic/tentacle/Cgigas_v9_gene-housekeeping.gff</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-comment">/Users/sr320/data-genomic/tentacle/Cgigas_v9_gene-env-response.gff</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-comment">```</span></span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 232px;"></div><div class="CodeMirror-gutters" style="display: none; height: 262px;"></div></div></div></div><div class="text_cell_render rendered_html" tabindex="-1"><p>Feature (from nb -03) </p>
<p><strong>tldr</strong> 4 "new" tracks
<img src="./Array-feature-overlap-05_files/IGV_and_Directory_Listing_of__halfshell_2015-02-hs-bedgraph__1AA51F1B.png" width="100%" alt="IGV_and_Directory_Listing_of__halfshell_2015-02-hs-bedgraph__1AA51F1B.png"></p>
<pre><code>/Users/sr320/data-genomic/tentacle/Cuffdiff_geneexp.sig.gtf
/Users/sr320/data-genomic/tentacle/rebuilt.gtf
/Users/sr320/data-genomic/tentacle/Cgigas_v9_gene-housekeeping.gff
/Users/sr320/data-genomic/tentacle/Cgigas_v9_gene-env-response.gff
</code></pre></div></div></div><div class="cell text_cell unselected rendered" tabindex="2"><div class="prompt input_prompt"></div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-default CodeMirror-wrap"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 5.59375px; left: 5.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="bottom: 0px; min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true" style=""><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; padding-right: 0px; padding-bottom: 0px; margin-bottom: 0px; border-right-width: 30px; min-height: 34px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors"><div class="CodeMirror-cursor" style="left: 0px; top: 0px; height: 23px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-header cm-header-1"># DEGs</span></span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 34px;"></div><div class="CodeMirror-gutters" style="display: none; height: 64px;"></div></div></div></div><div class="text_cell_render rendered_html" tabindex="-1"><h1 id="DEGs">DEGs<a class="anchor-link" href="http://localhost:8888/notebooks/ipynb/Array-feature-overlap-05.ipynb#DEGs">¶</a></h1>
</div></div></div><div class="cell text_cell rendered unselected" tabindex="2"><div class="prompt input_prompt"></div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-default CodeMirror-wrap"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 5.59375px; left: 5.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="bottom: 0px; min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true" style=""><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; padding-right: 0px; padding-bottom: 0px; margin-bottom: 0px; border-right-width: 30px; min-height: 45px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors"><div class="CodeMirror-cursor" style="left: 0px; top: 0px; height: 16.5px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-comment">`-wb<span class="cm-tab"> </span>Write the original entry in B for each overlap. Useful for knowing what A overlaps. Restricted by -f and -r.`</span></span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 45px;"></div><div class="CodeMirror-gutters" style="display: none; height: 75px;"></div></div></div></div><div class="text_cell_render rendered_html" tabindex="-1"><p><code>-wb Write the original entry in B for each overlap. Useful for knowing what A overlaps. Restricted by -f and -r.</code></p>
</div></div></div><div class="cell text_cell rendered unselected" tabindex="2"><div class="prompt input_prompt"></div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-default CodeMirror-wrap"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 22.59375px; left: 5.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true" style=""><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 30px; min-height: 96px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors"><div class="CodeMirror-cursor" style="left: 0px; top: 17px; height: 17px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;">tldr</span></pre><pre class=""><span style="padding-right: 0.1px;"><span></span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-tag cm-bracket"><</span><span class="cm-tag">img</span> <span class="cm-attribute">src</span>=<span class="cm-string">"</span><span class="cm-string cm-link">http://eagle.fish.washington.edu/cnidarian/skitch/Screenshot_4_3_15__7_22_AM_1ACED994.png</span><span class="cm-string">"</span> <span class="cm-attribute">alt</span>=<span class="cm-string">"Screenshot_4_3_15__7_22_AM_1ACED994.png"</span><span class="cm-tag cm-bracket">/></span></span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 96px;"></div><div class="CodeMirror-gutters" style="display: none; height: 126px;"></div></div></div></div><div class="text_cell_render rendered_html" tabindex="-1"><p>tldr</p>
<p><img src="./Array-feature-overlap-05_files/Screenshot_4_3_15__7_22_AM_1ACED994.png" alt="Screenshot_4_3_15__7_22_AM_1ACED994.png"></p>
</div></div></div><div class="cell text_cell rendered unselected" tabindex="2"><div class="prompt input_prompt"></div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-default CodeMirror-wrap"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 5.59375px; left: 36.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true" style=""><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 30px; min-height: 32px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors"><div class="CodeMirror-cursor" style="left: 31px; top: 0px; height: 21px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-header cm-header-2">## Separating HYPO and HYPER</span></span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 32px;"></div><div class="CodeMirror-gutters" style="display: none; height: 62px;"></div></div></div></div><div class="text_cell_render rendered_html" tabindex="-1"><h2 id="Separating-HYPO-and-HYPER">Separating HYPO and HYPER<a class="anchor-link" href="http://localhost:8888/notebooks/ipynb/Array-feature-overlap-05.ipynb#Separating-HYPO-and-HYPER">¶</a></h2>
</div></div></div><div class="cell code_cell rendered unselected" tabindex="2"><div class="input"><div class="prompt input_prompt">In [1]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 5.59375px; left: 778.515625px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true" style=""><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 775.921875px; margin-bottom: 0px; border-right-width: 30px; min-height: 28px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre>x</pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"><div class="CodeMirror-selected" style="position: absolute; left: 50.408203125px; top: 0px; width: 722.513671875px; height: 17px;"></div></div><div class="CodeMirror-cursors"></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">head</span> <span class="cm-error">.</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02</span>.<span class="cm-variable">colson</span><span class="cm-operator">/</span><span class="cm-variable">genomeBrowserTracks</span><span class="cm-operator">/</span><span class="cm-variable">logFC_HS</span><span class="cm-operator">-</span><span class="cm-variable">preHS</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02.2</span><span class="cm-variable">M_sig</span>.<span class="cm-variable">bedGraph</span></span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 28px;"></div><div class="CodeMirror-gutters" style="display: none; height: 58px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to expand output; double click to hide output" style=""></div><div class="output" style=""><div class="output_area"><div class="prompt"></div><div class="output_subarea output_text output_stream output_stdout"><pre>track type=bedGraph name="2M_sig" description="2M_sig" visibility=full color=100,100,0 altColor=0,100,200 priority=20
scaffold1 163391 163444 -1.19635354862016
scaffold1 167390 167448 -1.34858424227208
scaffold1 177036 177092 -1.32513261026528
scaffold1 180263 180313 -1.59644601437398
scaffold1 184151 184202 -1.36802539236446
scaffold1 207852 207911 -1.4489540693628
scaffold1 221645 221697 -1.19168816975966
scaffold100 20261 20311 -1.38705592724581
scaffold100 43707 43766 -1.94554287545546
</pre></div></div></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell code_cell unrendered unselected" tabindex="2"><div class="input"><div class="prompt input_prompt">In [1]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 22.59375px; left: 5.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true" style="right: 0px; left: 0px;"><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1" draggable="false"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 843px; margin-bottom: 0px; border-right-width: 30px; min-height: 62px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre>x</pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"><div class="CodeMirror-selected" style="position: absolute; left: 117.619140625px; top: 0px; width: 887.380859375px; height: 17px;"></div><div class="CodeMirror-selected" style="position: absolute; left: 0px; top: 17px; width: 0px; height: 17px;"></div></div><div class="CodeMirror-cursors" style="visibility: hidden;"></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">fgrep</span> <span class="cm-operator">-</span><span class="cm-variable">c</span> <span class="cm-string">"-"</span> <span class="cm-error">.</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02</span>.<span class="cm-variable">colson</span><span class="cm-operator">/</span><span class="cm-variable">genomeBrowserTracks</span><span class="cm-operator">/</span><span class="cm-variable">logFC_HS</span><span class="cm-operator">-</span><span class="cm-variable">preHS</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02.2</span><span class="cm-variable">M_sig</span>.<span class="cm-variable">bedGraph</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span></span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span></span></span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 62px;"></div><div class="CodeMirror-gutters" style="display: none; height: 92px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to scroll output; double click to hide" style=""></div><div class="output" style=""><div class="output_area"><div class="prompt"></div><div class="output_subarea output_text output_stream output_stdout"><pre>7224
</pre></div></div></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell code_cell rendered unselected" tabindex="2"><div class="input"><div class="prompt input_prompt">In [3]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 5.59375px; left: 820.5263671875px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true" style="right: 0px; left: 0px;"><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 876.734375px; margin-bottom: 0px; border-right-width: 30px; min-height: 28px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre>x</pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"><div class="CodeMirror-selected" style="position: absolute; left: 92.4150390625px; top: 0px; width: 722.5068359375px; height: 17px;"></div></div><div class="CodeMirror-cursors"></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">fgrep</span> <span class="cm-string">"-"</span> <span class="cm-error">.</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02</span>.<span class="cm-variable">colson</span><span class="cm-operator">/</span><span class="cm-variable">genomeBrowserTracks</span><span class="cm-operator">/</span><span class="cm-variable">logFC_HS</span><span class="cm-operator">-</span><span class="cm-variable">preHS</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02.2</span><span class="cm-variable">M_sig</span>.<span class="cm-variable">bedGraph</span> <span class="cm-operator">|</span> <span class="cm-variable">head</span></span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 28px;"></div><div class="CodeMirror-gutters" style="display: none; height: 58px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to scroll output; double click to hide" style=""></div><div class="output" style=""><div class="output_area"><div class="prompt"></div><div class="output_subarea output_text output_stream output_stdout"><pre>scaffold1 163391 163444 -1.19635354862016
scaffold1 167390 167448 -1.34858424227208
scaffold1 177036 177092 -1.32513261026528
scaffold1 180263 180313 -1.59644601437398
scaffold1 184151 184202 -1.36802539236446
scaffold1 207852 207911 -1.4489540693628
scaffold1 221645 221697 -1.19168816975966
scaffold100 20261 20311 -1.38705592724581
scaffold100 43707 43766 -1.94554287545546
scaffold100 46611 46670 -1.2435587162076
</pre></div></div></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell code_cell rendered unselected" tabindex="2"><div class="input"><div class="prompt input_prompt">In [4]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 56.59375px; left: 610.484375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true"><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1" draggable="false"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 742.3203125px; margin-bottom: 0px; border-right-width: 30px; min-height: 79px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre>x</pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"><div class="CodeMirror-selected" style="position: absolute; left: 0px; top: 0px; width: 1005px; height: 17px;"></div><div class="CodeMirror-selected" style="position: absolute; left: 0px; top: 51px; width: 604.890625px; height: 17px;"></div><div class="CodeMirror-selected" style="position: absolute; left: 0px; top: 17px; width: 1005px; height: 34px;"></div></div><div class="CodeMirror-cursors" style="visibility: hidden;"></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">fgrep</span> <span class="cm-string">"-"</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-error">.</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02</span>.<span class="cm-variable">colson</span><span class="cm-operator">/</span><span class="cm-variable">genomeBrowserTracks</span><span class="cm-operator">/</span><span class="cm-variable">logFC_HS</span><span class="cm-operator">-</span><span class="cm-variable">preHS</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02.2</span><span class="cm-variable">M_sig</span>.<span class="cm-variable">bedGraph</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">></span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02.2</span><span class="cm-variable">M_sig</span>.<span class="cm-variable">hypo</span>.<span class="cm-variable">bedGraph</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">head</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02.2</span><span class="cm-variable">M_sig</span>.<span class="cm-variable">hypo</span>.<span class="cm-variable">bedGraph</span></span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 79px;"></div><div class="CodeMirror-gutters" style="display: none; height: 109px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to scroll output; double click to hide" style=""></div><div class="output" style=""><div class="output_area"><div class="prompt"></div><div class="output_subarea output_text output_stream output_stdout"><pre>scaffold1 163391 163444 -1.19635354862016
scaffold1 167390 167448 -1.34858424227208
scaffold1 177036 177092 -1.32513261026528
scaffold1 180263 180313 -1.59644601437398
scaffold1 184151 184202 -1.36802539236446
scaffold1 207852 207911 -1.4489540693628
scaffold1 221645 221697 -1.19168816975966
scaffold100 20261 20311 -1.38705592724581
scaffold100 43707 43766 -1.94554287545546
scaffold100 46611 46670 -1.2435587162076
</pre></div></div></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell code_cell rendered unselected" tabindex="2"><div class="input"><div class="prompt input_prompt">In [6]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 5.59375px; left: 106.41015625px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true"><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 742.3203125px; margin-bottom: 0px; border-right-width: 30px; min-height: 79px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors" style="visibility: hidden;"><div class="CodeMirror-cursor" style="left: 100.81640625px; top: 0px; height: 17px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">fgrep</span> <span class="cm-string">"-"</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-error">.</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02</span>.<span class="cm-variable">colson</span><span class="cm-operator">/</span><span class="cm-variable">genomeBrowserTracks</span><span class="cm-operator">/</span><span class="cm-variable">logFC_HS</span><span class="cm-operator">-</span><span class="cm-variable">preHS</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02.4</span><span class="cm-variable">M_sig</span>.<span class="cm-variable">bedGraph</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">></span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02.4</span><span class="cm-variable">M_sig</span>.<span class="cm-variable">hypo</span>.<span class="cm-variable">bedGraph</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">head</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02.4</span><span class="cm-variable">M_sig</span>.<span class="cm-variable">hypo</span>.<span class="cm-variable">bedGraph</span></span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 79px;"></div><div class="CodeMirror-gutters" style="display: none; height: 109px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to scroll output; double click to hide" style=""></div><div class="output" style=""><div class="output_area"><div class="prompt"></div><div class="output_subarea output_text output_stream output_stdout"><pre>scaffold1 55723 55780 -1.14983078196614
scaffold1 165162 165215 -1.24601772855566
scaffold1 171392 171453 -1.22260744814979
scaffold1 174287 174343 -1.69319890151177
scaffold1 176273 176334 -1.72785163633438
scaffold1 183256 183318 -1.30551922539134
scaffold1 184661 184715 -1.4004518443988
scaffold1 214736 214786 -1.21921626270337
scaffold1 215096 215156 -1.24410534350034
scaffold1 218534 218584 -1.13230161854171
</pre></div></div></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell code_cell rendered unselected" tabindex="2"><div class="input"><div class="prompt input_prompt">In [7]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 56.59375px; left: 610.484375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true"><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 742.3203125px; margin-bottom: 0px; border-right-width: 30px; min-height: 79px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors" style="visibility: hidden;"><div class="CodeMirror-cursor" style="left: 604.890625px; top: 51px; height: 17px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">fgrep</span> <span class="cm-string">"-"</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-error">.</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02</span>.<span class="cm-variable">colson</span><span class="cm-operator">/</span><span class="cm-variable">genomeBrowserTracks</span><span class="cm-operator">/</span><span class="cm-variable">logFC_HS</span><span class="cm-operator">-</span><span class="cm-variable">preHS</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02.6</span><span class="cm-variable">M_sig</span>.<span class="cm-variable">bedGraph</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">></span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02.6</span><span class="cm-variable">M_sig</span>.<span class="cm-variable">hypo</span>.<span class="cm-variable">bedGraph</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">head</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02.6</span><span class="cm-variable">M_sig</span>.<span class="cm-variable">hypo</span>.<span class="cm-variable">bedGraph</span></span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 79px;"></div><div class="CodeMirror-gutters" style="display: none; height: 109px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to scroll output; double click to hide" style=""></div><div class="output" style=""><div class="output_area"><div class="prompt"></div><div class="output_subarea output_text output_stream output_stdout"><pre>scaffold1 54599 54654 -1.38187662416007
scaffold1 163536 163586 -1.15032035523765
scaffold1 174287 174343 -1.62903936976887
scaffold1 184271 184330 -1.20699853451878
scaffold1 184661 184715 -1.61107459826899
scaffold1 185141 185192 -1.19168730137504
scaffold1 210863 210918 -1.74282743323306
scaffold1 215839 215890 -1.34660189199927
scaffold1 224010 224070 -1.29699353038817
scaffold1 227414 227469 -1.17931294986337
</pre></div></div></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell code_cell rendered unselected" tabindex="2"><div class="input"><div class="prompt input_prompt">In [ ]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 5.59375px; left: 5.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true"><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 3px; margin-bottom: 0px; border-right-width: 30px; min-height: 28px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors"><div class="CodeMirror-cursor" style="left: 0px; top: 0px; height: 17px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span></span></span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 28px;"></div><div class="CodeMirror-gutters" style="display: none; height: 58px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to expand output; double click to hide output" style="display: none;"></div><div class="output" style="display: none;"></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell code_cell rendered unselected" tabindex="2"><div class="input"><div class="prompt input_prompt">In [ ]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 5.59375px; left: 5.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true"><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 3px; margin-bottom: 0px; border-right-width: 30px; min-height: 28px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors"><div class="CodeMirror-cursor" style="left: 0px; top: 0px; height: 17px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span></span></span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 28px;"></div><div class="CodeMirror-gutters" style="display: none; height: 58px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to expand output; double click to hide output" style="display: none;"></div><div class="output" style="display: none;"></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell code_cell rendered unselected" tabindex="2"><div class="input"><div class="prompt input_prompt">In [ ]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 5.59375px; left: 5.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true"><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 3px; margin-bottom: 0px; border-right-width: 30px; min-height: 28px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors"><div class="CodeMirror-cursor" style="left: 0px; top: 0px; height: 17px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span></span></span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 28px;"></div><div class="CodeMirror-gutters" style="display: none; height: 58px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to expand output; double click to hide output" style="display: none;"></div><div class="output" style="display: none;"></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell text_cell rendered unselected" tabindex="2"><div class="prompt input_prompt"></div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-default CodeMirror-wrap"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 5.59375px; left: 40.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true" style=""><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 30px; min-height: 31px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors"><div class="CodeMirror-cursor" style="left: 35px; top: 0px; height: 20px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-header cm-header-3">### HYPO</span></span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 31px;"></div><div class="CodeMirror-gutters" style="display: none; height: 61px;"></div></div></div></div><div class="text_cell_render rendered_html" tabindex="-1"><h3 id="HYPO">HYPO<a class="anchor-link" href="http://localhost:8888/notebooks/ipynb/Array-feature-overlap-05.ipynb#HYPO">¶</a></h3>
</div></div></div><div class="cell code_cell rendered unselected" tabindex="2"><div class="input"><div class="prompt input_prompt">In [5]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 5.59375px; left: 5.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true" style=""><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 599.4970703125px; margin-bottom: 0px; border-right-width: 30px; min-height: 113px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre>x</pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"><div class="CodeMirror-selected" style="position: absolute; left: 0px; top: 0px; width: 1005px; height: 17px;"></div><div class="CodeMirror-selected" style="position: absolute; left: 0px; top: 85px; width: 142.8232421875px; height: 17px;"></div><div class="CodeMirror-selected" style="position: absolute; left: 0px; top: 17px; width: 1005px; height: 68px;"></div></div><div class="CodeMirror-cursors" style="visibility: hidden;"></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">intersectbed</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">wb</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">a</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02.2</span><span class="cm-variable">M_sig</span>.<span class="cm-variable">hypo</span>.<span class="cm-variable">bedGraph</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">b</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-variable">Cuffdiff_geneexp</span>.<span class="cm-variable">sig</span>.<span class="cm-variable">gtf</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">cut</span> <span class="cm-operator">-</span><span class="cm-variable">f</span> <span class="cm-number">6</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">sort</span> <span class="cm-operator">|</span> <span class="cm-variable">uniq</span> <span class="cm-operator">-</span><span class="cm-variable">c</span> </span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 113px;"></div><div class="CodeMirror-gutters" style="display: none; height: 143px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to scroll output; double click to hide" style=""></div><div class="output" style=""><div class="output_area"><div class="prompt"></div><div class="output_subarea output_text output_stream output_stdout"><pre> 726 Cufflinks
