diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index ed0efde7f1b82319dcbc96fbf4d20f4ac3811040..4793817ff6896453c58b0d2029b64acb364e0d23 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -13,7 +13,7 @@ pages: - pip3 install sphinx - yum install -y make - pip3 install sphinx - - pip3 install sphinxcontrib-bibtex + - pip3 install sphinxcontrib-bibtex sphinx_rtd_theme sphinx-argparse - pip3 install -r jass_preprocessing/requirements.txt - cd doc - sphinx-apidoc -f -o ./source/_autosummary/ ../jass_preprocessing/ diff --git a/doc/_build/doctrees/_autosummary/jass_preprocessing.doctree b/doc/_build/doctrees/_autosummary/jass_preprocessing.doctree index d0913191263b087a2eb7716892dc73279b33e9cb..f63ae09cfdfcd8b45cc4aa8ea86a829b1d0de6f2 100644 Binary files a/doc/_build/doctrees/_autosummary/jass_preprocessing.doctree and b/doc/_build/doctrees/_autosummary/jass_preprocessing.doctree differ diff --git a/doc/_build/doctrees/_autosummary/modules.doctree b/doc/_build/doctrees/_autosummary/modules.doctree index d81bf9478aba49c75c023312084bedfb7da10a8b..27e69465a3f3a5f52f0a552a07a3b5fae79b0de3 100644 Binary files a/doc/_build/doctrees/_autosummary/modules.doctree and b/doc/_build/doctrees/_autosummary/modules.doctree differ diff --git a/doc/_build/doctrees/environment.pickle b/doc/_build/doctrees/environment.pickle index a25385815e8157b8176f6a3de98f8f3998f8d13c..37ed4b08a279ba895c90c7a1e3e3234dced8b63f 100644 Binary files a/doc/_build/doctrees/environment.pickle and b/doc/_build/doctrees/environment.pickle differ diff --git a/doc/_build/doctrees/index.doctree b/doc/_build/doctrees/index.doctree index 5b61a86be1dbf42d20c6b122cd6a38b0dc169d47..554b563fc216964e90e38f90aeecec5d7b9e4ca9 100644 Binary files a/doc/_build/doctrees/index.doctree and b/doc/_build/doctrees/index.doctree differ diff --git a/doc/_build/html/.buildinfo b/doc/_build/html/.buildinfo index 7973807d1c69071dd9427905d36f83acc0b30141..d4001700a5cc33291156a913bc4f82fc1f733f82 100644 --- a/doc/_build/html/.buildinfo +++ b/doc/_build/html/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: 4d7603fff8910e91226dddc14910dfe6 +config: 7890896c7cf0d3614ade393a5c103246 tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/doc/_build/html/_autosummary/jass_preprocessing.html b/doc/_build/html/_autosummary/jass_preprocessing.html index 875b0e9feb52089a9ac7c1559ccc57390f565637..573ab6b3f170548f62ad9a8f93e5098280342494 100644 --- a/doc/_build/html/_autosummary/jass_preprocessing.html +++ b/doc/_build/html/_autosummary/jass_preprocessing.html @@ -1,43 +1,83 @@ -<!doctype html> - -<html xmlns="http://www.w3.org/1999/xhtml"> - <head> - <meta http-equiv="X-UA-Compatible" content="IE=Edge" /> - <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> - <title>jass_preprocessing package — jass_preprocessing 1.0 documentation</title> - <link rel="stylesheet" href="../_static/bizstyle.css" type="text/css" /> - <link rel="stylesheet" href="../_static/pygments.css" type="text/css" /> - <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script> - <script type="text/javascript" src="../_static/jquery.js"></script> - <script type="text/javascript" src="../_static/underscore.js"></script> - <script type="text/javascript" src="../_static/doctools.js"></script> - <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script> - <script type="text/javascript" src="../_static/bizstyle.js"></script> +<!DOCTYPE html> +<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]--> +<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]--> +<head> + <meta charset="utf-8"> + + <meta name="viewport" content="width=device-width, initial-scale=1.0"> + + <title>jass_preprocessing package — jass_preprocessing 1.0 documentation</title> + + + + + + + + + + + + + + + + <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" /> + <link rel="stylesheet" href="../_static/pygments.css" type="text/css" /> <link rel="index" title="Index" href="../genindex.html" /> - <link rel="search" title="Search" href="../search.html" /> - <meta name="viewport" content="width=device-width,initial-scale=1.0"> - <!