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docs/_build/html/_modules/index.html

@@ -128,6 +128,7 @@
   <h1>All modules for which code is available</h1>
 <ul><li><a href="gseapy/algorithm.html">gseapy.algorithm</a></li>
 <li><a href="gseapy/gsea.html">gseapy.gsea</a></li>
+<li><a href="gseapy/parser.html">gseapy.parser</a></li>
 </ul>
 
            </div>

docs/_build/html/_sources/run.txt

@@ -41,14 +41,19 @@ Run gseapy inside python:
 This will import the following:
 
 * The :func:`replot` function to reproduce GSEA desktop results
-* The :func:`run` function to computing es,nes,pval,fdr,and generate plots *de novo*.
 
 .. code:: python
 
    # An example to reproduce figures using replot module.
    gseapy.replot('./Gsea.reports','test')
 
-   # calculate es, nes, pval,fdrs, and produce figures using gseapy.
+
+
+* The :func:`run` function to computing es,nes,pval,fdr,and generate plots *de novo*.
+
+.. code:: python
+
+   # An example to calculate es, nes, pval,fdrs, and produce figures using gseapy.
    gseapy.run(data = expression.txt, gene_sets = gene_sets.gmt,cls = test.cls, 
              min_size = 15, max_size = 1000, permutation_n = 1000, weighted_score_type = 1,
              permutation_type = 'gene_set', method = 'log2_ratio_of_classes',ascending = False, 
@@ -189,3 +194,9 @@ Algorithms
    :members:
 
 
+Parsers
+--------------------------
+
+.. automodule:: gseapy.parser
+   :members:
+

docs/_build/html/genindex.html

@@ -151,27 +151,47 @@ <h2 id="G">G</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%" valign="top"><dl>
 
+  <dt><a href="run.html#gseapy.parser.gsea_cls_parser">gsea_cls_parser() (in module gseapy.parser)</a>
+  </dt>
+
+
   <dt><a href="run.html#gseapy.algorithm.gsea_compute">gsea_compute() (in module gseapy.algorithm)</a>
   </dt>
 
 
-  <dt><a href="run.html#gseapy.algorithm.gsea_pval">gsea_pval() (in module gseapy.algorithm)</a>
+  <dt><a href="run.html#gseapy.parser.gsea_edb_parser">gsea_edb_parser() (in module gseapy.parser)</a>
   </dt>
 
 
-  <dt><a href="run.html#gseapy.algorithm.gsea_significance">gsea_significance() (in module gseapy.algorithm)</a>
+  <dt><a href="run.html#gseapy.parser.gsea_gmt_parser">gsea_gmt_parser() (in module gseapy.parser)</a>
+  </dt>
+
+
+  <dt><a href="run.html#gseapy.algorithm.gsea_pval">gsea_pval() (in module gseapy.algorithm)</a>
   </dt>
 
   </dl></td>
   <td style="width: 33%" valign="top"><dl>
 
+  <dt><a href="run.html#gseapy.parser.gsea_rank_metric">gsea_rank_metric() (in module gseapy.parser)</a>
+  </dt>
+
+
+  <dt><a href="run.html#gseapy.algorithm.gsea_significance">gsea_significance() (in module gseapy.algorithm)</a>
+  </dt>
+
+
   <dt><a href="run.html#module-gseapy">gseapy (module)</a>
   </dt>
 
 
   <dt><a href="run.html#module-gseapy.algorithm">gseapy.algorithm (module)</a>
   </dt>
 
+
+  <dt><a href="run.html#module-gseapy.parser">gseapy.parser (module)</a>
+  </dt>
+
   </dl></td>
 </tr></table>
 

docs/_build/html/objects.inv

@@ -2,7 +2,5 @@
 # Project: GSEAPY
 # Version: 0.3.1
 # The remainder of this file is compressed using zlib.
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+xڝ�1k�0�w���v�i�lJۡ:E>ˢ�I�����*�4���<��xO1
+?���5�Ax��S�Ek�R>BY�_[%�rA��.*��eg�b��LڞdԎ`s�qNB-��}\
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docs/_build/html/py-modindex.html

@@ -150,6 +150,11 @@ <h1>Python Module Index</h1>
        <td>&nbsp;&nbsp;&nbsp;
        <a href="run.html#module-gseapy.algorithm"><code class="xref">gseapy.algorithm</code></a></td><td>
        <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&nbsp;&nbsp;&nbsp;
+       <a href="run.html#module-gseapy.parser"><code class="xref">gseapy.parser</code></a></td><td>
+       <em></em></td></tr>
    </table>
 