</pre></div></div></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell code_cell rendered unselected" tabindex="2"><div class="input"><div class="prompt input_prompt">In [9]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 39.59375px; left: 316.4443359375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true" style="right: 0px; left: 0px;"><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 599.4970703125px; margin-bottom: 0px; border-right-width: 30px; min-height: 113px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre>x</pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors" style=""><div class="CodeMirror-cursor" style="left: 310.8505859375px; top: 34px; height: 17px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">intersectbed</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">wb</span> <span class="cm-error">\</span></span></pre><pre><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">a</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02.4</span><span class="cm-variable">M_sig</span>.<span class="cm-variable">hypo</span>.<span class="cm-variable">bedGraph</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">b</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-variable">Cuffdiff_geneexp</span>.<span class="cm-variable">sig</span>.<span class="cm-variable">gtf</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">cut</span> <span class="cm-operator">-</span><span class="cm-variable">f</span> <span class="cm-number">6</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">sort</span> <span class="cm-operator">|</span> <span class="cm-variable">uniq</span> <span class="cm-operator">-</span><span class="cm-variable">c</span> </span></pre><pre class="" style="display: none;"><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">wb</span> <span class="cm-error">\</span></span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 113px;"></div><div class="CodeMirror-gutters" style="display: none; height: 143px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to scroll output; double click to hide" style=""></div><div class="output" style=""><div class="output_area"><div class="prompt"></div><div class="output_subarea output_text output_stream output_stdout"><pre> 426 Cufflinks
</pre></div></div></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell code_cell rendered unselected" tabindex="2"><div class="input"><div class="prompt input_prompt">In [10]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 39.59375px; left: 517.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true" style=""><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 599.4970703125px; margin-bottom: 0px; border-right-width: 30px; min-height: 113px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre>x</pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors" style="visibility: hidden;"><div class="CodeMirror-cursor" style="left: 512px; top: 34px; height: 17px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">intersectbed</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">wb</span> <span class="cm-error">\</span></span></pre><pre><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">a</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02.6</span><span class="cm-variable">M_sig</span>.<span class="cm-variable">hypo</span>.<span class="cm-variable">bedGraph</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">b</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-variable">Cuffdiff_geneexp</span>.<span class="cm-variable">sig</span>.<span class="cm-variable">gtf</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">cut</span> <span class="cm-operator">-</span><span class="cm-variable">f</span> <span class="cm-number">6</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">sort</span> <span class="cm-operator">|</span> <span class="cm-variable">uniq</span> <span class="cm-operator">-</span><span class="cm-variable">c</span> </span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 113px;"></div><div class="CodeMirror-gutters" style="display: none; height: 143px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to scroll output; double click to hide" style=""></div><div class="output" style=""><div class="output_area"><div class="prompt"></div><div class="output_subarea output_text output_stream output_stdout"><pre> 372 Cufflinks
</pre></div></div></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell code_cell rendered unselected" tabindex="2"><div class="input"><div class="prompt input_prompt">In [10]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 5.59375px; left: 5.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true" style="right: 0px; left: 0px;"><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 826.333984375px; margin-bottom: 0px; border-right-width: 30px; min-height: 113px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre>x</pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"><div class="CodeMirror-selected" style="position: absolute; left: 0px; top: 0px; width: 1005px; height: 17px;"></div><div class="CodeMirror-selected" style="position: absolute; left: 0px; top: 85px; width: 142.8232421875px; height: 17px;"></div><div class="CodeMirror-selected" style="position: absolute; left: 0px; top: 17px; width: 1005px; height: 68px;"></div></div><div class="CodeMirror-cursors"></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">intersectbed</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">wb</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">a</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">git</span><span class="cm-operator">-</span><span class="cm-variable">repos</span><span class="cm-operator">/</span><span class="cm-variable">paper</span><span class="cm-operator">-</span><span class="cm-variable">Temp</span><span class="cm-operator">-</span><span class="cm-variable">stress</span><span class="cm-operator">/</span><span class="cm-variable">ipynb</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">/</span><span class="cm-variable">array</span><span class="cm-operator">-</span><span class="cm-variable">design</span><span class="cm-operator">/</span><span class="cm-variable">OID40453_probe_locations</span>.<span class="cm-variable">gff</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">b</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-variable">Cuffdiff_geneexp</span>.<span class="cm-variable">sig</span>.<span class="cm-variable">gtf</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">cut</span> <span class="cm-operator">-</span><span class="cm-variable">f</span> <span class="cm-number">11</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">sort</span> <span class="cm-operator">|</span> <span class="cm-variable">uniq</span> <span class="cm-operator">-</span><span class="cm-variable">c</span> </span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 113px;"></div><div class="CodeMirror-gutters" style="display: none; height: 143px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to expand output; double click to hide output" style=""></div><div class="output" style=""><div class="output_area"><div class="prompt"></div><div class="output_subarea output_text output_stream output_stdout"><pre>117460 Cufflinks
</pre></div></div></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell code_cell unrendered unselected" tabindex="2"><div class="input"><div class="prompt input_prompt">In [21]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 175.59375px; left: 954.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true" style="right: 0px; left: 0px;"><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 952px; margin-bottom: 0px; border-right-width: 30px; min-height: 198px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre>x</pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"><div class="CodeMirror-selected" style="position: absolute; left: 0px; top: 0px; width: 1005px; height: 17px;"></div><div class="CodeMirror-selected" style="position: absolute; left: 0px; top: 170px; width: 949px; height: 17px;"></div><div class="CodeMirror-selected" style="position: absolute; left: 0px; top: 17px; width: 1005px; height: 153px;"></div></div><div class="CodeMirror-cursors"></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-comment"># Enter the data comparing Oyster 2 then Probes</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-variable">obs</span> = <span class="cm-variable">array</span>([[<span class="cm-number">726</span>, <span class="cm-number">7224</span>], [<span class="cm-number">117460</span>, <span class="cm-number">697753</span>]])</span></pre><pre class=""><span style="padding-right: 0.1px;"><span></span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-comment"># Calculate the chi-square test</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-variable">chi2_corrected</span> = <span class="cm-variable">stats</span>.<span class="cm-variable">chi2_contingency</span>(<span class="cm-variable">obs</span>, <span class="cm-variable">correction</span>=<span class="cm-builtin">True</span>)</span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-variable">chi2_uncorrected</span> = <span class="cm-variable">stats</span>.<span class="cm-variable">chi2_contingency</span>(<span class="cm-variable">obs</span>, <span class="cm-variable">correction</span>=<span class="cm-builtin">False</span>)</span></pre><pre class=""><span style="padding-right: 0.1px;"><span></span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-comment"># Print the result</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-keyword">print</span>(<span class="cm-string">'CHI SQUARE'</span>)</span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-keyword">print</span>(<span class="cm-string">'The corrected chi2 value is {0:5.3f}, with p={1:5.3f}'</span>.<span class="cm-builtin">format</span>(<span class="cm-variable">chi2_corrected</span>[<span class="cm-number">0</span>], <span class="cm-variable">chi2_corrected</span>[<span class="cm-number">1</span>]))</span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-keyword">print</span>(<span class="cm-string">'The uncorrected chi2 value is {0:5.3f}, with p={1:5.3f}'</span>.<span class="cm-builtin">format</span>(<span class="cm-variable">chi2_uncorrected</span>[<span class="cm-number">0</span>], <span class="cm-variable">chi2_uncorrected</span>[<span class="cm-number">1</span>]))</span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 198px;"></div><div class="CodeMirror-gutters" style="display: none; height: 228px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to scroll output; double click to hide" style=""></div><div class="output" style=""><div class="output_area"><div class="prompt"></div><div class="output_subarea output_text output_stream output_stdout"><pre>CHI SQUARE
The corrected chi2 value is 177.835, with p=0.000
The uncorrected chi2 value is 178.264, with p=0.000
</pre></div></div></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell code_cell rendered unselected" tabindex="2"><div class="input"><div class="prompt input_prompt">In [22]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 22.59375px; left: 198.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true" style="right: 0px; left: 0px;"><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 952px; margin-bottom: 0px; border-right-width: 30px; min-height: 198px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre>x</pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors"><div class="CodeMirror-cursor" style="left: 193px; top: 17px; height: 17px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-comment"># Enter the data comparing Oyster 4 then Probes</span></span></pre><pre><span style="padding-right: 0.1px;"><span class="cm-variable">obs</span> = <span class="cm-variable">array</span>([[<span class="cm-number">426</span>, <span class="cm-number">6560</span>], [<span class="cm-number">117460</span>, <span class="cm-number">697753</span>]])</span></pre><pre class=""><span style="padding-right: 0.1px;"><span></span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-comment"># Calculate the chi-square test</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-variable">chi2_corrected</span> = <span class="cm-variable">stats</span>.<span class="cm-variable">chi2_contingency</span>(<span class="cm-variable">obs</span>, <span class="cm-variable">correction</span>=<span class="cm-builtin">True</span>)</span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-variable">chi2_uncorrected</span> = <span class="cm-variable">stats</span>.<span class="cm-variable">chi2_contingency</span>(<span class="cm-variable">obs</span>, <span class="cm-variable">correction</span>=<span class="cm-builtin">False</span>)</span></pre><pre class=""><span style="padding-right: 0.1px;"><span></span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-comment"># Print the result</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-keyword">print</span>(<span class="cm-string">'CHI SQUARE'</span>)</span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-keyword">print</span>(<span class="cm-string">'The corrected chi2 value is {0:5.3f}, with p={1:5.3f}'</span>.<span class="cm-builtin">format</span>(<span class="cm-variable">chi2_corrected</span>[<span class="cm-number">0</span>], <span class="cm-variable">chi2_corrected</span>[<span class="cm-number">1</span>]))</span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-keyword">print</span>(<span class="cm-string">'The uncorrected chi2 value is {0:5.3f}, with p={1:5.3f}'</span>.<span class="cm-builtin">format</span>(<span class="cm-variable">chi2_uncorrected</span>[<span class="cm-number">0</span>], <span class="cm-variable">chi2_uncorrected</span>[<span class="cm-number">1</span>]))</span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 198px;"></div><div class="CodeMirror-gutters" style="display: none; height: 228px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to scroll output; double click to hide" style=""></div><div class="output" style=""><div class="output_area"><div class="prompt"></div><div class="output_subarea output_text output_stream output_stdout"><pre>CHI SQUARE
The corrected chi2 value is 388.828, with p=0.000
The uncorrected chi2 value is 389.505, with p=0.000
</pre></div></div></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell code_cell rendered unselected" tabindex="2"><div class="input"><div class="prompt input_prompt">In [23]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 22.59375px; left: 198.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true" style="right: 0px; left: 0px;"><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 952px; margin-bottom: 0px; border-right-width: 30px; min-height: 198px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre>x</pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors"><div class="CodeMirror-cursor" style="left: 193px; top: 17px; height: 17px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-comment"># Enter the data comparing Oyster 6 then Probes</span></span></pre><pre><span style="padding-right: 0.1px;"><span class="cm-variable">obs</span> = <span class="cm-variable">array</span>([[<span class="cm-number">372</span>, <span class="cm-number">7645</span>], [<span class="cm-number">117460</span>, <span class="cm-number">697753</span>]])</span></pre><pre class=""><span style="padding-right: 0.1px;"><span></span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-comment"># Calculate the chi-square test</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-variable">chi2_corrected</span> = <span class="cm-variable">stats</span>.<span class="cm-variable">chi2_contingency</span>(<span class="cm-variable">obs</span>, <span class="cm-variable">correction</span>=<span class="cm-builtin">True</span>)</span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-variable">chi2_uncorrected</span> = <span class="cm-variable">stats</span>.<span class="cm-variable">chi2_contingency</span>(<span class="cm-variable">obs</span>, <span class="cm-variable">correction</span>=<span class="cm-builtin">False</span>)</span></pre><pre class=""><span style="padding-right: 0.1px;"><span></span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-comment"># Print the result</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-keyword">print</span>(<span class="cm-string">'CHI SQUARE'</span>)</span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-keyword">print</span>(<span class="cm-string">'The corrected chi2 value is {0:5.3f}, with p={1:5.3f}'</span>.<span class="cm-builtin">format</span>(<span class="cm-variable">chi2_corrected</span>[<span class="cm-number">0</span>], <span class="cm-variable">chi2_corrected</span>[<span class="cm-number">1</span>]))</span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-keyword">print</span>(<span class="cm-string">'The uncorrected chi2 value is {0:5.3f}, with p={1:5.3f}'</span>.<span class="cm-builtin">format</span>(<span class="cm-variable">chi2_uncorrected</span>[<span class="cm-number">0</span>], <span class="cm-variable">chi2_uncorrected</span>[<span class="cm-number">1</span>]))</span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 198px;"></div><div class="CodeMirror-gutters" style="display: none; height: 228px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to scroll output; double click to hide" style=""></div><div class="output" style=""><div class="output_area"><div class="prompt"></div><div class="output_subarea output_text output_stream output_stdout"><pre>CHI SQUARE
The corrected chi2 value is 616.865, with p=0.000
The uncorrected chi2 value is 617.661, with p=0.000
</pre></div></div></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell text_cell rendered unselected" tabindex="2"><div class="prompt input_prompt"></div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-default CodeMirror-wrap"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 5.59375px; left: 111.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true" style=""><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 30px; min-height: 32px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors"><div class="CodeMirror-cursor" style="left: 106px; top: 0px; height: 21px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-header cm-header-2">## HYPER</span></span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 32px;"></div><div class="CodeMirror-gutters" style="display: none; height: 62px;"></div></div></div></div><div class="text_cell_render rendered_html" tabindex="-1"><h2 id="HYPER">HYPER<a class="anchor-link" href="http://localhost:8888/notebooks/ipynb/Array-feature-overlap-05.ipynb#HYPER">¶</a></h2>
</div></div></div><div class="cell code_cell rendered unselected" tabindex="2"><div class="input"><div class="prompt input_prompt">In [13]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 73.59375px; left: 627.28125px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true"><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1" draggable="false"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 742.3203125px; margin-bottom: 0px; border-right-width: 30px; min-height: 96px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre>x</pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"><div class="CodeMirror-selected" style="position: absolute; left: 0px; top: 68px; width: 621.6875px; height: 17px;"></div></div><div class="CodeMirror-cursors"></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">fgrep</span> <span class="cm-operator">-</span><span class="cm-variable">v</span> <span class="cm-string">"-"</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-error">.</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02</span>.<span class="cm-variable">colson</span><span class="cm-operator">/</span><span class="cm-variable">genomeBrowserTracks</span><span class="cm-operator">/</span><span class="cm-variable">logFC_HS</span><span class="cm-operator">-</span><span class="cm-variable">preHS</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02.2</span><span class="cm-variable">M_sig</span>.<span class="cm-variable">bedGraph</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">></span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02.2</span><span class="cm-variable">M_sig</span>.<span class="cm-variable">hyper</span>.<span class="cm-variable">bedGraph</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">head</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02.2</span><span class="cm-variable">M_sig</span>.<span class="cm-variable">hyper</span>.<span class="cm-variable">bedGraph</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">wc</span> <span class="cm-operator">-</span><span class="cm-variable">l</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02.2</span><span class="cm-variable">M_sig</span>.<span class="cm-variable">hyper</span>.<span class="cm-variable">bedGraph</span></span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 96px;"></div><div class="CodeMirror-gutters" style="display: none; height: 126px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to scroll output; double click to hide" style=""></div><div class="output" style=""><div class="output_area"><div class="prompt"></div><div class="output_subarea output_text output_stream output_stdout"><pre>track type=bedGraph name="2M_sig" description="2M_sig" visibility=full color=100,100,0 altColor=0,100,200 priority=20
scaffold100 250533 250586 1.72713841645018
scaffold100 362779 362836 1.24792813025432
scaffold100 437627 437684 1.26968497656438
scaffold100 439363 439415 1.8535900440036
scaffold100 458442 458498 1.33779652899652
scaffold100 636974 637034 1.47573175617257
scaffold100 637084 637143 1.24656795811596
scaffold100 642110 642170 1.32784939242625
scaffold100 676066 676117 2.0744756115782
2804 /Users/sr320/data-genomic/tentacle/2014.07.02.2M_sig.hyper.bedGraph
</pre></div></div></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell code_cell rendered unselected" tabindex="2"><div class="input"><div class="prompt input_prompt">In [12]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 73.59375px; left: 459.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true"><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 742.3203125px; margin-bottom: 0px; border-right-width: 30px; min-height: 96px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors" style="visibility: hidden;"><div class="CodeMirror-cursor" style="left: 454px; top: 68px; height: 17px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">fgrep</span> <span class="cm-operator">-</span><span class="cm-variable">v</span> <span class="cm-string">"-"</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-error">.</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02</span>.<span class="cm-variable">colson</span><span class="cm-operator">/</span><span class="cm-variable">genomeBrowserTracks</span><span class="cm-operator">/</span><span class="cm-variable">logFC_HS</span><span class="cm-operator">-</span><span class="cm-variable">preHS</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02.4</span><span class="cm-variable">M_sig</span>.<span class="cm-variable">bedGraph</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">></span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02.4</span><span class="cm-variable">M_sig</span>.<span class="cm-variable">hyper</span>.<span class="cm-variable">bedGraph</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">head</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02.4</span><span class="cm-variable">M_sig</span>.<span class="cm-variable">hyper</span>.<span class="cm-variable">bedGraph</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">wc</span> <span class="cm-operator">-</span><span class="cm-variable">l</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02.4</span><span class="cm-variable">M_sig</span>.<span class="cm-variable">hyper</span>.<span class="cm-variable">bedGraph</span></span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 96px;"></div><div class="CodeMirror-gutters" style="display: none; height: 126px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to scroll output; double click to hide" style=""></div><div class="output" style=""><div class="output_area"><div class="prompt"></div><div class="output_subarea output_text output_stream output_stdout"><pre>track type=bedGraph name="4M_sig" description="4M_sig" visibility=full color=100,100,0 altColor=0,100,200 priority=20
scaffold1 162896 162952 1.31051906307266
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scaffold1 178210 178267 1.2199265031441
scaffold1 208737 208792 1.31462945133609
scaffold100 91713 91767 1.16773934117713
scaffold100 250282 250335 1.35652322667099
scaffold100 300103 300158 1.23146709929105
scaffold100 303374 303434 1.44751323196346
scaffold100 306375 306430 1.14267878234681
3588 /Users/sr320/data-genomic/tentacle/2014.07.02.4M_sig.hyper.bedGraph