--[if lt IE 9]> - <script type="text/javascript" src="_static/css3-mediaqueries.js"></script> - <![endif]--> - </head><body> - <div class="related" role="navigation" aria-label="related navigation"> - <h3>Navigation</h3> - <ul> - <li class="right" style="margin-right: 10px"> - <a href="../genindex.html" title="General Index" - accesskey="I">index</a></li> - <li class="right" > - <a href="../py-modindex.html" title="Python Module Index" - >modules</a> |</li> - <li class="nav-item nav-item-0"><a href="../index.html">jass_preprocessing 1.0 documentation</a> »</li> - </ul> - </div> - <div class="sphinxsidebar" role="navigation" aria-label="main navigation"> - <div class="sphinxsidebarwrapper"> - <h3><a href="../index.html">Table Of Contents</a></h3> - <ul> + <link rel="search" title="Search" href="../search.html" /> + + + <script src="../_static/js/modernizr.min.js"></script> + +</head> + +<body class="wy-body-for-nav"> + + + <div class="wy-grid-for-nav"> + + + <nav data-toggle="wy-nav-shift" class="wy-nav-side"> + <div class="wy-side-scroll"> + <div class="wy-side-nav-search"> + + + + <a href="../index.html" class="icon icon-home"> jass_preprocessing + + + + </a> + + + + + + + +<div role="search"> + <form id="rtd-search-form" class="wy-form" action="../search.html" method="get"> + <input type="text" name="q" placeholder="Search docs" /> + <input type="hidden" name="check_keywords" value="yes" /> + <input type="hidden" name="area" value="default" /> + </form> +</div> + + + </div> + + <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation"> + + + + + + + <!-- Local TOC --> + <div class="local-toc"><ul> <li><a class="reference internal" href="#">jass_preprocessing package</a><ul> <li><a class="reference internal" href="#submodules">Submodules</a></li> <li><a class="reference internal" href="#module-jass_preprocessing.compute_score">jass_preprocessing.compute_score module</a></li> @@ -49,33 +89,68 @@ </ul> </li> </ul> - - <div role="note" aria-label="source link"> - <h3>This Page</h3> - <ul class="this-page-menu"> - <li><a href="../_sources/_autosummary/jass_preprocessing.rst.txt" - rel="nofollow">Show Source</a></li> - </ul> - </div> -<div id="searchbox" style="display: none" role="search"> - <h3>Quick search</h3> - <div class="searchformwrapper"> - <form class="search" action="../search.html" method="get"> - <input type="text" name="q" /> - <input type="submit" value="Go" /> - <input type="hidden" name="check_keywords" value="yes" /> - <input type="hidden" name="area" value="default" /> - </form> - </div> </div> -<script type="text/javascript">$('#searchbox').show(0);</script> + + </div> </div> + </nav> + + <section data-toggle="wy-nav-shift" 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class="headerlink" href="#jass-preprocessing-package" title="Permalink to this headline">¶</a></h1> @@ -336,26 +411,52 @@ Make sure that the same SNPs are in the reference panel and the gwas</p> </div> + </div> + </div> + <footer> + + + <hr/> + + <div role="contentinfo"> + <p> + © Copyright 2018, Hanna Julienne + + </p> + </div> + Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/rtfd/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. + +</footer> + </div> </div> - <div class="clearer"></div> - </div> - <div class="related" role="navigation" aria-label="related navigation"> - <h3>Navigation</h3> - <ul> - <li class="right" style="margin-right: 10px"> - <a href="../genindex.html" title="General Index" - >index</a></li> - <li class="right" > - <a href="../py-modindex.html" title="Python Module Index" - >modules</a> |</li> - <li class="nav-item nav-item-0"><a href="../index.html">jass_preprocessing 1.0 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type="text/javascript">$('#searchbox').show(0);</script> + + + </div> + + <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation"> + + + + + + + <!