 

docs/_build/html/run.html

@@ -95,6 +95,7 @@
 <li class="toctree-l4"><a class="reference internal" href="#to-see-help-information-of-gseapy">To See help information of GSEAPY</a></li>
 <li class="toctree-l4"><a class="reference internal" href="#module-apis">Module APIs</a></li>
 <li class="toctree-l4"><a class="reference internal" href="#module-gseapy.algorithm">Algorithms</a></li>
+<li class="toctree-l4"><a class="reference internal" href="#module-gseapy.parser">Parsers</a></li>
 </ul>
 </li>
 </ul>
@@ -113,6 +114,7 @@
 </li>
 <li class="toctree-l2"><a class="reference internal" href="#module-apis">Module APIs</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#module-gseapy.algorithm">Algorithms</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#module-gseapy.parser">Parsers</a></li>
 </ul>
 </li>
 </ul>
@@ -186,12 +188,15 @@ <h2>Run gseapy inside python:<a class="headerlink" href="#run-gseapy-inside-pyth
 <p>This will import the following:</p>
 <ul class="simple">
 <li>The <a class="reference internal" href="#gseapy.replot" title="gseapy.replot"><code class="xref py py-func docutils literal"><span class="pre">replot()</span></code></a> function to reproduce GSEA desktop results</li>
-<li>The <a class="reference internal" href="#gseapy.run" title="gseapy.run"><code class="xref py py-func docutils literal"><span class="pre">run()</span></code></a> function to computing es,nes,pval,fdr,and generate plots <em>de novo</em>.</li>
 </ul>
 <div class="code python highlight-python"><div class="highlight"><pre><span class="c"># An example to reproduce figures using replot module.</span>
 <span class="n">gseapy</span><span class="o">.</span><span class="n">replot</span><span class="p">(</span><span class="s">&#39;./Gsea.reports&#39;</span><span class="p">,</span><span class="s">&#39;test&#39;</span><span class="p">)</span>
-
-<span class="c"># calculate es, nes, pval,fdrs, and produce figures using gseapy.</span>
+</pre></div>
+</div>
+<ul class="simple">
+<li>The <a class="reference internal" href="#gseapy.run" title="gseapy.run"><code class="xref py py-func docutils literal"><span class="pre">run()</span></code></a> function to computing es,nes,pval,fdr,and generate plots <em>de novo</em>.</li>
+</ul>
+<div class="code python highlight-python"><div class="highlight"><pre><span class="c"># An example to calculate es, nes, pval,fdrs, and produce figures using gseapy.</span>
 <span class="n">gseapy</span><span class="o">.</span><span class="n">run</span><span class="p">(</span><span class="n">data</span> <span class="o">=</span> <span class="n">expression</span><span class="o">.</span><span class="n">txt</span><span class="p">,</span> <span class="n">gene_sets</span> <span class="o">=</span> <span class="n">gene_sets</span><span class="o">.</span><span class="n">gmt</span><span class="p">,</span><span class="n">cls</span> <span class="o">=</span> <span class="n">test</span><span class="o">.</span><span class="n">cls</span><span class="p">,</span>
           <span class="n">min_size</span> <span class="o">=</span> <span class="mi">15</span><span class="p">,</span> <span class="n">max_size</span> <span class="o">=</span> <span class="mi">1000</span><span class="p">,</span> <span class="n">permutation_n</span> <span class="o">=</span> <span class="mi">1000</span><span class="p">,</span> <span class="n">weighted_score_type</span> <span class="o">=</span> <span class="mi">1</span><span class="p">,</span>
           <span class="n">permutation_type</span> <span class="o">=</span> <span class="s">&#39;gene_set&#39;</span><span class="p">,</span> <span class="n">method</span> <span class="o">=</span> <span class="s">&#39;log2_ratio_of_classes&#39;</span><span class="p">,</span><span class="n">ascending</span> <span class="o">=</span> <span class="bp">False</span><span class="p">,</span>
@@ -505,7 +510,7 @@ <h2>Module APIs<a class="headerlink" href="#module-apis" title="Permalink to thi
 