</pre></div></div></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell code_cell rendered unselected" tabindex="2"><div class="input"><div class="prompt input_prompt">In [14]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 56.59375px; left: 232.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true"><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 742.3203125px; margin-bottom: 0px; border-right-width: 30px; min-height: 96px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors" style="visibility: hidden;"><div class="CodeMirror-cursor" style="left: 227px; top: 51px; height: 17px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">fgrep</span> <span class="cm-operator">-</span><span class="cm-variable">v</span> <span class="cm-string">"-"</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-error">.</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02</span>.<span class="cm-variable">colson</span><span class="cm-operator">/</span><span class="cm-variable">genomeBrowserTracks</span><span class="cm-operator">/</span><span class="cm-variable">logFC_HS</span><span class="cm-operator">-</span><span class="cm-variable">preHS</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02.6</span><span class="cm-variable">M_sig</span>.<span class="cm-variable">bedGraph</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">></span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02.6</span><span class="cm-variable">M_sig</span>.<span class="cm-variable">hyper</span>.<span class="cm-variable">bedGraph</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">head</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02.6</span><span class="cm-variable">M_sig</span>.<span class="cm-variable">hyper</span>.<span class="cm-variable">bedGraph</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">wc</span> <span class="cm-operator">-</span><span class="cm-variable">l</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02.6</span><span class="cm-variable">M_sig</span>.<span class="cm-variable">hyper</span>.<span class="cm-variable">bedGraph</span></span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 96px;"></div><div class="CodeMirror-gutters" style="display: none; height: 126px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to scroll output; double click to hide" style=""></div><div class="output" style=""><div class="output_area"><div class="prompt"></div><div class="output_subarea output_text output_stream output_stdout"><pre>track type=bedGraph name="6M_sig" description="6M_sig" visibility=full color=100,100,0 altColor=0,100,200 priority=20
scaffold1 162129 162191 1.85685479189849
scaffold1 172654 172714 1.33561271440876
scaffold1 178075 178128 1.42323539316231
scaffold1 178685 178740 1.30886296151914
scaffold1 214231 214288 1.23355990867606
scaffold1 219034 219092 1.34001786676384
scaffold1 223041 223094 1.32669837521425
scaffold1 230131 230189 1.41307400393928
scaffold100 244541 244592 2.500239239607
4045 /Users/sr320/data-genomic/tentacle/2014.07.02.6M_sig.hyper.bedGraph
</pre></div></div></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell code_cell rendered unselected" tabindex="2"><div class="input"><div class="prompt input_prompt">In [15]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 39.59375px; left: 30.7978515625px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true"><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1" draggable="false"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 607.8984375px; margin-bottom: 0px; border-right-width: 30px; min-height: 113px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre>x</pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"><div class="CodeMirror-selected" style="position: absolute; left: 25.2041015625px; top: 34px; width: 562.7958984375px; height: 17px;"></div></div><div class="CodeMirror-cursors" style="visibility: hidden;"></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">intersectbed</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">wb</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">a</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02.2</span><span class="cm-variable">M_sig</span>.<span class="cm-variable">hyper</span>.<span class="cm-variable">bedGraph</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">b</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-variable">Cuffdiff_geneexp</span>.<span class="cm-variable">sig</span>.<span class="cm-variable">gtf</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">cut</span> <span class="cm-operator">-</span><span class="cm-variable">f</span> <span class="cm-number">6</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">sort</span> <span class="cm-operator">|</span> <span class="cm-variable">uniq</span> <span class="cm-operator">-</span><span class="cm-variable">c</span> </span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 113px;"></div><div class="CodeMirror-gutters" style="display: none; height: 143px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to scroll output; double click to hide" style=""></div><div class="output" style=""><div class="output_area"><div class="prompt"></div><div class="output_subarea output_text output_stream output_stdout"><pre> 154 Cufflinks
</pre></div></div></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell code_cell rendered unselected" tabindex="2"><div class="input"><div class="prompt input_prompt">In [16]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 90.59375px; left: 148.4169921875px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true"><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 607.8984375px; margin-bottom: 0px; border-right-width: 30px; min-height: 113px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors" style="visibility: hidden;"><div class="CodeMirror-cursor" style="left: 142.8232421875px; top: 85px; height: 17px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">intersectbed</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">wb</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">a</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02.4</span><span class="cm-variable">M_sig</span>.<span class="cm-variable">hyper</span>.<span class="cm-variable">bedGraph</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">b</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-variable">Cuffdiff_geneexp</span>.<span class="cm-variable">sig</span>.<span class="cm-variable">gtf</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">cut</span> <span class="cm-operator">-</span><span class="cm-variable">f</span> <span class="cm-number">6</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">sort</span> <span class="cm-operator">|</span> <span class="cm-variable">uniq</span> <span class="cm-operator">-</span><span class="cm-variable">c</span> </span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 113px;"></div><div class="CodeMirror-gutters" style="display: none; height: 143px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to scroll output; double click to hide" style=""></div><div class="output" style=""><div class="output_area"><div class="prompt"></div><div class="output_subarea output_text output_stream output_stdout"><pre> 278 Cufflinks
</pre></div></div></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell code_cell rendered unselected" tabindex="2"><div class="input"><div class="prompt input_prompt">In [17]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 39.59375px; left: 425.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true"><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 607.8984375px; margin-bottom: 0px; border-right-width: 30px; min-height: 113px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors" style="visibility: hidden;"><div class="CodeMirror-cursor" style="left: 420px; top: 34px; height: 17px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">intersectbed</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">wb</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">a</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02.6</span><span class="cm-variable">M_sig</span>.<span class="cm-variable">hyper</span>.<span class="cm-variable">bedGraph</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">b</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-variable">Cuffdiff_geneexp</span>.<span class="cm-variable">sig</span>.<span class="cm-variable">gtf</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">cut</span> <span class="cm-operator">-</span><span class="cm-variable">f</span> <span class="cm-number">6</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">sort</span> <span class="cm-operator">|</span> <span class="cm-variable">uniq</span> <span class="cm-operator">-</span><span class="cm-variable">c</span> </span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 113px;"></div><div class="CodeMirror-gutters" style="display: none; height: 143px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to scroll output; double click to hide" style=""></div><div class="output" style=""><div class="output_area"><div class="prompt"></div><div class="output_subarea output_text output_stream output_stdout"><pre> 260 Cufflinks
</pre></div></div></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell code_cell rendered unselected" tabindex="2"><div class="input"><div class="prompt input_prompt">In [18]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 90.59375px; left: 148.4169921875px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true" style="right: 0px; left: 0px;"><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 826.333984375px; margin-bottom: 0px; border-right-width: 30px; min-height: 113px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors"><div class="CodeMirror-cursor" style="left: 142.8232421875px; top: 85px; height: 17px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">intersectbed</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">wb</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">a</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">git</span><span class="cm-operator">-</span><span class="cm-variable">repos</span><span class="cm-operator">/</span><span class="cm-variable">paper</span><span class="cm-operator">-</span><span class="cm-variable">Temp</span><span class="cm-operator">-</span><span class="cm-variable">stress</span><span class="cm-operator">/</span><span class="cm-variable">ipynb</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">/</span><span class="cm-variable">array</span><span class="cm-operator">-</span><span class="cm-variable">design</span><span class="cm-operator">/</span><span class="cm-variable">OID40453_probe_locations</span>.<span class="cm-variable">gff</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">b</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-variable">Cuffdiff_geneexp</span>.<span class="cm-variable">sig</span>.<span class="cm-variable">gtf</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">cut</span> <span class="cm-operator">-</span><span class="cm-variable">f</span> <span class="cm-number">11</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">sort</span> <span class="cm-operator">|</span> <span class="cm-variable">uniq</span> <span class="cm-operator">-</span><span class="cm-variable">c</span> </span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 113px;"></div><div class="CodeMirror-gutters" style="display: none; height: 143px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to scroll output; double click to hide" style=""></div><div class="output" style=""><div class="output_area"><div class="prompt"></div><div class="output_subarea output_text output_stream output_stdout"><pre>117460 Cufflinks
</pre></div></div></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell code_cell rendered unselected" tabindex="2"><div class="input"><div class="prompt input_prompt">In [24]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 22.59375px; left: 148.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true" style="right: 0px; left: 0px;"><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 952px; margin-bottom: 0px; border-right-width: 30px; min-height: 198px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre>x</pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors"><div class="CodeMirror-cursor" style="left: 143px; top: 17px; height: 17px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-comment"># Enter the data comparing Oyster 2 then Probes</span></span></pre><pre><span style="padding-right: 0.1px;"><span class="cm-variable">obs</span> = <span class="cm-variable">array</span>([[<span class="cm-number">154</span>, <span class="cm-number">2803</span>], [<span class="cm-number">117460</span>, <span class="cm-number">697753</span>]])</span></pre><pre class=""><span style="padding-right: 0.1px;"><span></span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-comment"># Calculate the chi-square test</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-variable">chi2_corrected</span> = <span class="cm-variable">stats</span>.<span class="cm-variable">chi2_contingency</span>(<span class="cm-variable">obs</span>, <span class="cm-variable">correction</span>=<span class="cm-builtin">True</span>)</span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-variable">chi2_uncorrected</span> = <span class="cm-variable">stats</span>.<span class="cm-variable">chi2_contingency</span>(<span class="cm-variable">obs</span>, <span class="cm-variable">correction</span>=<span class="cm-builtin">False</span>)</span></pre><pre class=""><span style="padding-right: 0.1px;"><span></span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-comment"># Print the result</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-keyword">print</span>(<span class="cm-string">'CHI SQUARE'</span>)</span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-keyword">print</span>(<span class="cm-string">'The corrected chi2 value is {0:5.3f}, with p={1:5.3f}'</span>.<span class="cm-builtin">format</span>(<span class="cm-variable">chi2_corrected</span>[<span class="cm-number">0</span>], <span class="cm-variable">chi2_corrected</span>[<span class="cm-number">1</span>]))</span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-keyword">print</span>(<span class="cm-string">'The uncorrected chi2 value is {0:5.3f}, with p={1:5.3f}'</span>.<span class="cm-builtin">format</span>(<span class="cm-variable">chi2_uncorrected</span>[<span class="cm-number">0</span>], <span class="cm-variable">chi2_uncorrected</span>[<span class="cm-number">1</span>]))</span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 198px;"></div><div class="CodeMirror-gutters" style="display: none; height: 228px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to scroll output; double click to hide" style=""></div><div class="output" style=""><div class="output_area"><div class="prompt"></div><div class="output_subarea output_text output_stream output_stdout"><pre>CHI SQUARE
The corrected chi2 value is 201.876, with p=0.000
The uncorrected chi2 value is 202.623, with p=0.000
</pre></div></div></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell code_cell rendered unselected" tabindex="2"><div class="input"><div class="prompt input_prompt">In [25]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 22.59375px; left: 198.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true" style="right: 0px; left: 0px;"><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 952px; margin-bottom: 0px; border-right-width: 30px; min-height: 198px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre>x</pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors"><div class="CodeMirror-cursor" style="left: 193px; top: 17px; height: 17px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-comment"># Enter the data comparing Oyster 2 then Probes</span></span></pre><pre><span style="padding-right: 0.1px;"><span class="cm-variable">obs</span> = <span class="cm-variable">array</span>([[<span class="cm-number">278</span>, <span class="cm-number">3587</span>], [<span class="cm-number">117460</span>, <span class="cm-number">697753</span>]])</span></pre><pre class=""><span style="padding-right: 0.1px;"><span></span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-comment"># Calculate the chi-square test</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-variable">chi2_corrected</span> = <span class="cm-variable">stats</span>.<span class="cm-variable">chi2_contingency</span>(<span class="cm-variable">obs</span>, <span class="cm-variable">correction</span>=<span class="cm-builtin">True</span>)</span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-variable">chi2_uncorrected</span> = <span class="cm-variable">stats</span>.<span class="cm-variable">chi2_contingency</span>(<span class="cm-variable">obs</span>, <span class="cm-variable">correction</span>=<span class="cm-builtin">False</span>)</span></pre><pre class=""><span style="padding-right: 0.1px;"><span></span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-comment"># Print the result</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-keyword">print</span>(<span class="cm-string">'CHI SQUARE'</span>)</span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-keyword">print</span>(<span class="cm-string">'The corrected chi2 value is {0:5.3f}, with p={1:5.3f}'</span>.<span class="cm-builtin">format</span>(<span class="cm-variable">chi2_corrected</span>[<span class="cm-number">0</span>], <span class="cm-variable">chi2_corrected</span>[<span class="cm-number">1</span>]))</span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-keyword">print</span>(<span class="cm-string">'The uncorrected chi2 value is {0:5.3f}, with p={1:5.3f}'</span>.<span class="cm-builtin">format</span>(<span class="cm-variable">chi2_uncorrected</span>[<span class="cm-number">0</span>], <span class="cm-variable">chi2_uncorrected</span>[<span class="cm-number">1</span>]))</span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 198px;"></div><div class="CodeMirror-gutters" style="display: none; height: 228px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to scroll output; double click to hide" style=""></div><div class="output" style=""><div class="output_area"><div class="prompt"></div><div class="output_subarea output_text output_stream output_stdout"><pre>CHI SQUARE
The corrected chi2 value is 162.143, with p=0.000
The uncorrected chi2 value is 162.728, with p=0.000
</pre></div></div></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell code_cell rendered unselected" tabindex="2"><div class="input"><div class="prompt input_prompt">In [26]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 22.59375px; left: 198.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true" style="right: 0px; left: 0px;"><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 952px; margin-bottom: 0px; border-right-width: 30px; min-height: 198px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre>x</pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors" style="visibility: hidden;"><div class="CodeMirror-cursor" style="left: 193px; top: 17px; height: 17px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-comment"># Enter the data comparing Oyster 2 then Probes</span></span></pre><pre><span style="padding-right: 0.1px;"><span class="cm-variable">obs</span> = <span class="cm-variable">array</span>([[<span class="cm-number">260</span>, <span class="cm-number">4044</span>], [<span class="cm-number">117460</span>, <span class="cm-number">697753</span>]])</span></pre><pre class=""><span style="padding-right: 0.1px;"><span></span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-comment"># Calculate the chi-square test</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-variable">chi2_corrected</span> = <span class="cm-variable">stats</span>.<span class="cm-variable">chi2_contingency</span>(<span class="cm-variable">obs</span>, <span class="cm-variable">correction</span>=<span class="cm-builtin">True</span>)</span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-variable">chi2_uncorrected</span> = <span class="cm-variable">stats</span>.<span class="cm-variable">chi2_contingency</span>(<span class="cm-variable">obs</span>, <span class="cm-variable">correction</span>=<span class="cm-builtin">False</span>)</span></pre><pre class=""><span style="padding-right: 0.1px;"><span></span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-comment"># Print the result</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-keyword">print</span>(<span class="cm-string">'CHI SQUARE'</span>)</span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-keyword">print</span>(<span class="cm-string">'The corrected chi2 value is {0:5.3f}, with p={1:5.3f}'</span>.<span class="cm-builtin">format</span>(<span class="cm-variable">chi2_corrected</span>[<span class="cm-number">0</span>], <span class="cm-variable">chi2_corrected</span>[<span class="cm-number">1</span>]))</span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-keyword">print</span>(<span class="cm-string">'The uncorrected chi2 value is {0:5.3f}, with p={1:5.3f}'</span>.<span class="cm-builtin">format</span>(<span class="cm-variable">chi2_uncorrected</span>[<span class="cm-number">0</span>], <span class="cm-variable">chi2_uncorrected</span>[<span class="cm-number">1</span>]))</span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 198px;"></div><div class="CodeMirror-gutters" style="display: none; height: 228px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to scroll output; double click to hide" style=""></div><div class="output" style=""><div class="output_area"><div class="prompt"></div><div class="output_subarea output_text output_stream output_stdout"><pre>CHI SQUARE
The corrected chi2 value is 243.013, with p=0.000
The uncorrected chi2 value is 243.693, with p=0.000
</pre></div></div></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell code_cell rendered unselected" tabindex="2"><div class="input"><div class="prompt input_prompt">In [ ]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 5.59375px; left: 5.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true"><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 3px; margin-bottom: 0px; border-right-width: 30px; min-height: 28px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors" style="visibility: hidden;"><div class="CodeMirror-cursor" style="left: 0px; top: 0px; height: 17px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span></span></span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 28px;"></div><div class="CodeMirror-gutters" style="display: none; height: 58px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to expand output; double click to hide output" style="display: none;"></div><div class="output" style="display: none;"></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell code_cell rendered unselected" tabindex="2"><div class="input"><div class="prompt input_prompt">In [ ]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 5.59375px; left: 5.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true"><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 3px; margin-bottom: 0px; border-right-width: 30px; min-height: 28px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors"><div class="CodeMirror-cursor" style="left: 0px; top: 0px; height: 17px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span></span></span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 28px;"></div><div class="CodeMirror-gutters" style="display: none; height: 58px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to expand output; double click to hide output" style="display: none;"></div><div class="output" style="display: none;"></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell code_cell rendered unselected" tabindex="2"><div class="input"><div class="prompt input_prompt">In [ ]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 5.59375px; left: 5.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true"><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 3px; margin-bottom: 0px; border-right-width: 30px; min-height: 28px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors"><div class="CodeMirror-cursor" style="left: 0px; top: 0px; height: 17px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span></span></span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 28px;"></div><div class="CodeMirror-gutters" style="display: none; height: 58px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to expand output; double click to hide output" style="display: none;"></div><div class="output" style="display: none;"></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell text_cell unselected rendered" tabindex="2"><div class="prompt input_prompt"></div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-default CodeMirror-wrap"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 5.59375px; left: 5.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="bottom: 0px; min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true" style=""><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; padding-right: 0px; padding-bottom: 0px; margin-bottom: 0px; border-right-width: 30px; min-height: 34px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors"><div class="CodeMirror-cursor" style="left: 0px; top: 0px; height: 23px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-header cm-header-1"># Rebuilt (new gtf based on RNAseq data)</span></span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 34px;"></div><div class="CodeMirror-gutters" style="display: none; height: 64px;"></div></div></div></div><div class="text_cell_render rendered_html" tabindex="-1"><h1 id="Rebuilt-(new-gtf-based-on-RNAseq-data)">Rebuilt (new gtf based on RNAseq data)<a class="anchor-link" href="http://localhost:8888/notebooks/ipynb/Array-feature-overlap-05.ipynb#Rebuilt-(new-gtf-based-on-RNAseq-data)">¶</a></h1>
</div></div></div><div class="cell code_cell unselected rendered" tabindex="2"><div class="input"><div class="prompt input_prompt">In [15]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 5.59375px; left: 5.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true" style=""><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 767.5244140625px; margin-bottom: 0px; border-right-width: 30px; min-height: 113px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors"><div class="CodeMirror-cursor" style="left: 0px; top: 0px; height: 17px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">intersectbed</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">wb</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">a</span> <span class="cm-error">.</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02</span>.<span class="cm-variable">colson</span><span class="cm-operator">/</span><span class="cm-variable">genomeBrowserTracks</span><span class="cm-operator">/</span><span class="cm-variable">logFC_HS</span><span class="cm-operator">-</span><span class="cm-variable">preHS</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02.2</span><span class="cm-variable">M_sig</span>.<span class="cm-variable">bedGraph</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">b</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-variable">rebuilt</span>.<span class="cm-variable">gtf</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">cut</span> <span class="cm-operator">-</span><span class="cm-variable">f</span> <span class="cm-number">6</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">sort</span> <span class="cm-operator">|</span> <span class="cm-variable">uniq</span> <span class="cm-operator">-</span><span class="cm-variable">c</span> </span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 113px;"></div><div class="CodeMirror-gutters" style="display: none; height: 143px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to expand output; double click to hide output" style=""></div><div class="output" style=""><div class="output_area"><div class="prompt"></div><div class="output_subarea output_text output_stream output_stdout"><pre>8768 Cufflinks
