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ebic v0.4: updating documentation
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athril committed Jan 3, 2018
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2 changes: 1 addition & 1 deletion docs/index.html
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Expand Up @@ -168,5 +168,5 @@ <h1 id="ebic">EBIC</h1>

<!--
MkDocs version : 0.16.3
Build Date UTC : 2018-01-03 19:54:32
Build Date UTC : 2018-01-03 19:59:14
-->
4 changes: 2 additions & 2 deletions docs/mkdocs/search_index.json
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},
{
"location": "/usage/",
"text": "Using ebic\n\n\nCurrently \nebic\n can be used only as a command line tool.\n\n\nIn order to build a program simply run:\n\n\n$ make\n\n\n\n\nCheck our 'input.txt' data file to see the required input file format. In order to run an example simply type:\n\n\n$ ./ebic -i input.txt\n\n\n\n\nThe basic usage of ebic is:\n\n\n$ ./ebic [OPTIONS]\n\n\n\n\nTo override any of default options extra arguments should be added:\n\n\nOptions:\n -i,--input TEXT input file (required!)\n -n,--iterations INT number of iterations [default: 5000]\n -b,--biclusters INT number of biclusters [100]\n -x,--overlap FLOAT overlap threshold [0.75]\n -g,--gpus INT number of gpus [1]\n -a,--approx FLOAT approximate trends acceptance ratio [0.85]\n -m,--negative-trends INT negative trends [1]\n -l,--log is logging enabled [false]\n\n\nInput\n\n\nInput files are expected to have a row and a column headers, the values need to be separated by whitespace. \nThe current release of \nebic\n doesn't handle missing values.\nCheck our toy file (input.txt) for the required file format.\n\n\nOutputs\n\n\nebic\n writes to its working directory two text files: [input_filename]-res and [input_filename]-blocks.\n\n\nThe first output file contains in its first line the number of detected biclusters and in consecutive lines each bicluster identifiers in the following format.\n\n\nBicluster([row0 row1 ... ],[column0, column1, ...])\n\n\n\n\nThe second file extracts the actual values of the bicluster from the dataset. Its format is as follows:\n\n\nBC[bicluster_number] [number_of_rows x number_of columns]\nExtracted part of the input dataset with rows and columns labels of the bicluster.",
"text": "Using ebic\n\n\nCurrently \nebic\n can be used only as a command line tool.\n\n\nIn order to build a program simply run:\n\n\n$ make\n\n\n\n\nCheck our 'input.txt' data file to see the required input file format. In order to run an example simply type:\n\n\n$ ./ebic -i input.txt\n\n\n\n\nThe basic usage of ebic is:\n\n\n$ ./ebic [OPTIONS]\n\n\n\n\nTo override any of default options extra arguments should be added:\n\n\nOptions:\n\n\n\n\n\n\n-i,--input TEXT input file (required!)\n\n\n\n\n\n\n-n,--iterations INT number of iterations [default: 5000]\n\n\n\n\n\n\n-b,--biclusters INT number of biclusters [100]\n\n\n\n\n\n\n-x,--overlap FLOAT overlap threshold [0.75]\n\n\n\n\n\n\n-g,--gpus INT number of gpus [1]\n\n\n\n\n\n\n-a,--approx FLOAT approximate trends acceptance ratio [0.85]\n\n\n\n\n\n\n-t,--negative-trends INT negative trends [1]\n\n\n\n\n\n\n-l,--log is logging enabled [false]\n\n\n\n\n\n\nInput\n\n\nInput files are expected to have a row and a column headers, the values need to be separated by whitespace. \nThe current release of \nebic\n doesn't handle missing values.\nCheck our toy file (input.txt) for the required file format.\n\n\nOutputs\n\n\nebic\n writes to its working directory two text files: [input_filename]-res and [input_filename]-blocks.\n\n\nThe first output file contains in its first line the number of detected biclusters and in consecutive lines each bicluster identifiers in the following format.\n\n\nBicluster([row0 row1 ... ],[column0, column1, ...])\n\n\n\n\nThe second file extracts the actual values of the bicluster from the dataset. Its format is as follows:\n\n\nBC[bicluster_number] [number_of_rows x number_of columns]\nExtracted part of the input dataset with rows and columns labels of the bicluster.",
"title": "How to use"
},
{
"location": "/usage/#using-ebic",
"text": "Currently ebic can be used only as a command line tool. In order to build a program simply run: $ make Check our 'input.txt' data file to see the required input file format. In order to run an example simply type: $ ./ebic -i input.txt The basic usage of ebic is: $ ./ebic [OPTIONS] To override any of default options extra arguments should be added: Options:\n -i,--input TEXT input file (required!)\n -n,--iterations INT number of iterations [default: 5000]\n -b,--biclusters INT number of biclusters [100]\n -x,--overlap FLOAT overlap threshold [0.75]\n -g,--gpus INT number of gpus [1]\n -a,--approx FLOAT approximate trends acceptance ratio [0.85]\n -m,--negative-trends INT negative trends [1]\n -l,--log is logging enabled [false]",
"text": "Currently ebic can be used only as a command line tool. In order to build a program simply run: $ make Check our 'input.txt' data file to see the required input file format. In order to run an example simply type: $ ./ebic -i input.txt The basic usage of ebic is: $ ./ebic [OPTIONS] To override any of default options extra arguments should be added: Options: -i,--input TEXT input file (required!) -n,--iterations INT number of iterations [default: 5000] -b,--biclusters INT number of biclusters [100] -x,--overlap FLOAT overlap threshold [0.75] -g,--gpus INT number of gpus [1] -a,--approx FLOAT approximate trends acceptance ratio [0.85] -t,--negative-trends INT negative trends [1] -l,--log is logging enabled [false]",
"title": "Using ebic"
},
{
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36 changes: 27 additions & 9 deletions docs/usage/index.html
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Expand Up @@ -134,15 +134,33 @@ <h2 id="using-ebic">Using ebic</h2>
</code></pre>