 <dl class="function">
 <dt id="gseapy.algorithm.shuffle_list">
-<code class="descclassname">gseapy.algorithm.</code><code class="descname">shuffle_list</code><span class="sig-paren">(</span><em>gene_list</em>, <em>rand=&lt;random.Random object at 0x0000022911F63FF8&gt;</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/gseapy/algorithm.html#shuffle_list"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#gseapy.algorithm.shuffle_list" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">gseapy.algorithm.</code><code class="descname">shuffle_list</code><span class="sig-paren">(</span><em>gene_list</em>, <em>rand=&lt;random.Random object at 0x0000018178FAB7A8&gt;</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/gseapy/algorithm.html#shuffle_list"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#gseapy.algorithm.shuffle_list" title="Permalink to this definition">¶</a></dt>
 <dd><p>Returns a copy of a shuffled input gene_list.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
@@ -524,6 +529,92 @@ <h2>Module APIs<a class="headerlink" href="#module-apis" title="Permalink to thi
 </table>
 </dd></dl>
 
+</div>
+<div class="section" id="module-gseapy.parser">
+<span id="parsers"></span><h2>Parsers<a class="headerlink" href="#module-gseapy.parser" title="Permalink to this headline">¶</a></h2>
+<dl class="function">
+<dt id="gseapy.parser.gsea_cls_parser">
+<code class="descclassname">gseapy.parser.</code><code class="descname">gsea_cls_parser</code><span class="sig-paren">(</span><em>cls</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/gseapy/parser.html#gsea_cls_parser"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#gseapy.parser.gsea_cls_parser" title="Permalink to this definition">¶</a></dt>
+<dd><p>Extact class(phenotype) name from .cls file.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>cls</strong> &#8211; the location of GSEA-P .cls file.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">phenotype name and a list of class vector.</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="function">
+<dt id="gseapy.parser.gsea_edb_parser">
+<code class="descclassname">gseapy.parser.</code><code class="descname">gsea_edb_parser</code><span class="sig-paren">(</span><em>results_path</em>, <em>index=0</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/gseapy/parser.html#gsea_edb_parser"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#gseapy.parser.gsea_edb_parser" title="Permalink to this definition">¶</a></dt>
+<dd><p>Parse results.edb file stored under <strong>edb</strong> file folder.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>results_path</strong> &#8211; location of GSEA Desktop results.</li>
+<li><strong>index</strong> &#8211; gene_set index of gmt database, used for iterating items.</li>
+</ul>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">enrichment_term, hit_index,nes, pval, fdr.</p>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="function">
+<dt id="gseapy.parser.gsea_gmt_parser">
+<code class="descclassname">gseapy.parser.</code><code class="descname">gsea_gmt_parser</code><span class="sig-paren">(</span><em>gmt</em>, <em>min_size=3</em>, <em>max_size=5000</em>, <em>gene_list=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/gseapy/parser.html#gsea_gmt_parser"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#gseapy.parser.gsea_gmt_parser" title="Permalink to this definition">¶</a></dt>
+<dd><p>parser gene_sets.gmt(gene set database) file.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>gmt</strong> &#8211; Location of gene_sets.gmt file.</li>
+<li><strong>min_size</strong> &#8211; Minimum allowed number of genes from gene set also the data set. Default: 3.</li>
+<li><strong>max_size</strong> &#8211; Maximum allowed number of genes from gene set also the data set. Default: 5000.</li>
+</ul>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Gene_list:</th><td class="field-body"><p class="first">Used for filtering gene set. Only used this argument for <code class="xref py py-func docutils literal"><span class="pre">run()</span></code> method.</p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">Return a new filtered gene set database dictionary.</p>
+</td>
+</tr>
+</tbody>
+</table>
+<p><strong>DO NOT</strong> filtering gene sets, when use <code class="xref py py-func docutils literal"><span class="pre">replot()</span></code>. Because <code class="docutils literal"><span class="pre">GSEA</span></code> Desktop have already
+do this for you.</p>
+</dd></dl>
+
+<dl class="function">
+<dt id="gseapy.parser.gsea_rank_metric">
+<code class="descclassname">gseapy.parser.</code><code class="descname">gsea_rank_metric</code><span class="sig-paren">(</span><em>rnk</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/gseapy/parser.html#gsea_rank_metric"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#gseapy.parser.gsea_rank_metric" title="Permalink to this definition">¶</a></dt>
+<dd><p>parse .rnk file. This file contains ranking correlation vector and gene names or ids.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>rnk</strong> &#8211; location of GSEA-P .rnk file</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">a pandas DataFrame with 3 columns names are:<div class="highlight-python"><div class="highlight"><pre>&#39;gene_name&#39;,&#39;rank&#39;,rank2&#39;
+</pre></div>
+</div>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
 </div>
 </div>