</pre></div></div></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell code_cell unselected rendered" tabindex="2"><div class="input"><div class="prompt input_prompt">In [16]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 5.59375px; left: 5.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true" style=""><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 767.5244140625px; margin-bottom: 0px; border-right-width: 30px; min-height: 113px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors"><div class="CodeMirror-cursor" style="left: 0px; top: 0px; height: 17px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">intersectbed</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">wb</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">a</span> <span class="cm-error">.</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02</span>.<span class="cm-variable">colson</span><span class="cm-operator">/</span><span class="cm-variable">genomeBrowserTracks</span><span class="cm-operator">/</span><span class="cm-variable">logFC_HS</span><span class="cm-operator">-</span><span class="cm-variable">preHS</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02.4</span><span class="cm-variable">M_sig</span>.<span class="cm-variable">bedGraph</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">b</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-variable">rebuilt</span>.<span class="cm-variable">gtf</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">cut</span> <span class="cm-operator">-</span><span class="cm-variable">f</span> <span class="cm-number">6</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">sort</span> <span class="cm-operator">|</span> <span class="cm-variable">uniq</span> <span class="cm-operator">-</span><span class="cm-variable">c</span> </span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 113px;"></div><div class="CodeMirror-gutters" style="display: none; height: 143px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to expand output; double click to hide output" style=""></div><div class="output" style=""><div class="output_area"><div class="prompt"></div><div class="output_subarea output_text output_stream output_stdout"><pre>7694 Cufflinks
</pre></div></div></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell code_cell unselected rendered" tabindex="2"><div class="input"><div class="prompt input_prompt">In [17]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 5.59375px; left: 5.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true" style=""><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 767.5244140625px; margin-bottom: 0px; border-right-width: 30px; min-height: 113px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors"><div class="CodeMirror-cursor" style="left: 0px; top: 0px; height: 17px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">intersectbed</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">wb</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">a</span> <span class="cm-error">.</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02</span>.<span class="cm-variable">colson</span><span class="cm-operator">/</span><span class="cm-variable">genomeBrowserTracks</span><span class="cm-operator">/</span><span class="cm-variable">logFC_HS</span><span class="cm-operator">-</span><span class="cm-variable">preHS</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02.6</span><span class="cm-variable">M_sig</span>.<span class="cm-variable">bedGraph</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">b</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-variable">rebuilt</span>.<span class="cm-variable">gtf</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">cut</span> <span class="cm-operator">-</span><span class="cm-variable">f</span> <span class="cm-number">6</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">sort</span> <span class="cm-operator">|</span> <span class="cm-variable">uniq</span> <span class="cm-operator">-</span><span class="cm-variable">c</span> </span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 113px;"></div><div class="CodeMirror-gutters" style="display: none; height: 143px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to expand output; double click to hide output" style=""></div><div class="output" style=""><div class="output_area"><div class="prompt"></div><div class="output_subarea output_text output_stream output_stdout"><pre>6160 Cufflinks
</pre></div></div></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell code_cell unselected rendered" tabindex="2"><div class="input"><div class="prompt input_prompt">In [18]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 5.59375px; left: 5.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true" style="right: 0px; left: 0px;"><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 826.333984375px; margin-bottom: 0px; border-right-width: 30px; min-height: 113px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors"><div class="CodeMirror-cursor" style="left: 0px; top: 0px; height: 17px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">intersectbed</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">wb</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">a</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">git</span><span class="cm-operator">-</span><span class="cm-variable">repos</span><span class="cm-operator">/</span><span class="cm-variable">paper</span><span class="cm-operator">-</span><span class="cm-variable">Temp</span><span class="cm-operator">-</span><span class="cm-variable">stress</span><span class="cm-operator">/</span><span class="cm-variable">ipynb</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">/</span><span class="cm-variable">array</span><span class="cm-operator">-</span><span class="cm-variable">design</span><span class="cm-operator">/</span><span class="cm-variable">OID40453_probe_locations</span>.<span class="cm-variable">gff</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">b</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-variable">rebuilt</span>.<span class="cm-variable">gtf</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">cut</span> <span class="cm-operator">-</span><span class="cm-variable">f</span> <span class="cm-number">11</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">sort</span> <span class="cm-operator">|</span> <span class="cm-variable">uniq</span> <span class="cm-operator">-</span><span class="cm-variable">c</span> </span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 113px;"></div><div class="CodeMirror-gutters" style="display: none; height: 143px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to expand output; double click to hide output" style=""></div><div class="output" style=""><div class="output_area"><div class="prompt"></div><div class="output_subarea output_text output_stream output_stdout"><pre>1197818 Cufflinks
</pre></div></div></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell code_cell rendered unselected" tabindex="2"><div class="input"><div class="prompt input_prompt">In [39]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 5.59375px; left: 5.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true" style="right: 0px; left: 0px;"><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 952px; margin-bottom: 0px; border-right-width: 30px; min-height: 198px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre>x</pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"><div class="CodeMirror-selected" style="position: absolute; left: 0px; top: 0px; width: 1005px; height: 17px;"></div><div class="CodeMirror-selected" style="position: absolute; left: 0px; top: 170px; width: 949px; height: 17px;"></div><div class="CodeMirror-selected" style="position: absolute; left: 0px; top: 17px; width: 1005px; height: 153px;"></div></div><div class="CodeMirror-cursors"></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-comment"># Enter the data comparing Oyster 2 then Probes</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-variable">obs</span> = <span class="cm-variable">array</span>([[<span class="cm-number">8768</span>, <span class="cm-number">10028</span>], [<span class="cm-number">1197818</span>, <span class="cm-number">697753</span>]])</span></pre><pre class=""><span style="padding-right: 0.1px;"><span></span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-comment"># Calculate the chi-square test</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-variable">chi2_corrected</span> = <span class="cm-variable">stats</span>.<span class="cm-variable">chi2_contingency</span>(<span class="cm-variable">obs</span>, <span class="cm-variable">correction</span>=<span class="cm-builtin">True</span>)</span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-variable">chi2_uncorrected</span> = <span class="cm-variable">stats</span>.<span class="cm-variable">chi2_contingency</span>(<span class="cm-variable">obs</span>, <span class="cm-variable">correction</span>=<span class="cm-builtin">False</span>)</span></pre><pre class=""><span style="padding-right: 0.1px;"><span></span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-comment"># Print the result</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-keyword">print</span>(<span class="cm-string">'CHI SQUARE'</span>)</span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-keyword">print</span>(<span class="cm-string">'The corrected chi2 value is {0:5.3f}, with p={1:5.3f}'</span>.<span class="cm-builtin">format</span>(<span class="cm-variable">chi2_corrected</span>[<span class="cm-number">0</span>], <span class="cm-variable">chi2_corrected</span>[<span class="cm-number">1</span>]))</span></pre><pre><span style="padding-right: 0.1px;"><span class="cm-keyword">print</span>(<span class="cm-string">'The uncorrected chi2 value is {0:5.3f}, with p={1:5.3f}'</span>.<span class="cm-builtin">format</span>(<span class="cm-variable">chi2_uncorrected</span>[<span class="cm-number">0</span>], <span class="cm-variable">chi2_uncorrected</span>[<span class="cm-number">1</span>]))</span></pre><pre class="" style="display: none;"><span style="padding-right: 0.1px;"><span class="cm-variable">chi2_corrected</span> = <span class="cm-variable">stats</span>.<span class="cm-variable">chi2_contingency</span>(<span class="cm-variable">obs</span>, <span class="cm-variable">correction</span>=<span class="cm-builtin">True</span>)</span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 198px;"></div><div class="CodeMirror-gutters" style="display: none; height: 228px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to expand output; double click to hide output" style=""></div><div class="output" style=""><div class="output_area"><div class="prompt"></div><div class="output_subarea output_text output_stream output_stdout"><pre>CHI SQUARE
The corrected chi2 value is 2184.818, with p=0.000
The uncorrected chi2 value is 2185.528, with p=0.000
</pre></div></div></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell code_cell unselected rendered" tabindex="2"><div class="input"><div class="prompt input_prompt">In [40]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 5.59375px; left: 5.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true" style="right: 0px; left: 0px;"><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 952px; margin-bottom: 0px; border-right-width: 30px; min-height: 198px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors"><div class="CodeMirror-cursor" style="left: 0px; top: 0px; height: 17px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-comment"># Enter the data comparing Oyster 4 then Probes</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-variable">obs</span> = <span class="cm-variable">array</span>([[<span class="cm-number">7694</span>, <span class="cm-number">10148</span>], [<span class="cm-number">1197818</span>, <span class="cm-number">697753</span>]])</span></pre><pre class=""><span style="padding-right: 0.1px;"><span></span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-comment"># Calculate the chi-square test</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-variable">chi2_corrected</span> = <span class="cm-variable">stats</span>.<span class="cm-variable">chi2_contingency</span>(<span class="cm-variable">obs</span>, <span class="cm-variable">correction</span>=<span class="cm-builtin">True</span>)</span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-variable">chi2_uncorrected</span> = <span class="cm-variable">stats</span>.<span class="cm-variable">chi2_contingency</span>(<span class="cm-variable">obs</span>, <span class="cm-variable">correction</span>=<span class="cm-builtin">False</span>)</span></pre><pre class=""><span style="padding-right: 0.1px;"><span></span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-comment"># Print the result</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-keyword">print</span>(<span class="cm-string">'CHI SQUARE'</span>)</span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-keyword">print</span>(<span class="cm-string">'The corrected chi2 value is {0:5.3f}, with p={1:5.3f}'</span>.<span class="cm-builtin">format</span>(<span class="cm-variable">chi2_corrected</span>[<span class="cm-number">0</span>], <span class="cm-variable">chi2_corrected</span>[<span class="cm-number">1</span>]))</span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-keyword">print</span>(<span class="cm-string">'The uncorrected chi2 value is {0:5.3f}, with p={1:5.3f}'</span>.<span class="cm-builtin">format</span>(<span class="cm-variable">chi2_uncorrected</span>[<span class="cm-number">0</span>], <span class="cm-variable">chi2_uncorrected</span>[<span class="cm-number">1</span>]))</span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 198px;"></div><div class="CodeMirror-gutters" style="display: none; height: 228px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to expand output; double click to hide output" style=""></div><div class="output" style=""><div class="output_area"><div class="prompt"></div><div class="output_subarea output_text output_stream output_stdout"><pre>CHI SQUARE
The corrected chi2 value is 3052.863, with p=0.000
The uncorrected chi2 value is 3053.724, with p=0.000
</pre></div></div></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell code_cell unselected rendered" tabindex="2"><div class="input"><div class="prompt input_prompt">In [41]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 5.59375px; left: 5.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true" style="right: 0px; left: 0px;"><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 952px; margin-bottom: 0px; border-right-width: 30px; min-height: 198px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors"><div class="CodeMirror-cursor" style="left: 0px; top: 0px; height: 17px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-comment"># Enter the data comparing Oyster 6 then Probes</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-variable">obs</span> = <span class="cm-variable">array</span>([[<span class="cm-number">6160</span>, <span class="cm-number">11690</span>], [<span class="cm-number">1197818</span>, <span class="cm-number">697753</span>]])</span></pre><pre class=""><span style="padding-right: 0.1px;"><span></span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-comment"># Calculate the chi-square test</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-variable">chi2_corrected</span> = <span class="cm-variable">stats</span>.<span class="cm-variable">chi2_contingency</span>(<span class="cm-variable">obs</span>, <span class="cm-variable">correction</span>=<span class="cm-builtin">True</span>)</span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-variable">chi2_uncorrected</span> = <span class="cm-variable">stats</span>.<span class="cm-variable">chi2_contingency</span>(<span class="cm-variable">obs</span>, <span class="cm-variable">correction</span>=<span class="cm-builtin">False</span>)</span></pre><pre class=""><span style="padding-right: 0.1px;"><span></span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-comment"># Print the result</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-keyword">print</span>(<span class="cm-string">'CHI SQUARE'</span>)</span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-keyword">print</span>(<span class="cm-string">'The corrected chi2 value is {0:5.3f}, with p={1:5.3f}'</span>.<span class="cm-builtin">format</span>(<span class="cm-variable">chi2_corrected</span>[<span class="cm-number">0</span>], <span class="cm-variable">chi2_corrected</span>[<span class="cm-number">1</span>]))</span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-keyword">print</span>(<span class="cm-string">'The uncorrected chi2 value is {0:5.3f}, with p={1:5.3f}'</span>.<span class="cm-builtin">format</span>(<span class="cm-variable">chi2_uncorrected</span>[<span class="cm-number">0</span>], <span class="cm-variable">chi2_uncorrected</span>[<span class="cm-number">1</span>]))</span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 198px;"></div><div class="CodeMirror-gutters" style="display: none; height: 228px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to expand output; double click to hide output" style=""></div><div class="output" style=""><div class="output_area"><div class="prompt"></div><div class="output_subarea output_text output_stream output_stdout"><pre>CHI SQUARE
The corrected chi2 value is 6233.645, with p=0.000
The uncorrected chi2 value is 6234.874, with p=0.000
</pre></div></div></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell text_cell rendered unselected" tabindex="2"><div class="prompt input_prompt"></div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-default CodeMirror-wrap"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 5.59375px; left: 5.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="bottom: 0px; min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true" style=""><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; padding-right: 0px; padding-bottom: 0px; margin-bottom: 0px; border-right-width: 30px; min-height: 34px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors"><div class="CodeMirror-cursor" style="left: 0px; top: 0px; height: 23px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-header cm-header-1"># Housekeeping Genes</span></span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 34px;"></div><div class="CodeMirror-gutters" style="display: none; height: 64px;"></div></div></div></div><div class="text_cell_render rendered_html" tabindex="-1"><h1 id="Housekeeping-Genes">Housekeeping Genes<a class="anchor-link" href="http://localhost:8888/notebooks/ipynb/Array-feature-overlap-05.ipynb#Housekeeping-Genes">¶</a></h1>
</div></div></div><div class="cell text_cell rendered unselected" tabindex="2"><div class="prompt input_prompt"></div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-default CodeMirror-wrap"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 5.59375px; left: 249.21875px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true" style=""><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 30px; min-height: 28px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors"><div class="CodeMirror-cursor" style="left: 243.625px; top: 0px; height: 17px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;">Separating out hypo and hyper</span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 28px;"></div><div class="CodeMirror-gutters" style="display: none; height: 58px;"></div></div></div></div><div class="text_cell_render rendered_html" tabindex="-1"><p>Separating out hypo and hyper</p>
</div></div></div><div class="cell text_cell rendered unselected" tabindex="2"><div class="prompt input_prompt"></div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-default CodeMirror-wrap"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 39.09375px; left: 417.25px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true" style=""><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 30px; min-height: 62px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors"><div class="CodeMirror-cursor" style="left: 411.65625px; top: 33.5px; height: 17.5px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-tag cm-bracket"><</span><span class="cm-tag">img</span> <span class="cm-attribute">src</span>=<span class="cm-string">"</span><span class="cm-string cm-link">http://eagle.fish.washington.edu/cnidarian/skitch/Screenshot_4_3_15__7_23_AM_1ACED9DD.png</span><span class="cm-string">"</span> <span class="cm-attribute">alt</span>=<span class="cm-string">"Screenshot_4_3_15__7_23_AM_1ACED9DD.png"</span><span class="cm-tag cm-bracket">/></span></span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 62px;"></div><div class="CodeMirror-gutters" style="display: none; height: 92px;"></div></div></div></div><div class="text_cell_render rendered_html" tabindex="-1"><p><img src="./Array-feature-overlap-05_files/Screenshot_4_3_15__7_23_AM_1ACED9DD.png" alt="Screenshot_4_3_15__7_23_AM_1ACED9DD.png"></p>
</div></div></div><div class="cell code_cell rendered unselected" tabindex="2"><div class="input"><div class="prompt input_prompt">In [29]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 5.59375px; left: 5.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true" style=""><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1" draggable="false"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 607.8984375px; margin-bottom: 0px; border-right-width: 30px; min-height: 215px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre>x</pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"><div class="CodeMirror-selected" style="position: absolute; left: 0px; top: 0px; width: 1005px; height: 17px;"></div><div class="CodeMirror-selected" style="position: absolute; left: 0px; top: 187px; width: 142.8232421875px; height: 17px;"></div><div class="CodeMirror-selected" style="position: absolute; left: 0px; top: 17px; width: 1005px; height: 170px;"></div></div><div class="CodeMirror-cursors" style="visibility: hidden;"></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">intersectbed</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">wb</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">a</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02.2</span><span class="cm-variable">M_sig</span>.<span class="cm-variable">hypo</span>.<span class="cm-variable">bedGraph</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">b</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-variable">Cgigas_v9_gene</span><span class="cm-operator">-</span><span class="cm-variable">housekeeping</span>.<span class="cm-variable">gff</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">cut</span> <span class="cm-operator">-</span><span class="cm-variable">f</span> <span class="cm-number">6</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">sort</span> <span class="cm-operator">|</span> <span class="cm-variable">uniq</span> <span class="cm-operator">-</span><span class="cm-variable">c</span> </span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">intersectbed</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">wb</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">a</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02.2</span><span class="cm-variable">M_sig</span>.<span class="cm-variable">hyper</span>.<span class="cm-variable">bedGraph</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">b</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-variable">Cgigas_v9_gene</span><span class="cm-operator">-</span><span class="cm-variable">housekeeping</span>.<span class="cm-variable">gff</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">cut</span> <span class="cm-operator">-</span><span class="cm-variable">f</span> <span class="cm-number">6</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">sort</span> <span class="cm-operator">|</span> <span class="cm-variable">uniq</span> <span class="cm-operator">-</span><span class="cm-variable">c</span> </span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 215px;"></div><div class="CodeMirror-gutters" style="display: none; height: 245px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to scroll output; double click to hide" style=""></div><div class="output" style=""><div class="output_area"><div class="prompt"></div><div class="output_subarea output_text output_stream output_stdout"><pre>2172 GLEAN
1038 GLEAN