<p>To override any of default options extra arguments should be added:</p>
<p>Options:
-i,--input TEXT input file (required!)
-n,--iterations INT number of iterations [default: 5000]
-b,--biclusters INT number of biclusters [100]
-x,--overlap FLOAT overlap threshold [0.75]
-g,--gpus INT number of gpus [1]
-a,--approx FLOAT approximate trends acceptance ratio [0.85]
-m,--negative-trends INT negative trends [1]
-l,--log is logging enabled [false]</p>
<p>Options:</p>
<ul>
<li>
<p>-i,--input TEXT input file (required!)</p>
</li>
<li>
<p>-n,--iterations INT number of iterations [default: 5000]</p>
</li>
<li>
<p>-b,--biclusters INT number of biclusters [100]</p>
</li>
<li>
<p>-x,--overlap FLOAT overlap threshold [0.75]</p>
</li>
<li>
<p>-g,--gpus INT number of gpus [1]</p>
</li>
<li>
<p>-a,--approx FLOAT approximate trends acceptance ratio [0.85]</p>
</li>
<li>
<p>-t,--negative-trends INT negative trends [1]</p>
</li>
<li>
<p>-l,--log is logging enabled [false]</p>
</li>
</ul>
<h2 id="input">Input</h2>
<p>Input files are expected to have a row and a column headers, the values need to be separated by whitespace.
The current release of <em>ebic</em> doesn't handle missing values.
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24 changes: 16 additions & 8 deletions docs_sources/usage.md
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Expand Up @@ -20,14 +20,22 @@ $ ./ebic [OPTIONS]
To override any of default options extra arguments should be added:

Options:
-i,--input TEXT input file (required!)
-n,--iterations INT number of iterations [default: 5000]
-b,--biclusters INT number of biclusters [100]
-x,--overlap FLOAT overlap threshold [0.75]
-g,--gpus INT number of gpus [1]
-a,--approx FLOAT approximate trends acceptance ratio [0.85]
-m,--negative-trends INT negative trends [1]
-l,--log is logging enabled [false]

* -i,--input TEXT input file (required!)

* -n,--iterations INT number of iterations [default: 5000]

* -b,--biclusters INT number of biclusters [100]

* -x,--overlap FLOAT overlap threshold [0.75]

* -g,--gpus INT number of gpus [1]

* -a,--approx FLOAT approximate trends acceptance ratio [0.85]

* -t,--negative-trends INT negative trends [1]

* -l,--log is logging enabled [false]


## Input
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