</pre></div></div></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell code_cell rendered unselected" tabindex="2"><div class="input"><div class="prompt input_prompt">In [30]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 5.59375px; left: 5.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true" style=""><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 607.8984375px; margin-bottom: 0px; border-right-width: 30px; min-height: 215px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre>x</pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"><div class="CodeMirror-selected" style="position: absolute; left: 0px; top: 0px; width: 1005px; height: 17px;"></div><div class="CodeMirror-selected" style="position: absolute; left: 0px; top: 187px; width: 142.8232421875px; height: 17px;"></div><div class="CodeMirror-selected" style="position: absolute; left: 0px; top: 17px; width: 1005px; height: 170px;"></div></div><div class="CodeMirror-cursors"></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">intersectbed</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">wb</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">a</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02.4</span><span class="cm-variable">M_sig</span>.<span class="cm-variable">hypo</span>.<span class="cm-variable">bedGraph</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">b</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-variable">Cgigas_v9_gene</span><span class="cm-operator">-</span><span class="cm-variable">housekeeping</span>.<span class="cm-variable">gff</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">cut</span> <span class="cm-operator">-</span><span class="cm-variable">f</span> <span class="cm-number">6</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">sort</span> <span class="cm-operator">|</span> <span class="cm-variable">uniq</span> <span class="cm-operator">-</span><span class="cm-variable">c</span> </span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">intersectbed</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">wb</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">a</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02.4</span><span class="cm-variable">M_sig</span>.<span class="cm-variable">hyper</span>.<span class="cm-variable">bedGraph</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">b</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-variable">Cgigas_v9_gene</span><span class="cm-operator">-</span><span class="cm-variable">housekeeping</span>.<span class="cm-variable">gff</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">cut</span> <span class="cm-operator">-</span><span class="cm-variable">f</span> <span class="cm-number">6</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">sort</span> <span class="cm-operator">|</span> <span class="cm-variable">uniq</span> <span class="cm-operator">-</span><span class="cm-variable">c</span> </span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 215px;"></div><div class="CodeMirror-gutters" style="display: none; height: 245px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to scroll output; double click to hide" style=""></div><div class="output" style=""><div class="output_area"><div class="prompt"></div><div class="output_subarea output_text output_stream output_stdout"><pre>1988 GLEAN
1381 GLEAN
</pre></div></div></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell code_cell rendered unselected" tabindex="2"><div class="input"><div class="prompt input_prompt">In [31]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 141.59375px; left: 425.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true" style=""><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 607.8984375px; margin-bottom: 0px; border-right-width: 30px; min-height: 215px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre>x</pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors"><div class="CodeMirror-cursor" style="left: 420px; top: 136px; height: 17px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">intersectbed</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">wb</span> <span class="cm-error">\</span></span></pre><pre><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">a</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02.6</span><span class="cm-variable">M_sig</span>.<span class="cm-variable">hypo</span>.<span class="cm-variable">bedGraph</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">b</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-variable">Cgigas_v9_gene</span><span class="cm-operator">-</span><span class="cm-variable">housekeeping</span>.<span class="cm-variable">gff</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">cut</span> <span class="cm-operator">-</span><span class="cm-variable">f</span> <span class="cm-number">6</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">sort</span> <span class="cm-operator">|</span> <span class="cm-variable">uniq</span> <span class="cm-operator">-</span><span class="cm-variable">c</span> </span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">intersectbed</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">wb</span> <span class="cm-error">\</span></span></pre><pre><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">a</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02.6</span><span class="cm-variable">M_sig</span>.<span class="cm-variable">hyper</span>.<span class="cm-variable">bedGraph</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">b</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-variable">Cgigas_v9_gene</span><span class="cm-operator">-</span><span class="cm-variable">housekeeping</span>.<span class="cm-variable">gff</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">cut</span> <span class="cm-operator">-</span><span class="cm-variable">f</span> <span class="cm-number">6</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">sort</span> <span class="cm-operator">|</span> <span class="cm-variable">uniq</span> <span class="cm-operator">-</span><span class="cm-variable">c</span> </span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 215px;"></div><div class="CodeMirror-gutters" style="display: none; height: 245px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to scroll output; double click to hide" style=""></div><div class="output" style=""><div class="output_area"><div class="prompt"></div><div class="output_subarea output_text output_stream output_stdout"><pre>2367 GLEAN
1452 GLEAN
</pre></div></div></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell code_cell rendered unselected" tabindex="2"><div class="input"><div class="prompt input_prompt">In [26]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 5.59375px; left: 5.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true" style="right: 0px; left: 0px;"><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 826.333984375px; margin-bottom: 0px; border-right-width: 30px; min-height: 113px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors"><div class="CodeMirror-cursor" style="left: 0px; top: 0px; height: 17px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">intersectbed</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">wb</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">a</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">git</span><span class="cm-operator">-</span><span class="cm-variable">repos</span><span class="cm-operator">/</span><span class="cm-variable">paper</span><span class="cm-operator">-</span><span class="cm-variable">Temp</span><span class="cm-operator">-</span><span class="cm-variable">stress</span><span class="cm-operator">/</span><span class="cm-variable">ipynb</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">/</span><span class="cm-variable">array</span><span class="cm-operator">-</span><span class="cm-variable">design</span><span class="cm-operator">/</span><span class="cm-variable">OID40453_probe_locations</span>.<span class="cm-variable">gff</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">b</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-variable">Cgigas_v9_gene</span><span class="cm-operator">-</span><span class="cm-variable">housekeeping</span>.<span class="cm-variable">gff</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">cut</span> <span class="cm-operator">-</span><span class="cm-variable">f</span> <span class="cm-number">11</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">sort</span> <span class="cm-operator">|</span> <span class="cm-variable">uniq</span> <span class="cm-operator">-</span><span class="cm-variable">c</span> </span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 113px;"></div><div class="CodeMirror-gutters" style="display: none; height: 143px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to expand output; double click to hide output" style=""></div><div class="output" style=""><div class="output_area"><div class="prompt"></div><div class="output_subarea output_text output_stream output_stdout"><pre>251970 GLEAN
</pre></div></div></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell code_cell unselected rendered" tabindex="2"><div class="input"><div class="prompt input_prompt">In [42]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 5.59375px; left: 5.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true" style="right: 0px; left: 0px;"><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 952px; margin-bottom: 0px; border-right-width: 30px; min-height: 198px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors"><div class="CodeMirror-cursor" style="left: 0px; top: 0px; height: 17px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-comment"># Enter the data comparing Oyster 2 then Probes</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-variable">obs</span> = <span class="cm-variable">array</span>([[<span class="cm-number">3210</span>, <span class="cm-number">10028</span>], [<span class="cm-number">251970</span>, <span class="cm-number">697753</span>]])</span></pre><pre class=""><span style="padding-right: 0.1px;"><span></span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-comment"># Calculate the chi-square test</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-variable">chi2_corrected</span> = <span class="cm-variable">stats</span>.<span class="cm-variable">chi2_contingency</span>(<span class="cm-variable">obs</span>, <span class="cm-variable">correction</span>=<span class="cm-builtin">True</span>)</span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-variable">chi2_uncorrected</span> = <span class="cm-variable">stats</span>.<span class="cm-variable">chi2_contingency</span>(<span class="cm-variable">obs</span>, <span class="cm-variable">correction</span>=<span class="cm-builtin">False</span>)</span></pre><pre class=""><span style="padding-right: 0.1px;"><span></span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-comment"># Print the result</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-keyword">print</span>(<span class="cm-string">'CHI SQUARE'</span>)</span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-keyword">print</span>(<span class="cm-string">'The corrected chi2 value is {0:5.3f}, with p={1:5.3f}'</span>.<span class="cm-builtin">format</span>(<span class="cm-variable">chi2_corrected</span>[<span class="cm-number">0</span>], <span class="cm-variable">chi2_corrected</span>[<span class="cm-number">1</span>]))</span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-keyword">print</span>(<span class="cm-string">'The uncorrected chi2 value is {0:5.3f}, with p={1:5.3f}'</span>.<span class="cm-builtin">format</span>(<span class="cm-variable">chi2_uncorrected</span>[<span class="cm-number">0</span>], <span class="cm-variable">chi2_uncorrected</span>[<span class="cm-number">1</span>]))</span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 198px;"></div><div class="CodeMirror-gutters" style="display: none; height: 228px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to expand output; double click to hide output" style=""></div><div class="output" style=""><div class="output_area"><div class="prompt"></div><div class="output_subarea output_text output_stream output_stdout"><pre>CHI SQUARE
The corrected chi2 value is 34.806, with p=0.000
The uncorrected chi2 value is 34.923, with p=0.000
</pre></div></div></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell code_cell unselected rendered" tabindex="2"><div class="input"><div class="prompt input_prompt">In [43]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 5.59375px; left: 5.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true" style="right: 0px; left: 0px;"><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 952px; margin-bottom: 0px; border-right-width: 30px; min-height: 198px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors"><div class="CodeMirror-cursor" style="left: 0px; top: 0px; height: 17px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-comment"># Enter the data comparing Oyster 4 then Probes</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-variable">obs</span> = <span class="cm-variable">array</span>([[<span class="cm-number">3369</span>, <span class="cm-number">10148</span>], [<span class="cm-number">251970</span>, <span class="cm-number">697753</span>]])</span></pre><pre class=""><span style="padding-right: 0.1px;"><span></span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-comment"># Calculate the chi-square test</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-variable">chi2_corrected</span> = <span class="cm-variable">stats</span>.<span class="cm-variable">chi2_contingency</span>(<span class="cm-variable">obs</span>, <span class="cm-variable">correction</span>=<span class="cm-builtin">True</span>)</span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-variable">chi2_uncorrected</span> = <span class="cm-variable">stats</span>.<span class="cm-variable">chi2_contingency</span>(<span class="cm-variable">obs</span>, <span class="cm-variable">correction</span>=<span class="cm-builtin">False</span>)</span></pre><pre class=""><span style="padding-right: 0.1px;"><span></span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-comment"># Print the result</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-keyword">print</span>(<span class="cm-string">'CHI SQUARE'</span>)</span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-keyword">print</span>(<span class="cm-string">'The corrected chi2 value is {0:5.3f}, with p={1:5.3f}'</span>.<span class="cm-builtin">format</span>(<span class="cm-variable">chi2_corrected</span>[<span class="cm-number">0</span>], <span class="cm-variable">chi2_corrected</span>[<span class="cm-number">1</span>]))</span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-keyword">print</span>(<span class="cm-string">'The uncorrected chi2 value is {0:5.3f}, with p={1:5.3f}'</span>.<span class="cm-builtin">format</span>(<span class="cm-variable">chi2_uncorrected</span>[<span class="cm-number">0</span>], <span class="cm-variable">chi2_uncorrected</span>[<span class="cm-number">1</span>]))</span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 198px;"></div><div class="CodeMirror-gutters" style="display: none; height: 228px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to expand output; double click to hide output" style=""></div><div class="output" style=""><div class="output_area"><div class="prompt"></div><div class="output_subarea output_text output_stream output_stdout"><pre>CHI SQUARE
The corrected chi2 value is 17.578, with p=0.000
The uncorrected chi2 value is 17.661, with p=0.000
</pre></div></div></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell code_cell unselected rendered" tabindex="2"><div class="input"><div class="prompt input_prompt">In [47]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 5.59375px; left: 5.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true" style="right: 0px; left: 0px;"><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 952px; margin-bottom: 0px; border-right-width: 30px; min-height: 198px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors"><div class="CodeMirror-cursor" style="left: 0px; top: 0px; height: 17px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-comment"># Enter the data comparing Oyster 6 then Probes</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-variable">obs</span> = <span class="cm-variable">array</span>([[<span class="cm-number">3819</span>, <span class="cm-number">11690</span>], [<span class="cm-number">251970</span>, <span class="cm-number">697753</span>]])</span></pre><pre class=""><span style="padding-right: 0.1px;"><span></span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-comment"># Calculate the chi-square test</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-variable">chi2_corrected</span> = <span class="cm-variable">stats</span>.<span class="cm-variable">chi2_contingency</span>(<span class="cm-variable">obs</span>, <span class="cm-variable">correction</span>=<span class="cm-builtin">True</span>)</span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-variable">chi2_uncorrected</span> = <span class="cm-variable">stats</span>.<span class="cm-variable">chi2_contingency</span>(<span class="cm-variable">obs</span>, <span class="cm-variable">correction</span>=<span class="cm-builtin">False</span>)</span></pre><pre class=""><span style="padding-right: 0.1px;"><span></span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-comment"># Print the result</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-keyword">print</span>(<span class="cm-string">'CHI SQUARE'</span>)</span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-keyword">print</span>(<span class="cm-string">'The corrected chi2 value is {0:5.3f}, with p={1:5.3f}'</span>.<span class="cm-builtin">format</span>(<span class="cm-variable">chi2_corrected</span>[<span class="cm-number">0</span>], <span class="cm-variable">chi2_corrected</span>[<span class="cm-number">1</span>]))</span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-keyword">print</span>(<span class="cm-string">'The uncorrected chi2 value is {0:5.3f}, with p={1:5.3f}'</span>.<span class="cm-builtin">format</span>(<span class="cm-variable">chi2_uncorrected</span>[<span class="cm-number">0</span>], <span class="cm-variable">chi2_uncorrected</span>[<span class="cm-number">1</span>]))</span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 198px;"></div><div class="CodeMirror-gutters" style="display: none; height: 228px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to expand output; double click to hide output" style=""></div><div class="output" style=""><div class="output_area"><div class="prompt"></div><div class="output_subarea output_text output_stream output_stdout"><pre>CHI SQUARE
The corrected chi2 value is 28.378, with p=0.000
The uncorrected chi2 value is 28.476, with p=0.000
</pre></div></div></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell code_cell unselected rendered" tabindex="2"><div class="input"><div class="prompt input_prompt">In [ ]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 5.59375px; left: 5.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true" style=""><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 3px; margin-bottom: 0px; border-right-width: 30px; min-height: 28px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors"><div class="CodeMirror-cursor" style="left: 0px; top: 0px; height: 17px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span></span></span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 28px;"></div><div class="CodeMirror-gutters" style="display: none; height: 58px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to expand output; double click to hide output" style="display: none;"></div><div class="output" style="display: none;"></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell code_cell unselected rendered" tabindex="2"><div class="input"><div class="prompt input_prompt">In [ ]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 5.59375px; left: 5.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true" style=""><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 3px; margin-bottom: 0px; border-right-width: 30px; min-height: 28px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors"><div class="CodeMirror-cursor" style="left: 0px; top: 0px; height: 17px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span></span></span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 28px;"></div><div class="CodeMirror-gutters" style="display: none; height: 58px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to expand output; double click to hide output" style="display: none;"></div><div class="output" style="display: none;"></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell text_cell rendered unselected" tabindex="2"><div class="prompt input_prompt"></div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-default CodeMirror-wrap"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 5.59375px; left: 89.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="bottom: 0px; min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true" style=""><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; padding-right: 0px; padding-bottom: 0px; margin-bottom: 0px; border-right-width: 30px; min-height: 34px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors" style="visibility: hidden;"><div class="CodeMirror-cursor" style="left: 84px; top: 0px; height: 23px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-header cm-header-1"># Environmental Response Genes</span></span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 34px;"></div><div class="CodeMirror-gutters" style="display: none; height: 64px;"></div></div></div></div><div class="text_cell_render rendered_html" tabindex="-1"><h1 id="Environmental-Response-Genes">Environmental Response Genes<a class="anchor-link" href="http://localhost:8888/notebooks/ipynb/Array-feature-overlap-05.ipynb#Environmental-Response-Genes">¶</a></h1>
</div></div></div><div class="cell text_cell rendered unselected" tabindex="2"><div class="prompt input_prompt"></div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-default CodeMirror-wrap"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 5.59375px; left: 215.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true" style=""><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 30px; min-height: 28px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors"><div class="CodeMirror-cursor" style="left: 210px; top: 0px; height: 17px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;">separating Hypo and Hyper</span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 28px;"></div><div class="CodeMirror-gutters" style="display: none; height: 58px;"></div></div></div></div><div class="text_cell_render rendered_html" tabindex="-1"><p>separating Hypo and Hyper</p>
</div></div></div><div class="cell text_cell rendered unselected" tabindex="2"><div class="prompt input_prompt"></div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-default CodeMirror-wrap"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 56.09375px; left: 417.25px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true" style=""><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 30px; min-height: 79px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors"><div class="CodeMirror-cursor" style="left: 411.65625px; top: 50.5px; height: 17.5px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;">tldr</span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-tag cm-bracket"><</span><span class="cm-tag">img</span> <span class="cm-attribute">src</span>=<span class="cm-string">"</span><span class="cm-string cm-link">http://eagle.fish.washington.edu/cnidarian/skitch/Screenshot_4_3_15__7_28_AM_1ACEDB27.png</span><span class="cm-string">"</span> <span class="cm-attribute">alt</span>=<span class="cm-string">"Screenshot_4_3_15__7_28_AM_1ACEDB27.png"</span><span class="cm-tag cm-bracket">/></span></span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 79px;"></div><div class="CodeMirror-gutters" style="display: none; height: 109px;"></div></div></div></div><div class="text_cell_render rendered_html" tabindex="-1"><p>tldr
<img src="./Array-feature-overlap-05_files/Screenshot_4_3_15__7_28_AM_1ACEDB27.png" alt="Screenshot_4_3_15__7_28_AM_1ACEDB27.png"></p>
</div></div></div><div class="cell code_cell rendered unselected" tabindex="2"><div class="input"><div class="prompt input_prompt">In [ ]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 5.59375px; left: 5.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true"><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 3px; margin-bottom: 0px; border-right-width: 30px; min-height: 28px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors"><div class="CodeMirror-cursor" style="left: 0px; top: 0px; height: 17px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span></span></span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 28px;"></div><div class="CodeMirror-gutters" style="display: none; height: 58px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to expand output; double click to hide output" style="display: none;"></div><div class="output" style="display: none;"></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell code_cell rendered unselected" tabindex="2"><div class="input"><div class="prompt input_prompt">In [33]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 5.59375px; left: 5.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true" style="right: 0px; left: 0px;"><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 607.8984375px; margin-bottom: 0px; border-right-width: 30px; min-height: 215px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre>x</pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"><div class="CodeMirror-selected" style="position: absolute; left: 0px; top: 0px; width: 1005px; height: 17px;"></div><div class="CodeMirror-selected" style="position: absolute; left: 0px; top: 187px; width: 142.8232421875px; height: 17px;"></div><div class="CodeMirror-selected" style="position: absolute; left: 0px; top: 17px; width: 1005px; height: 170px;"></div></div><div class="CodeMirror-cursors"></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">intersectbed</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">wb</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">a</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02.2</span><span class="cm-variable">M_sig</span>.<span class="cm-variable">hypo</span>.<span class="cm-variable">bedGraph</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">b</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-variable">Cgigas_v9_gene</span><span class="cm-operator">-</span><span class="cm-variable">env</span><span class="cm-operator">-</span><span class="cm-variable">response</span>.<span class="cm-variable">gff</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">cut</span> <span class="cm-operator">-</span><span class="cm-variable">f</span> <span class="cm-number">6</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">sort</span> <span class="cm-operator">|</span> <span class="cm-variable">uniq</span> <span class="cm-operator">-</span><span class="cm-variable">c</span> </span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">intersectbed</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">wb</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">a</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02.2</span><span class="cm-variable">M_sig</span>.<span class="cm-variable">hyper</span>.<span class="cm-variable">bedGraph</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">b</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-variable">Cgigas_v9_gene</span><span class="cm-operator">-</span><span class="cm-variable">env</span><span class="cm-operator">-</span><span class="cm-variable">response</span>.<span class="cm-variable">gff</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">cut</span> <span class="cm-operator">-</span><span class="cm-variable">f</span> <span class="cm-number">6</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">sort</span> <span class="cm-operator">|</span> <span class="cm-variable">uniq</span> <span class="cm-operator">-</span><span class="cm-variable">c</span> </span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 215px;"></div><div class="CodeMirror-gutters" style="display: none; height: 245px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to scroll output; double click to hide" style=""></div><div class="output" style=""><div class="output_area"><div class="prompt"></div><div class="output_subarea output_text output_stream output_stdout"><pre>2063 GLEAN
746 GLEAN
</pre></div></div></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell code_cell rendered unselected" tabindex="2"><div class="input"><div class="prompt input_prompt">In [34]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 141.59375px; left: 417.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true" style=""><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 607.8984375px; margin-bottom: 0px; border-right-width: 30px; min-height: 215px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre>x</pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors" style=""><div class="CodeMirror-cursor" style="left: 412px; top: 136px; height: 17px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">intersectbed</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">wb</span> <span class="cm-error">\</span></span></pre><pre><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">a</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02.4</span><span class="cm-variable">M_sig</span>.<span class="cm-variable">hypo</span>.<span class="cm-variable">bedGraph</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">b</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-variable">Cgigas_v9_gene</span><span class="cm-operator">-</span><span class="cm-variable">env</span><span class="cm-operator">-</span><span class="cm-variable">response</span>.<span class="cm-variable">gff</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">cut</span> <span class="cm-operator">-</span><span class="cm-variable">f</span> <span class="cm-number">6</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">sort</span> <span class="cm-operator">|</span> <span class="cm-variable">uniq</span> <span class="cm-operator">-</span><span class="cm-variable">c</span> </span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">intersectbed</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">wb</span> <span class="cm-error">\</span></span></pre><pre><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">a</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02.4</span><span class="cm-variable">M_sig</span>.<span class="cm-variable">hyper</span>.<span class="cm-variable">bedGraph</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">b</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-variable">Cgigas_v9_gene</span><span class="cm-operator">-</span><span class="cm-variable">env</span><span class="cm-operator">-</span><span class="cm-variable">response</span>.<span class="cm-variable">gff</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">cut</span> <span class="cm-operator">-</span><span class="cm-variable">f</span> <span class="cm-number">6</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">sort</span> <span class="cm-operator">|</span> <span class="cm-variable">uniq</span> <span class="cm-operator">-</span><span class="cm-variable">c</span> </span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 215px;"></div><div class="CodeMirror-gutters" style="display: none; height: 245px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to scroll output; double click to hide" style=""></div><div class="output" style=""><div class="output_area"><div class="prompt"></div><div class="output_subarea output_text output_stream output_stdout"><pre>1873 GLEAN
865 GLEAN
</pre></div></div></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell code_cell rendered unselected" tabindex="2"><div class="input"><div class="prompt input_prompt">In [35]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 39.59375px; left: 30.7978515625px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true" style=""><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 607.8984375px; margin-bottom: 0px; border-right-width: 30px; min-height: 215px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre>x</pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"><div class="CodeMirror-selected" style="position: absolute; left: 25.2041015625px; top: 34px; width: 554.4833984375px; height: 17px;"></div></div><div class="CodeMirror-cursors"></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">intersectbed</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">wb</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">a</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02.6</span><span class="cm-variable">M_sig</span>.<span class="cm-variable">hypo</span>.<span class="cm-variable">bedGraph</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">b</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-variable">Cgigas_v9_gene</span><span class="cm-operator">-</span><span class="cm-variable">env</span><span class="cm-operator">-</span><span class="cm-variable">response</span>.<span class="cm-variable">gff</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">cut</span> <span class="cm-operator">-</span><span class="cm-variable">f</span> <span class="cm-number">6</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">sort</span> <span class="cm-operator">|</span> <span class="cm-variable">uniq</span> <span class="cm-operator">-</span><span class="cm-variable">c</span> </span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">intersectbed</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">wb</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">a</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02.6</span><span class="cm-variable">M_sig</span>.<span class="cm-variable">hyper</span>.<span class="cm-variable">bedGraph</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">b</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-variable">Cgigas_v9_gene</span><span class="cm-operator">-</span><span class="cm-variable">env</span><span class="cm-operator">-</span><span class="cm-variable">response</span>.<span class="cm-variable">gff</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">cut</span> <span class="cm-operator">-</span><span class="cm-variable">f</span> <span class="cm-number">6</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">sort</span> <span class="cm-operator">|</span> <span class="cm-variable">uniq</span> <span class="cm-operator">-</span><span class="cm-variable">c</span> </span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 215px;"></div><div class="CodeMirror-gutters" style="display: none; height: 245px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to scroll output; double click to hide" style=""></div><div class="output" style=""><div class="output_area"><div class="prompt"></div><div class="output_subarea output_text output_stream output_stdout"><pre>2175 GLEAN
1041 GLEAN
</pre></div></div></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell code_cell rendered unselected" tabindex="2"><div class="input"><div class="prompt input_prompt">In [27]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 5.59375px; left: 5.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true" style="right: 0px; left: 0px;"><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 826.333984375px; margin-bottom: 0px; border-right-width: 30px; min-height: 113px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors"><div class="CodeMirror-cursor" style="left: 0px; top: 0px; height: 17px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">intersectbed</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">wb</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">a</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">git</span><span class="cm-operator">-</span><span class="cm-variable">repos</span><span class="cm-operator">/</span><span class="cm-variable">paper</span><span class="cm-operator">-</span><span class="cm-variable">Temp</span><span class="cm-operator">-</span><span class="cm-variable">stress</span><span class="cm-operator">/</span><span class="cm-variable">ipynb</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">/</span><span class="cm-variable">array</span><span class="cm-operator">-</span><span class="cm-variable">design</span><span class="cm-operator">/</span><span class="cm-variable">OID40453_probe_locations</span>.<span class="cm-variable">gff</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">b</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-variable">Cgigas_v9_gene</span><span class="cm-operator">-</span><span class="cm-variable">env</span><span class="cm-operator">-</span><span class="cm-variable">response</span>.<span class="cm-variable">gff</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">cut</span> <span class="cm-operator">-</span><span class="cm-variable">f</span> <span class="cm-number">11</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">sort</span> <span class="cm-operator">|</span> <span class="cm-variable">uniq</span> <span class="cm-operator">-</span><span class="cm-variable">c</span> </span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 113px;"></div><div class="CodeMirror-gutters" style="display: none; height: 143px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to expand output; double click to hide output" style=""></div><div class="output" style=""><div class="output_area"><div class="prompt"></div><div class="output_subarea output_text output_stream output_stdout"><pre>190475 GLEAN
</pre></div></div></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell code_cell unselected rendered" tabindex="2"><div class="input"><div class="prompt input_prompt">In [45]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 5.59375px; left: 5.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true" style="right: 0px; left: 0px;"><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 952px; margin-bottom: 0px; border-right-width: 30px; min-height: 198px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors"><div class="CodeMirror-cursor" style="left: 0px; top: 0px; height: 17px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-comment"># Enter the data comparing Oyster 2 then Probes</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-variable">obs</span> = <span class="cm-variable">array</span>([[<span class="cm-number">2809</span>, <span class="cm-number">10028</span>], [<span class="cm-number">190475</span>, <span class="cm-number">697753</span>]])</span></pre><pre class=""><span style="padding-right: 0.1px;"><span></span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-comment"># Calculate the chi-square test</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-variable">chi2_corrected</span> = <span class="cm-variable">stats</span>.<span class="cm-variable">chi2_contingency</span>(<span class="cm-variable">obs</span>, <span class="cm-variable">correction</span>=<span class="cm-builtin">True</span>)</span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-variable">chi2_uncorrected</span> = <span class="cm-variable">stats</span>.<span class="cm-variable">chi2_contingency</span>(<span class="cm-variable">obs</span>, <span class="cm-variable">correction</span>=<span class="cm-builtin">False</span>)</span></pre><pre class=""><span style="padding-right: 0.1px;"><span></span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-comment"># Print the result</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-keyword">print</span>(<span class="cm-string">'CHI SQUARE'</span>)</span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-keyword">print</span>(<span class="cm-string">'The corrected chi2 value is {0:5.3f}, with p={1:5.3f}'</span>.<span class="cm-builtin">format</span>(<span class="cm-variable">chi2_corrected</span>[<span class="cm-number">0</span>], <span class="cm-variable">chi2_corrected</span>[<span class="cm-number">1</span>]))</span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-keyword">print</span>(<span class="cm-string">'The uncorrected chi2 value is {0:5.3f}, with p={1:5.3f}'</span>.<span class="cm-builtin">format</span>(<span class="cm-variable">chi2_uncorrected</span>[<span class="cm-number">0</span>], <span class="cm-variable">chi2_uncorrected</span>[<span class="cm-number">1</span>]))</span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 198px;"></div><div class="CodeMirror-gutters" style="display: none; height: 228px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to expand output; double click to hide output" style=""></div><div class="output" style=""><div class="output_area"><div class="prompt"></div><div class="output_subarea output_text output_stream output_stdout"><pre>CHI SQUARE
The corrected chi2 value is 1.413, with p=0.235
The uncorrected chi2 value is 1.439, with p=0.230
</pre></div></div></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell code_cell unselected rendered" tabindex="2"><div class="input"><div class="prompt input_prompt">In [48]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 5.59375px; left: 5.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true" style="right: 0px; left: 0px;"><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 952px; margin-bottom: 0px; border-right-width: 30px; min-height: 198px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors"><div class="CodeMirror-cursor" style="left: 0px; top: 0px; height: 17px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-comment"># Enter the data comparing Oyster 4 then Probes</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-variable">obs</span> = <span class="cm-variable">array</span>([[<span class="cm-number">2738</span>, <span class="cm-number">10148</span>], [<span class="cm-number">190475</span>, <span class="cm-number">697753</span>]])</span></pre><pre class=""><span style="padding-right: 0.1px;"><span></span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-comment"># Calculate the chi-square test</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-variable">chi2_corrected</span> = <span class="cm-variable">stats</span>.<span class="cm-variable">chi2_contingency</span>(<span class="cm-variable">obs</span>, <span class="cm-variable">correction</span>=<span class="cm-builtin">True</span>)</span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-variable">chi2_uncorrected</span> = <span class="cm-variable">stats</span>.<span class="cm-variable">chi2_contingency</span>(<span class="cm-variable">obs</span>, <span class="cm-variable">correction</span>=<span class="cm-builtin">False</span>)</span></pre><pre class=""><span style="padding-right: 0.1px;"><span></span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-comment"># Print the result</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-keyword">print</span>(<span class="cm-string">'CHI SQUARE'</span>)</span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-keyword">print</span>(<span class="cm-string">'The corrected chi2 value is {0:5.3f}, with p={1:5.3f}'</span>.<span class="cm-builtin">format</span>(<span class="cm-variable">chi2_corrected</span>[<span class="cm-number">0</span>], <span class="cm-variable">chi2_corrected</span>[<span class="cm-number">1</span>]))</span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-keyword">print</span>(<span class="cm-string">'The uncorrected chi2 value is {0:5.3f}, with p={1:5.3f}'</span>.<span class="cm-builtin">format</span>(<span class="cm-variable">chi2_uncorrected</span>[<span class="cm-number">0</span>], <span class="cm-variable">chi2_uncorrected</span>[<span class="cm-number">1</span>]))</span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 198px;"></div><div class="CodeMirror-gutters" style="display: none; height: 228px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to expand output; double click to hide output" style=""></div><div class="output" style=""><div class="output_area"><div class="prompt"></div><div class="output_subarea output_text output_stream output_stdout"><pre>CHI SQUARE
The corrected chi2 value is 0.280, with p=0.597
The uncorrected chi2 value is 0.291, with p=0.589
</pre></div></div></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell code_cell unselected rendered" tabindex="2"><div class="input"><div class="prompt input_prompt">In [49]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 5.59375px; left: 5.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true" style="right: 0px; left: 0px;"><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 952px; margin-bottom: 0px; border-right-width: 30px; min-height: 198px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors"><div class="CodeMirror-cursor" style="left: 0px; top: 0px; height: 17px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-comment"># Enter the data comparing Oyster 6 then Probes</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-variable">obs</span> = <span class="cm-variable">array</span>([[<span class="cm-number">3216</span>, <span class="cm-number">11690</span>], [<span class="cm-number">190475</span>, <span class="cm-number">697753</span>]])</span></pre><pre class=""><span style="padding-right: 0.1px;"><span></span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-comment"># Calculate the chi-square test</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-variable">chi2_corrected</span> = <span class="cm-variable">stats</span>.<span class="cm-variable">chi2_contingency</span>(<span class="cm-variable">obs</span>, <span class="cm-variable">correction</span>=<span class="cm-builtin">True</span>)</span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-variable">chi2_uncorrected</span> = <span class="cm-variable">stats</span>.<span class="cm-variable">chi2_contingency</span>(<span class="cm-variable">obs</span>, <span class="cm-variable">correction</span>=<span class="cm-builtin">False</span>)</span></pre><pre class=""><span style="padding-right: 0.1px;"><span></span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-comment"># Print the result</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-keyword">print</span>(<span class="cm-string">'CHI SQUARE'</span>)</span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-keyword">print</span>(<span class="cm-string">'The corrected chi2 value is {0:5.3f}, with p={1:5.3f}'</span>.<span class="cm-builtin">format</span>(<span class="cm-variable">chi2_corrected</span>[<span class="cm-number">0</span>], <span class="cm-variable">chi2_corrected</span>[<span class="cm-number">1</span>]))</span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-keyword">print</span>(<span class="cm-string">'The uncorrected chi2 value is {0:5.3f}, with p={1:5.3f}'</span>.<span class="cm-builtin">format</span>(<span class="cm-variable">chi2_uncorrected</span>[<span class="cm-number">0</span>], <span class="cm-variable">chi2_uncorrected</span>[<span class="cm-number">1</span>]))</span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 198px;"></div><div class="CodeMirror-gutters" style="display: none; height: 228px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to expand output; double click to hide output" style=""></div><div class="output" style=""><div class="output_area"><div class="prompt"></div><div class="output_subarea output_text output_stream output_stdout"><pre>CHI SQUARE
The corrected chi2 value is 0.141, with p=0.707
The uncorrected chi2 value is 0.149, with p=0.700
</pre></div></div></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell text_cell rendered unselected" tabindex="2"><div class="prompt input_prompt"></div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-default CodeMirror-wrap"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 5.59375px; left: 27.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true" style=""><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 30px; min-height: 34px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors"><div class="CodeMirror-cursor" style="left: 22px; top: 0px; height: 23px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-header cm-header-1"># TE-Blast</span></span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 34px;"></div><div class="CodeMirror-gutters" style="display: none; height: 64px;"></div></div></div></div><div class="text_cell_render rendered_html" tabindex="-1"><h1 id="TE-Blast">TE-Blast<a class="anchor-link" href="http://localhost:8888/notebooks/ipynb/Array-feature-overlap-05.ipynb#TE-Blast">¶</a></h1>
</div></div></div><div class="cell text_cell rendered unselected" tabindex="2"><div class="prompt input_prompt"></div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-default CodeMirror-wrap"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 22.09375px; left: 400.453125px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true" style=""><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 30px; min-height: 45px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors"><div class="CodeMirror-cursor" style="left: 394.859375px; top: 16.5px; height: 17.5px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-tag cm-bracket"><</span><span class="cm-tag">img</span> <span class="cm-attribute">src</span>=<span class="cm-string">"</span><span class="cm-string cm-link">http://eagle.fish.washington.edu/cnidarian/skitch/Screenshot_4_3_15__7_42_AM_1ACEDE69.png</span><span class="cm-string">"</span> <span class="cm-attribute">alt</span>=<span class="cm-string">"Screenshot_4_3_15__7_42_AM_1ACEDE69.png"</span><span class="cm-tag cm-bracket">/></span></span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 45px;"></div><div class="CodeMirror-gutters" style="display: none; height: 75px;"></div></div></div></div><div class="text_cell_render rendered_html" tabindex="-1"><p><img src="./Array-feature-overlap-05_files/Screenshot_4_3_15__7_42_AM_1ACEDE69.png" alt="Screenshot_4_3_15__7_42_AM_1ACEDE69.png"></p>
</div></div></div><div class="cell code_cell rendered unselected" tabindex="2"><div class="input"><div class="prompt input_prompt">In [37]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 5.59375px; left: 5.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true"><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 700.3134765625px; margin-bottom: 0px; border-right-width: 30px; min-height: 215px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre>x</pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"><div class="CodeMirror-selected" style="position: absolute; left: 0px; top: 0px; width: 1005px; height: 17px;"></div><div class="CodeMirror-selected" style="position: absolute; left: 0px; top: 187px; width: 243.625px; height: 17px;"></div><div class="CodeMirror-selected" style="position: absolute; left: 0px; top: 17px; width: 1005px; height: 170px;"></div></div><div class="CodeMirror-cursors" style="visibility: hidden;"></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">intersectbed</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">wb</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">a</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02.2</span><span class="cm-variable">M_sig</span>.<span class="cm-variable">hypo</span>.<span class="cm-variable">bedGraph</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">b</span> <span class="cm-operator">/</span><span class="cm-variable">Volumes</span><span class="cm-operator">/</span><span class="cm-variable">web</span><span class="cm-operator">-</span><span class="cm-number">1</span><span class="cm-operator">/</span><span class="cm-variable">trilobite</span><span class="cm-operator">/</span><span class="cm-variable">Crassostrea_gigas_v9_tracks</span><span class="cm-operator">/</span><span class="cm-variable">Cgigas_v9_TE</span><span class="cm-operator">-</span><span class="cm-variable">WUBLASTX</span>.<span class="cm-variable">gff</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">cut</span> <span class="cm-operator">-</span><span class="cm-variable">f</span> <span class="cm-number">6</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">sort</span> <span class="cm-operator">|</span> <span class="cm-variable">uniq</span> <span class="cm-operator">-</span><span class="cm-variable">c</span> <span class="cm-operator">|</span> <span class="cm-variable">sed</span> <span class="cm-string">'/#/d'</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">intersectbed</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">wb</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">a</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02.2</span><span class="cm-variable">M_sig</span>.<span class="cm-variable">hyper</span>.<span class="cm-variable">bedGraph</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">b</span> <span class="cm-operator">/</span><span class="cm-variable">Volumes</span><span class="cm-operator">/</span><span class="cm-variable">web</span><span class="cm-operator">-</span><span class="cm-number">1</span><span class="cm-operator">/</span><span class="cm-variable">trilobite</span><span class="cm-operator">/</span><span class="cm-variable">Crassostrea_gigas_v9_tracks</span><span class="cm-operator">/</span><span class="cm-variable">Cgigas_v9_TE</span><span class="cm-operator">-</span><span class="cm-variable">WUBLASTX</span>.<span class="cm-variable">gff</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">cut</span> <span class="cm-operator">-</span><span class="cm-variable">f</span> <span class="cm-number">6</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">sort</span> <span class="cm-operator">|</span> <span class="cm-variable">uniq</span> <span class="cm-operator">-</span><span class="cm-variable">c</span> <span class="cm-operator">|</span> <span class="cm-variable">sed</span> <span class="cm-string">'/#/d'</span></span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 215px;"></div><div class="CodeMirror-gutters" style="display: none; height: 245px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to scroll output; double click to hide" style=""></div><div class="output" style=""><div class="output_area"><div class="prompt"></div><div class="output_subarea output_text output_stream output_stdout"><pre> 368 WUBlastX
15 WUBlastX
</pre></div></div></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell code_cell rendered unselected" tabindex="2"><div class="input"><div class="prompt input_prompt">In [38]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 124.59375px; left: 47.6005859375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true"><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 700.3134765625px; margin-bottom: 0px; border-right-width: 30px; min-height: 215px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors"><div class="CodeMirror-cursor" style="left: 42.0068359375px; top: 119px; height: 17px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">intersectbed</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">wb</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">a</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02.4</span><span class="cm-variable">M_sig</span>.<span class="cm-variable">hypo</span>.<span class="cm-variable">bedGraph</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">b</span> <span class="cm-operator">/</span><span class="cm-variable">Volumes</span><span class="cm-operator">/</span><span class="cm-variable">web</span><span class="cm-operator">-</span><span class="cm-number">1</span><span class="cm-operator">/</span><span class="cm-variable">trilobite</span><span class="cm-operator">/</span><span class="cm-variable">Crassostrea_gigas_v9_tracks</span><span class="cm-operator">/</span><span class="cm-variable">Cgigas_v9_TE</span><span class="cm-operator">-</span><span class="cm-variable">WUBLASTX</span>.<span class="cm-variable">gff</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">cut</span> <span class="cm-operator">-</span><span class="cm-variable">f</span> <span class="cm-number">6</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">sort</span> <span class="cm-operator">|</span> <span class="cm-variable">uniq</span> <span class="cm-operator">-</span><span class="cm-variable">c</span> <span class="cm-operator">|</span> <span class="cm-variable">sed</span> <span class="cm-string">'/#/d'</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">intersectbed</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">wb</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">a</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02.4</span><span class="cm-variable">M_sig</span>.<span class="cm-variable">hyper</span>.<span class="cm-variable">bedGraph</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">b</span> <span class="cm-operator">/</span><span class="cm-variable">Volumes</span><span class="cm-operator">/</span><span class="cm-variable">web</span><span class="cm-operator">-</span><span class="cm-number">1</span><span class="cm-operator">/</span><span class="cm-variable">trilobite</span><span class="cm-operator">/</span><span class="cm-variable">Crassostrea_gigas_v9_tracks</span><span class="cm-operator">/</span><span class="cm-variable">Cgigas_v9_TE</span><span class="cm-operator">-</span><span class="cm-variable">WUBLASTX</span>.<span class="cm-variable">gff</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">cut</span> <span class="cm-operator">-</span><span class="cm-variable">f</span> <span class="cm-number">6</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">sort</span> <span class="cm-operator">|</span> <span class="cm-variable">uniq</span> <span class="cm-operator">-</span><span class="cm-variable">c</span> <span class="cm-operator">|</span> <span class="cm-variable">sed</span> <span class="cm-string">'/#/d'</span></span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 215px;"></div><div class="CodeMirror-gutters" style="display: none; height: 245px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to scroll output; double click to hide" style=""></div><div class="output" style=""><div class="output_area"><div class="prompt"></div><div class="output_subarea output_text output_stream output_stdout"><pre> 251 WUBlastX
3 WUBlastX
</pre></div></div></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell code_cell rendered unselected" tabindex="2"><div class="input"><div class="prompt input_prompt">In [39]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 39.59375px; left: 30.7978515625px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true"><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1" draggable="false"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 700.3134765625px; margin-bottom: 0px; border-right-width: 30px; min-height: 215px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre>x</pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"><div class="CodeMirror-selected" style="position: absolute; left: 25.2041015625px; top: 34px; width: 554.4833984375px; height: 17px;"></div></div><div class="CodeMirror-cursors" style="visibility: hidden;"></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">intersectbed</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">wb</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">a</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02.6</span><span class="cm-variable">M_sig</span>.<span class="cm-variable">hypo</span>.<span class="cm-variable">bedGraph</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">b</span> <span class="cm-operator">/</span><span class="cm-variable">Volumes</span><span class="cm-operator">/</span><span class="cm-variable">web</span><span class="cm-operator">-</span><span class="cm-number">1</span><span class="cm-operator">/</span><span class="cm-variable">trilobite</span><span class="cm-operator">/</span><span class="cm-variable">Crassostrea_gigas_v9_tracks</span><span class="cm-operator">/</span><span class="cm-variable">Cgigas_v9_TE</span><span class="cm-operator">-</span><span class="cm-variable">WUBLASTX</span>.<span class="cm-variable">gff</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">cut</span> <span class="cm-operator">-</span><span class="cm-variable">f</span> <span class="cm-number">6</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">sort</span> <span class="cm-operator">|</span> <span class="cm-variable">uniq</span> <span class="cm-operator">-</span><span class="cm-variable">c</span> <span class="cm-operator">|</span> <span class="cm-variable">sed</span> <span class="cm-string">'/#/d'</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">intersectbed</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">wb</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">a</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02.6</span><span class="cm-variable">M_sig</span>.<span class="cm-variable">hyper</span>.<span class="cm-variable">bedGraph</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">b</span> <span class="cm-operator">/</span><span class="cm-variable">Volumes</span><span class="cm-operator">/</span><span class="cm-variable">web</span><span class="cm-operator">-</span><span class="cm-number">1</span><span class="cm-operator">/</span><span class="cm-variable">trilobite</span><span class="cm-operator">/</span><span class="cm-variable">Crassostrea_gigas_v9_tracks</span><span class="cm-operator">/</span><span class="cm-variable">Cgigas_v9_TE</span><span class="cm-operator">-</span><span class="cm-variable">WUBLASTX</span>.<span class="cm-variable">gff</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">cut</span> <span class="cm-operator">-</span><span class="cm-variable">f</span> <span class="cm-number">6</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">sort</span> <span class="cm-operator">|</span> <span class="cm-variable">uniq</span> <span class="cm-operator">-</span><span class="cm-variable">c</span> <span class="cm-operator">|</span> <span class="cm-variable">sed</span> <span class="cm-string">'/#/d'</span></span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 215px;"></div><div class="CodeMirror-gutters" style="display: none; height: 245px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to scroll output; double click to hide" style=""></div><div class="output" style=""><div class="output_area"><div class="prompt"></div><div class="output_subarea output_text output_stream output_stdout"><pre> 141 WUBlastX
27 WUBlastX
</pre></div></div></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell text_cell rendered unselected" tabindex="2"><div class="prompt input_prompt"></div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-default CodeMirror-wrap"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 5.59375px; left: 144.1875px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true" style=""><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 30px; min-height: 34px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors" style="visibility: hidden;"><div class="CodeMirror-cursor" style="left: 138.59375px; top: 0px; height: 23px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-header cm-header-1"># Promoter</span></span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 34px;"></div><div class="CodeMirror-gutters" style="display: none; height: 64px;"></div></div></div></div><div class="text_cell_render rendered_html" tabindex="-1"><h1 id="Promoter">Promoter<a class="anchor-link" href="http://localhost:8888/notebooks/ipynb/Array-feature-overlap-05.ipynb#Promoter">¶</a></h1>
</div></div></div><div class="cell text_cell rendered unselected" tabindex="2"><div class="prompt input_prompt"></div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-default CodeMirror-wrap"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 5.59375px; left: 5.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true" style=""><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 30px; min-height: 45px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors"><div class="CodeMirror-cursor" style="left: 0px; top: 0px; height: 16.5px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-tag cm-bracket"><</span><span class="cm-tag">img</span> <span class="cm-attribute">src</span>=<span class="cm-string">"</span><span class="cm-string cm-link">http://eagle.fish.washington.edu/cnidarian/skitch/Screenshot_4_3_15__7_48_AM_1ACEDFD9.png</span><span class="cm-string">"</span> <span class="cm-attribute">alt</span>=<span class="cm-string">"Screenshot_4_3_15__7_48_AM_1ACEDFD9.png"</span><span class="cm-tag cm-bracket">/></span></span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 45px;"></div><div class="CodeMirror-gutters" style="display: none; height: 75px;"></div></div></div></div><div class="text_cell_render rendered_html" tabindex="-1"><p><img src="./Array-feature-overlap-05_files/Screenshot_4_3_15__7_48_AM_1ACEDFD9.png" alt="Screenshot_4_3_15__7_48_AM_1ACEDFD9.png"></p>
</div></div></div><div class="cell code_cell rendered unselected" tabindex="2"><div class="input"><div class="prompt input_prompt">In [40]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 5.59375px; left: 5.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true"><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1" draggable="false"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 759.123046875px; margin-bottom: 0px; border-right-width: 30px; min-height: 215px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre>x</pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"><div class="CodeMirror-selected" style="position: absolute; left: 0px; top: 0px; width: 1005px; height: 17px;"></div><div class="CodeMirror-selected" style="position: absolute; left: 0px; top: 187px; width: 243.625px; height: 17px;"></div><div class="CodeMirror-selected" style="position: absolute; left: 0px; top: 17px; width: 1005px; height: 170px;"></div></div><div class="CodeMirror-cursors"></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">intersectbed</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">wb</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">a</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02.2</span><span class="cm-variable">M_sig</span>.<span class="cm-variable">hypo</span>.<span class="cm-variable">bedGraph</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">b</span> <span class="cm-operator">/</span><span class="cm-variable">Volumes</span><span class="cm-operator">/</span><span class="cm-variable">web</span><span class="cm-operator">-</span><span class="cm-number">1</span><span class="cm-operator">/</span><span class="cm-variable">trilobite</span><span class="cm-operator">/</span><span class="cm-variable">Crassostrea_gigas_v9_tracks</span><span class="cm-operator">/</span><span class="cm-variable">Cgigas_v9_1k5p_gene_promoter</span>.<span class="cm-variable">gff</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">cut</span> <span class="cm-operator">-</span><span class="cm-variable">f</span> <span class="cm-number">6</span>,<span class="cm-number">7</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">sort</span> <span class="cm-operator">|</span> <span class="cm-variable">uniq</span> <span class="cm-operator">-</span><span class="cm-variable">c</span> <span class="cm-operator">|</span> <span class="cm-variable">sed</span> <span class="cm-string">'/#/d'</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">intersectbed</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">wb</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">a</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02.2</span><span class="cm-variable">M_sig</span>.<span class="cm-variable">hyper</span>.<span class="cm-variable">bedGraph</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">b</span> <span class="cm-operator">/</span><span class="cm-variable">Volumes</span><span class="cm-operator">/</span><span class="cm-variable">web</span><span class="cm-operator">-</span><span class="cm-number">1</span><span class="cm-operator">/</span><span class="cm-variable">trilobite</span><span class="cm-operator">/</span><span class="cm-variable">Crassostrea_gigas_v9_tracks</span><span class="cm-operator">/</span><span class="cm-variable">Cgigas_v9_1k5p_gene_promoter</span>.<span class="cm-variable">gff</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">cut</span> <span class="cm-operator">-</span><span class="cm-variable">f</span> <span class="cm-number">6</span>,<span class="cm-number">7</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">sort</span> <span class="cm-operator">|</span> <span class="cm-variable">uniq</span> <span class="cm-operator">-</span><span class="cm-variable">c</span> <span class="cm-operator">|</span> <span class="cm-variable">sed</span> <span class="cm-string">'/#/d'</span></span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 215px;"></div><div class="CodeMirror-gutters" style="display: none; height: 245px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to scroll output; double click to hide" style=""></div><div class="output" style=""><div class="output_area"><div class="prompt"></div><div class="output_subarea output_text output_stream output_stdout"><pre> 720 flankbed promoter
256 flankbed promoter
</pre></div></div></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell code_cell rendered unselected" tabindex="2"><div class="input"><div class="prompt input_prompt">In [41]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 39.59375px; left: 30.7978515625px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true"><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 759.123046875px; margin-bottom: 0px; border-right-width: 30px; min-height: 215px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre>x</pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"><div class="CodeMirror-selected" style="position: absolute; left: 25.2041015625px; top: 34px; width: 554.4833984375px; height: 17px;"></div></div><div class="CodeMirror-cursors"></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">intersectbed</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">wb</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">a</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02.4</span><span class="cm-variable">M_sig</span>.<span class="cm-variable">hypo</span>.<span class="cm-variable">bedGraph</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">b</span> <span class="cm-operator">/</span><span class="cm-variable">Volumes</span><span class="cm-operator">/</span><span class="cm-variable">web</span><span class="cm-operator">-</span><span class="cm-number">1</span><span class="cm-operator">/</span><span class="cm-variable">trilobite</span><span class="cm-operator">/</span><span class="cm-variable">Crassostrea_gigas_v9_tracks</span><span class="cm-operator">/</span><span class="cm-variable">Cgigas_v9_1k5p_gene_promoter</span>.<span class="cm-variable">gff</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">cut</span> <span class="cm-operator">-</span><span class="cm-variable">f</span> <span class="cm-number">6</span>,<span class="cm-number">7</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">sort</span> <span class="cm-operator">|</span> <span class="cm-variable">uniq</span> <span class="cm-operator">-</span><span class="cm-variable">c</span> <span class="cm-operator">|</span> <span class="cm-variable">sed</span> <span class="cm-string">'/#/d'</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">intersectbed</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">wb</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">a</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02.4</span><span class="cm-variable">M_sig</span>.<span class="cm-variable">hyper</span>.<span class="cm-variable">bedGraph</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">b</span> <span class="cm-operator">/</span><span class="cm-variable">Volumes</span><span class="cm-operator">/</span><span class="cm-variable">web</span><span class="cm-operator">-</span><span class="cm-number">1</span><span class="cm-operator">/</span><span class="cm-variable">trilobite</span><span class="cm-operator">/</span><span class="cm-variable">Crassostrea_gigas_v9_tracks</span><span class="cm-operator">/</span><span class="cm-variable">Cgigas_v9_1k5p_gene_promoter</span>.<span class="cm-variable">gff</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">cut</span> <span class="cm-operator">-</span><span class="cm-variable">f</span> <span class="cm-number">6</span>,<span class="cm-number">7</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">sort</span> <span class="cm-operator">|</span> <span class="cm-variable">uniq</span> <span class="cm-operator">-</span><span class="cm-variable">c</span> <span class="cm-operator">|</span> <span class="cm-variable">sed</span> <span class="cm-string">'/#/d'</span></span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 215px;"></div><div class="CodeMirror-gutters" style="display: none; height: 245px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to scroll output; double click to hide" style=""></div><div class="output" style=""><div class="output_area"><div class="prompt"></div><div class="output_subarea output_text output_stream output_stdout"><pre> 684 flankbed promoter
308 flankbed promoter
</pre></div></div></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell text_cell rendered unselected" tabindex="2"><div class="prompt input_prompt"></div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-default CodeMirror-wrap"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 141.59375px; left: 425.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px; bottom: 0px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true" style=""><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 30px; min-height: 215px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors"><div class="CodeMirror-cursor" style="left: 420px; top: 136px; height: 17px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;">!intersectbed \</span></pre><pre class=""><span style="padding-right: 0.1px;">-wb \</span></pre><pre class=""><span style="padding-right: 0.1px;">-a /Users/sr320/data-genomic/tentacle/2014.07.02.6M_sig.hypo.bedGraph \</span></pre><pre class=""><span style="padding-right: 0.1px;">-b /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_1k5p_gene_promoter.gff \</span></pre><pre class=""><span style="padding-right: 0.1px;">| cut -f 6,7 \</span></pre><pre class=""><span style="padding-right: 0.1px;">| sort | uniq -c | sed '/#/d'</span></pre><pre class=""><span style="padding-right: 0.1px;">!intersectbed \</span></pre><pre class=""><span style="padding-right: 0.1px;">-wb \</span></pre><pre class=""><span style="padding-right: 0.1px;">-a /Users/sr320/data-genomic/tentacle/2014.07.02.6M_sig.hyper.bedGraph \</span></pre><pre class=""><span style="padding-right: 0.1px;">-b /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_1k5p_gene_promoter.gff \</span></pre><pre class=""><span style="padding-right: 0.1px;">| cut -f 6,7 \</span></pre><pre class=""><span style="padding-right: 0.1px;">| sort | uniq -c | sed '/#/d'</span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 215px;"></div><div class="CodeMirror-gutters" style="display: none; height: 245px;"></div></div></div></div><div class="text_cell_render rendered_html" tabindex="-1"><p>!intersectbed \
-wb \
-a /Users/sr320/data-genomic/tentacle/2014.07.02.6M_sig.hypo.bedGraph \
-b /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_1k5p_gene_promoter.gff \
| cut -f 6,7 \
| sort | uniq -c | sed '/#/d'
!intersectbed \
-wb \
-a /Users/sr320/data-genomic/tentacle/2014.07.02.6M_sig.hyper.bedGraph \
-b /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_1k5p_gene_promoter.gff \
| cut -f 6,7 \
| sort | uniq -c | sed '/#/d'</p>
</div></div></div><div class="cell text_cell rendered unselected" tabindex="2"><div class="prompt input_prompt"></div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-default CodeMirror-wrap"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 5.59375px; left: 27.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true" style=""><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 30px; min-height: 34px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors"><div class="CodeMirror-cursor" style="left: 22px; top: 0px; height: 23px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-header cm-header-1"># Chi2 test to compare hypo v hyper?</span></span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 34px;"></div><div class="CodeMirror-gutters" style="display: none; height: 64px;"></div></div></div></div><div class="text_cell_render rendered_html" tabindex="-1"><h1 id="Chi2-test-to-compare-hypo-v-hyper?">Chi2 test to compare hypo v hyper?<a class="anchor-link" href="http://localhost:8888/notebooks/ipynb/Array-feature-overlap-05.ipynb#Chi2-test-to-compare-hypo-v-hyper?">¶</a></h1>
</div></div></div><div class="cell code_cell rendered unselected" tabindex="2"><div class="input"><div class="prompt input_prompt">In [43]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 175.59375px; left: 954.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true"><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 952px; margin-bottom: 0px; border-right-width: 30px; min-height: 198px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre>x</pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"><div class="CodeMirror-selected" style="position: absolute; left: 0px; top: 0px; width: 1005px; height: 17px;"></div><div class="CodeMirror-selected" style="position: absolute; left: 0px; top: 170px; width: 949px; height: 17px;"></div><div class="CodeMirror-selected" style="position: absolute; left: 0px; top: 17px; width: 1005px; height: 153px;"></div></div><div class="CodeMirror-cursors"></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-comment"># Enter the data comparing Oyster ALL hypo versus hyper -HOUSEKEEPING</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-variable">obs</span> = <span class="cm-variable">array</span>([[<span class="cm-number">6527</span>, <span class="cm-number">21429</span>], [<span class="cm-number">3871</span>, <span class="cm-number">10434</span>]])</span></pre><pre class=""><span style="padding-right: 0.1px;"><span></span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-comment"># Calculate the chi-square test</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-variable">chi2_corrected</span> = <span class="cm-variable">stats</span>.<span class="cm-variable">chi2_contingency</span>(<span class="cm-variable">obs</span>, <span class="cm-variable">correction</span>=<span class="cm-builtin">True</span>)</span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-variable">chi2_uncorrected</span> = <span class="cm-variable">stats</span>.<span class="cm-variable">chi2_contingency</span>(<span class="cm-variable">obs</span>, <span class="cm-variable">correction</span>=<span class="cm-builtin">False</span>)</span></pre><pre class=""><span style="padding-right: 0.1px;"><span></span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-comment"># Print the result</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-keyword">print</span>(<span class="cm-string">'CHI SQUARE'</span>)</span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-keyword">print</span>(<span class="cm-string">'The corrected chi2 value is {0:5.3f}, with p={1:5.3f}'</span>.<span class="cm-builtin">format</span>(<span class="cm-variable">chi2_corrected</span>[<span class="cm-number">0</span>], <span class="cm-variable">chi2_corrected</span>[<span class="cm-number">1</span>]))</span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-keyword">print</span>(<span class="cm-string">'The uncorrected chi2 value is {0:5.3f}, with p={1:5.3f}'</span>.<span class="cm-builtin">format</span>(<span class="cm-variable">chi2_uncorrected</span>[<span class="cm-number">0</span>], <span class="cm-variable">chi2_uncorrected</span>[<span class="cm-number">1</span>]))</span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 198px;"></div><div class="CodeMirror-gutters" style="display: none; height: 228px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to scroll output; double click to hide" style=""></div><div class="output" style=""><div class="output_area"><div class="prompt"></div><div class="output_subarea output_text output_stream output_stdout"><pre>CHI SQUARE
The corrected chi2 value is 70.128, with p=0.000
The uncorrected chi2 value is 70.329, with p=0.000
</pre></div></div></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell code_cell rendered unselected" tabindex="2"><div class="input"><div class="prompt input_prompt">In [44]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 5.59375px; left: 5.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true"><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 952px; margin-bottom: 0px; border-right-width: 30px; min-height: 198px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre>x</pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"><div class="CodeMirror-selected" style="position: absolute; left: 0px; top: 0px; width: 1005px; height: 17px;"></div><div class="CodeMirror-selected" style="position: absolute; left: 0px; top: 170px; width: 949px; height: 17px;"></div><div class="CodeMirror-selected" style="position: absolute; left: 0px; top: 17px; width: 1005px; height: 153px;"></div></div><div class="CodeMirror-cursors" style="visibility: hidden;"></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-comment"># Enter the data comparing Oyster ALL hypo versus hyper -DEGS</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-variable">obs</span> = <span class="cm-variable">array</span>([[<span class="cm-number">1524</span>, <span class="cm-number">21429</span>], [<span class="cm-number">692</span>, <span class="cm-number">10434</span>]])</span></pre><pre class=""><span style="padding-right: 0.1px;"><span></span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-comment"># Calculate the chi-square test</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-variable">chi2_corrected</span> = <span class="cm-variable">stats</span>.<span class="cm-variable">chi2_contingency</span>(<span class="cm-variable">obs</span>, <span class="cm-variable">correction</span>=<span class="cm-builtin">True</span>)</span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-variable">chi2_uncorrected</span> = <span class="cm-variable">stats</span>.<span class="cm-variable">chi2_contingency</span>(<span class="cm-variable">obs</span>, <span class="cm-variable">correction</span>=<span class="cm-builtin">False</span>)</span></pre><pre class=""><span style="padding-right: 0.1px;"><span></span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-comment"># Print the result</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-keyword">print</span>(<span class="cm-string">'CHI SQUARE'</span>)</span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-keyword">print</span>(<span class="cm-string">'The corrected chi2 value is {0:5.3f}, with p={1:5.3f}'</span>.<span class="cm-builtin">format</span>(<span class="cm-variable">chi2_corrected</span>[<span class="cm-number">0</span>], <span class="cm-variable">chi2_corrected</span>[<span class="cm-number">1</span>]))</span></pre><pre><span style="padding-right: 0.1px;"><span class="cm-keyword">print</span>(<span class="cm-string">'The uncorrected chi2 value is {0:5.3f}, with p={1:5.3f}'</span>.<span class="cm-builtin">format</span>(<span class="cm-variable">chi2_uncorrected</span>[<span class="cm-number">0</span>], <span class="cm-variable">chi2_uncorrected</span>[<span class="cm-number">1</span>]))</span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 198px;"></div><div class="CodeMirror-gutters" style="display: none; height: 228px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to scroll output; double click to hide" style=""></div><div class="output" style=""><div class="output_area"><div class="prompt"></div><div class="output_subarea output_text output_stream output_stdout"><pre>CHI SQUARE
The corrected chi2 value is 2.106, with p=0.147
The uncorrected chi2 value is 2.174, with p=0.140
</pre></div></div></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell code_cell rendered unselected" tabindex="2"><div class="input"><div class="prompt input_prompt">In [45]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 22.59375px; left: 257.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true"><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 952.3544921875px; margin-bottom: 0px; border-right-width: 30px; min-height: 198px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre>x</pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors" style="visibility: hidden;"><div class="CodeMirror-cursor" style="left: 252px; top: 17px; height: 17px;"> </div></div><div class="CodeMirror-code"><pre><span style="padding-right: 0.1px;"><span class="cm-comment"># Enter the data comparing Oyster ALL hypo versus hyper -TE blast</span></span></pre><pre><span style="padding-right: 0.1px;"><span class="cm-variable">obs</span> = <span class="cm-variable">array</span>([[<span class="cm-number">760</span>, <span class="cm-number">21429</span>], [<span class="cm-number">45</span>, <span class="cm-number">10434</span>]])</span></pre><pre class=""><span style="padding-right: 0.1px;"><span></span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-comment"># Calculate the chi-square test</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-variable">chi2_corrected</span> = <span class="cm-variable">stats</span>.<span class="cm-variable">chi2_contingency</span>(<span class="cm-variable">obs</span>, <span class="cm-variable">correction</span>=<span class="cm-builtin">True</span>)</span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-variable">chi2_uncorrected</span> = <span class="cm-variable">stats</span>.<span class="cm-variable">chi2_contingency</span>(<span class="cm-variable">obs</span>, <span class="cm-variable">correction</span>=<span class="cm-builtin">False</span>)</span></pre><pre class=""><span style="padding-right: 0.1px;"><span></span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-comment"># Print the result</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-keyword">print</span>(<span class="cm-string">'CHI SQUARE'</span>)</span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-keyword">print</span>(<span class="cm-string">'The corrected chi2 value is {0:5.3f}, with p={1:5.3f}'</span>.<span class="cm-builtin">format</span>(<span class="cm-variable">chi2_corrected</span>[<span class="cm-number">0</span>], <span class="cm-variable">chi2_corrected</span>[<span class="cm-number">1</span>]))</span></pre><pre><span style="padding-right: 0.1px;"><span class="cm-keyword">print</span>(<span class="cm-string">'The uncorrected chi2 value is {0:5.3f}, with p={1:5.3f}'</span>.<span class="cm-builtin">format</span>(<span class="cm-variable">chi2_uncorrected</span>[<span class="cm-number">0</span>], <span class="cm-variable">chi2_uncorrected</span>[<span class="cm-number">1</span>]))</span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 198px;"></div><div class="CodeMirror-gutters" style="display: none; height: 228px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to scroll output; double click to hide" style=""></div><div class="output" style=""><div class="output_area"><div class="prompt"></div><div class="output_subarea output_text output_stream output_stdout"><pre>CHI SQUARE
The corrected chi2 value is 264.516, with p=0.000
The uncorrected chi2 value is 265.761, with p=0.000
</pre></div></div></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell text_cell rendered unselected" tabindex="2"><div class="prompt input_prompt"></div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-default CodeMirror-wrap"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 5.59375px; left: 644.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true" style=""><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 30px; min-height: 45px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors"><div class="CodeMirror-cursor" style="left: 639px; top: 0px; height: 16.5px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-tag cm-bracket"><</span><span class="cm-tag">img</span> <span class="cm-attribute">src</span>=<span class="cm-string">"</span><span class="cm-string cm-link">http://eagle.fish.washington.edu/cnidarian/skitch/Screenshot_4_3_15__8_07_AM_1ACEE442.png</span><span class="cm-string">"</span> <span class="cm-attribute">alt</span>=<span class="cm-string">"Screenshot_4_3_15__8_07_AM_1ACEE442.png"</span><span class="cm-tag cm-bracket">/></span></span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 45px;"></div><div class="CodeMirror-gutters" style="display: none; height: 75px;"></div></div></div></div><div class="text_cell_render rendered_html" tabindex="-1"><p><img src="./Array-feature-overlap-05_files/Screenshot_4_3_15__8_07_AM_1ACEE442.png" alt="Screenshot_4_3_15__8_07_AM_1ACEE442.png"></p>
</div></div></div><div class="cell text_cell rendered unselected" tabindex="2"><div class="prompt input_prompt"></div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-default CodeMirror-wrap"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 5.59375px; left: 27.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true" style=""><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 30px; min-height: 34px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors"><div class="CodeMirror-cursor" style="left: 22px; top: 0px; height: 23px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-header cm-header-1"># Hypo v Hyper on Ensembl gff - gives data on gene body, and repeats</span></span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 34px;"></div><div class="CodeMirror-gutters" style="display: none; height: 64px;"></div></div></div></div><div class="text_cell_render rendered_html" tabindex="-1"><h1 id="Hypo-v-Hyper-on-Ensembl-gff---gives-data-on-gene-body,-and-repeats">Hypo v Hyper on Ensembl gff - gives data on gene body, and repeats<a class="anchor-link" href="http://localhost:8888/notebooks/ipynb/Array-feature-overlap-05.ipynb#Hypo-v-Hyper-on-Ensembl-gff---gives-data-on-gene-body,-and-repeats">¶</a></h1>
</div></div></div><div class="cell code_cell rendered unselected" tabindex="2"><div class="input"><div class="prompt input_prompt">In [48]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 5.59375px; left: 5.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true"><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1" draggable="false"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 935.5517578125px; margin-bottom: 0px; border-right-width: 30px; min-height: 249px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre>x</pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"><div class="CodeMirror-selected" style="position: absolute; left: 0px; top: 0px; width: 1005px; height: 17px;"></div><div class="CodeMirror-selected" style="position: absolute; left: 0px; top: 221px; width: 243.625px; height: 17px;"></div><div class="CodeMirror-selected" style="position: absolute; left: 0px; top: 17px; width: 1005px; height: 204px;"></div></div><div class="CodeMirror-cursors" style="visibility: hidden;"></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">echo</span> <span class="cm-string">"hypo"</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">intersectbed</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">wb</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">a</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02.2</span><span class="cm-variable">M_sig</span>.<span class="cm-variable">hypo</span>.<span class="cm-variable">bedGraph</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">b</span> <span class="cm-operator">/</span><span class="cm-variable">Volumes</span><span class="cm-operator">/</span><span class="cm-variable">web</span><span class="cm-operator">-</span><span class="cm-number">1</span><span class="cm-operator">/</span><span class="cm-variable">trilobite</span><span class="cm-operator">/</span><span class="cm-variable">Crassostrea_gigas_ensembl_tracks</span><span class="cm-operator">/</span><span class="cm-variable">Crassostrea_gigas</span>.<span class="cm-variable">GCA_000297895</span><span class="cm-number">.1.25</span>.<span class="cm-builtin">sorted</span>.<span class="cm-variable">gff3</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">cut</span> <span class="cm-operator">-</span><span class="cm-variable">f</span> <span class="cm-number">6</span>,<span class="cm-number">7</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">sort</span> <span class="cm-operator">|</span> <span class="cm-variable">uniq</span> <span class="cm-operator">-</span><span class="cm-variable">c</span> <span class="cm-operator">|</span> <span class="cm-variable">sed</span> <span class="cm-string">'/#/d'</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">echo</span> <span class="cm-string">"hyper"</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">intersectbed</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">wb</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">a</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02.2</span><span class="cm-variable">M_sig</span>.<span class="cm-variable">hyper</span>.<span class="cm-variable">bedGraph</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">b</span> <span class="cm-operator">/</span><span class="cm-variable">Volumes</span><span class="cm-operator">/</span><span class="cm-variable">web</span><span class="cm-operator">-</span><span class="cm-number">1</span><span class="cm-operator">/</span><span class="cm-variable">trilobite</span><span class="cm-operator">/</span><span class="cm-variable">Crassostrea_gigas_ensembl_tracks</span><span class="cm-operator">/</span><span class="cm-variable">Crassostrea_gigas</span>.<span class="cm-variable">GCA_000297895</span><span class="cm-number">.1.25</span>.<span class="cm-builtin">sorted</span>.<span class="cm-variable">gff3</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">cut</span> <span class="cm-operator">-</span><span class="cm-variable">f</span> <span class="cm-number">6</span>,<span class="cm-number">7</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">sort</span> <span class="cm-operator">|</span> <span class="cm-variable">uniq</span> <span class="cm-operator">-</span><span class="cm-variable">c</span> <span class="cm-operator">|</span> <span class="cm-variable">sed</span> <span class="cm-string">'/#/d'</span></span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 249px;"></div><div class="CodeMirror-gutters" style="display: none; height: 279px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to scroll output; double click to hide" style=""></div><div class="output" style=""><div class="output_area"><div class="prompt"></div><div class="output_subarea output_text output_stream output_stdout"><pre>hypo
1065 GigaDB CDS
1065 GigaDB exon
6094 GigaDB gene
6094 GigaDB transcript
918 dust repeat_region
819 trf repeat_region
hyper
308 GigaDB CDS
308 GigaDB exon
2374 GigaDB gene
2374 GigaDB transcript
322 dust repeat_region
156 trf repeat_region
</pre></div></div></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell code_cell rendered unselected" tabindex="2"><div class="input"><div class="prompt input_prompt">In [50]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 158.59375px; left: 47.6005859375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true"><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 935.5517578125px; margin-bottom: 0px; border-right-width: 30px; min-height: 249px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors" style="visibility: hidden;"><div class="CodeMirror-cursor" style="left: 42.0068359375px; top: 153px; height: 17px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">echo</span> <span class="cm-string">"hypo"</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">intersectbed</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">wb</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">a</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02.4</span><span class="cm-variable">M_sig</span>.<span class="cm-variable">hypo</span>.<span class="cm-variable">bedGraph</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">b</span> <span class="cm-operator">/</span><span class="cm-variable">Volumes</span><span class="cm-operator">/</span><span class="cm-variable">web</span><span class="cm-operator">-</span><span class="cm-number">1</span><span class="cm-operator">/</span><span class="cm-variable">trilobite</span><span class="cm-operator">/</span><span class="cm-variable">Crassostrea_gigas_ensembl_tracks</span><span class="cm-operator">/</span><span class="cm-variable">Crassostrea_gigas</span>.<span class="cm-variable">GCA_000297895</span><span class="cm-number">.1.25</span>.<span class="cm-builtin">sorted</span>.<span class="cm-variable">gff3</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">cut</span> <span class="cm-operator">-</span><span class="cm-variable">f</span> <span class="cm-number">6</span>,<span class="cm-number">7</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">sort</span> <span class="cm-operator">|</span> <span class="cm-variable">uniq</span> <span class="cm-operator">-</span><span class="cm-variable">c</span> <span class="cm-operator">|</span> <span class="cm-variable">sed</span> <span class="cm-string">'/#/d'</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">echo</span> <span class="cm-string">"hyper"</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">intersectbed</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">wb</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">a</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02.4</span><span class="cm-variable">M_sig</span>.<span class="cm-variable">hyper</span>.<span class="cm-variable">bedGraph</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">b</span> <span class="cm-operator">/</span><span class="cm-variable">Volumes</span><span class="cm-operator">/</span><span class="cm-variable">web</span><span class="cm-operator">-</span><span class="cm-number">1</span><span class="cm-operator">/</span><span class="cm-variable">trilobite</span><span class="cm-operator">/</span><span class="cm-variable">Crassostrea_gigas_ensembl_tracks</span><span class="cm-operator">/</span><span class="cm-variable">Crassostrea_gigas</span>.<span class="cm-variable">GCA_000297895</span><span class="cm-number">.1.25</span>.<span class="cm-builtin">sorted</span>.<span class="cm-variable">gff3</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">cut</span> <span class="cm-operator">-</span><span class="cm-variable">f</span> <span class="cm-number">6</span>,<span class="cm-number">7</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">sort</span> <span class="cm-operator">|</span> <span class="cm-variable">uniq</span> <span class="cm-operator">-</span><span class="cm-variable">c</span> <span class="cm-operator">|</span> <span class="cm-variable">sed</span> <span class="cm-string">'/#/d'</span></span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 249px;"></div><div class="CodeMirror-gutters" style="display: none; height: 279px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to scroll output; double click to hide" style=""></div><div class="output" style=""><div class="output_area"><div class="prompt"></div><div class="output_subarea output_text output_stream output_stdout"><pre>hypo
1 EnsemblGenomes exon
1 EnsemblGenomes pseudogenic_tRNA
1 EnsemblGenomes transcript
715 GigaDB CDS
715 GigaDB exon
5389 GigaDB gene
5389 GigaDB transcript
907 dust repeat_region
653 trf repeat_region
hyper
1 EnsemblGenomes exon
1 EnsemblGenomes tRNA_gene
1 EnsemblGenomes transcript
462 GigaDB CDS
462 GigaDB exon
3102 GigaDB gene
3102 GigaDB transcript
413 dust repeat_region
220 trf repeat_region
</pre></div></div></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell code_cell rendered selected" tabindex="2"><div class="input"><div class="prompt input_prompt">In [49]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 175.59375px; left: 425.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true"><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 935.5517578125px; margin-bottom: 0px; border-right-width: 30px; min-height: 249px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors"><div class="CodeMirror-cursor" style="left: 420px; top: 170px; height: 17px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">echo</span> <span class="cm-string">"hypo"</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">intersectbed</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">wb</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">a</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02.6</span><span class="cm-variable">M_sig</span>.<span class="cm-variable">hypo</span>.<span class="cm-variable">bedGraph</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">b</span> <span class="cm-operator">/</span><span class="cm-variable">Volumes</span><span class="cm-operator">/</span><span class="cm-variable">web</span><span class="cm-operator">-</span><span class="cm-number">1</span><span class="cm-operator">/</span><span class="cm-variable">trilobite</span><span class="cm-operator">/</span><span class="cm-variable">Crassostrea_gigas_ensembl_tracks</span><span class="cm-operator">/</span><span class="cm-variable">Crassostrea_gigas</span>.<span class="cm-variable">GCA_000297895</span><span class="cm-number">.1.25</span>.<span class="cm-builtin">sorted</span>.<span class="cm-variable">gff3</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">cut</span> <span class="cm-operator">-</span><span class="cm-variable">f</span> <span class="cm-number">6</span>,<span class="cm-number">7</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">sort</span> <span class="cm-operator">|</span> <span class="cm-variable">uniq</span> <span class="cm-operator">-</span><span class="cm-variable">c</span> <span class="cm-operator">|</span> <span class="cm-variable">sed</span> <span class="cm-string">'/#/d'</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">echo</span> <span class="cm-string">"hyper"</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">!</span><span class="cm-variable">intersectbed</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">wb</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">a</span> <span class="cm-operator">/</span><span class="cm-variable">Users</span><span class="cm-operator">/</span><span class="cm-variable">sr320</span><span class="cm-operator">/</span><span class="cm-variable">data</span><span class="cm-operator">-</span><span class="cm-variable">genomic</span><span class="cm-operator">/</span><span class="cm-variable">tentacle</span><span class="cm-operator">/</span><span class="cm-number">2014.07.02.6</span><span class="cm-variable">M_sig</span>.<span class="cm-variable">hyper</span>.<span class="cm-variable">bedGraph</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">-</span><span class="cm-variable">b</span> <span class="cm-operator">/</span><span class="cm-variable">Volumes</span><span class="cm-operator">/</span><span class="cm-variable">web</span><span class="cm-operator">-</span><span class="cm-number">1</span><span class="cm-operator">/</span><span class="cm-variable">trilobite</span><span class="cm-operator">/</span><span class="cm-variable">Crassostrea_gigas_ensembl_tracks</span><span class="cm-operator">/</span><span class="cm-variable">Crassostrea_gigas</span>.<span class="cm-variable">GCA_000297895</span><span class="cm-number">.1.25</span>.<span class="cm-builtin">sorted</span>.<span class="cm-variable">gff3</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">cut</span> <span class="cm-operator">-</span><span class="cm-variable">f</span> <span class="cm-number">6</span>,<span class="cm-number">7</span> <span class="cm-error">\</span></span></pre><pre class=""><span style="padding-right: 0.1px;"><span class="cm-operator">|</span> <span class="cm-variable">sort</span> <span class="cm-operator">|</span> <span class="cm-variable">uniq</span> <span class="cm-operator">-</span><span class="cm-variable">c</span> <span class="cm-operator">|</span> <span class="cm-variable">sed</span> <span class="cm-string">'/#/d'</span></span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 249px;"></div><div class="CodeMirror-gutters" style="display: none; height: 279px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to scroll output; double click to hide" style=""></div><div class="output" style=""><div class="output_area"><div class="prompt"></div><div class="output_subarea output_text output_stream output_stdout"><pre>hypo
1 EnsemblGenomes exon
1 EnsemblGenomes snRNA
1 EnsemblGenomes snRNA_gene
568 GigaDB CDS
568 GigaDB exon
6295 GigaDB gene
6295 GigaDB transcript
1052 dust repeat_region
550 trf repeat_region
hyper
379 GigaDB CDS
380 GigaDB exon
3394 GigaDB gene
3394 GigaDB transcript
539 dust repeat_region
314 trf repeat_region
</pre></div></div></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div><div class="cell code_cell unrendered unselected" tabindex="2"><div class="input"><div class="prompt input_prompt">In [ ]:</div><div class="inner_cell"><div class="ctb_hideshow"><div class="celltoolbar"></div></div><div class="input_area"><div class="CodeMirror cm-s-ipython"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 5.59375px; left: 5.59375px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-vscrollbar" not-content="true" style="min-width: 18px;"><div style="min-width: 1px; height: 0px;"></div></div><div class="CodeMirror-hscrollbar" not-content="true"><div style="height: 100%; min-height: 1px; width: 0px;"></div></div><div class="CodeMirror-scrollbar-filler" not-content="true"></div><div class="CodeMirror-gutter-filler" not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; min-width: 3px; margin-bottom: 0px; border-right-width: 30px; min-height: 28px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines"><div style="position: relative; outline: none;"><div class="CodeMirror-measure"></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-cursors"><div class="CodeMirror-cursor" style="left: 0px; top: 0px; height: 17px;"> </div></div><div class="CodeMirror-code"><pre class=""><span style="padding-right: 0.1px;"><span></span></span></pre></div></div></div></div></div><div style="position: absolute; height: 30px; width: 1px; top: 28px;"></div><div class="CodeMirror-gutters" style="display: none; height: 58px;"></div></div></div></div></div></div><div class="widget-area" style="display: none;"><div class="prompt"><button class="close">×</button></div><div class="widget-subarea"></div></div><div class="output_wrapper"><div class="out_prompt_overlay prompt" title="click to expand output; double click to hide output" style="display: none;"></div><div class="output" style="display: none;"></div><div class="btn btn-default output_collapsed" title="click to expand output" style="display: none;">. . .</div></div></div></div><div class="end_space"></div></div>
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