-- Local TOC --> + <div class="local-toc"></div> + + </div> </div> + </nav> + + <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"> + + + <nav class="wy-nav-top" aria-label="top navigation"> + + <i data-toggle="wy-nav-top" class="fa fa-bars"></i> + <a href="../index.html">jass_preprocessing</a> + + </nav> + + + <div class="wy-nav-content"> + + <div class="rst-content"> + + + + - <div class="document"> - <div class="documentwrapper"> - <div class="bodywrapper"> - <div class="body" role="main"> + + + + + + + + + + + + +<div role="navigation" aria-label="breadcrumbs navigation"> + + <ul class="wy-breadcrumbs"> + + <li><a href="../index.html">Docs</a> »</li> + + <li>Overview: module code</li> + + + <li class="wy-breadcrumbs-aside"> + + </li> + + </ul> + + + <hr/> +</div> + <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article"> + <div itemprop="articleBody"> <h1>All modules for which code is available</h1> <ul><li><a href="jass_preprocessing/compute_score.html">jass_preprocessing.compute_score</a></li> @@ -64,26 +144,52 @@ <li><a href="jass_preprocessing/save_output.html">jass_preprocessing.save_output</a></li> </ul> + </div> + </div> + <footer> + + + <hr/> + + <div role="contentinfo"> + <p> + © Copyright 2018, Hanna Julienne + + </p> + </div> + Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/rtfd/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. + +</footer> + </div> </div> - <div class="clearer"></div> - </div> - <div class="related" role="navigation" aria-label="related navigation"> - <h3>Navigation</h3> - <ul> - <li class="right" style="margin-right: 10px"> - <a href="../genindex.html" title="General Index" - >index</a></li> - <li class="right" > - <a href="../py-modindex.html" title="Python Module Index" - >modules</a> |</li> - <li class="nav-item nav-item-0"><a href="../index.html">jass_preprocessing 1.0 documentation</a> »</li> - </ul> - </div> - <div class="footer" role="contentinfo"> - © Copyright 2018, Hanna Julienne. - Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.7.7. - </div> - </body> + + </section> + + </div> + + + + + + + + <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script> + <script type="text/javascript" src="../_static/jquery.js"></script> + <script type="text/javascript" src="../_static/underscore.js"></script> + <script type="text/javascript" src="../_static/doctools.js"></script> + + + + + <script type="text/javascript" src="../_static/js/theme.js"></script> + + <script type="text/javascript"> + jQuery(function () { + SphinxRtdTheme.Navigation.enable(true); + }); + </script> + +</body> </html> \ No newline at end of file diff --git a/doc/_build/html/_modules/jass_preprocessing/compute_score.html b/doc/_build/html/_modules/jass_preprocessing/compute_score.html index edd89e010c576de2bb0869af407d2461698b780f..98653d3f499163f7bb332b1efe50b191951cc632 100644 --- a/doc/_build/html/_modules/jass_preprocessing/compute_score.html +++ b/doc/_build/html/_modules/jass_preprocessing/compute_score.html @@ -1,61 +1,142 @@ -<!doctype html> - -<html xmlns="http://www.w3.org/1999/xhtml"> - <head> - <meta http-equiv="X-UA-Compatible" content="IE=Edge" /> - <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> - <title>jass_preprocessing.compute_score — jass_preprocessing 1.0 documentation</title> - <link rel="stylesheet" href="../../_static/bizstyle.css" type="text/css" /> - <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" /> - <script type="text/javascript" id="documentation_options" data-url_root="../../" src="../../_static/documentation_options.js"></script> - <script type="text/javascript" src="../../_static/jquery.js"></script> - <script type="text/javascript" src="../../_static/underscore.js"></script> - <script type="text/javascript" src="../../_static/doctools.js"></script> - <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script> - <script type="text/javascript" src="../../_static/bizstyle.js"></script> +<!DOCTYPE html> +<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]--> +<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]--> +<head> + <meta charset="utf-8"> + + <meta name="viewport" content="width=device-width, initial-scale=1.0"> + + <title>jass_preprocessing.compute_score — jass_preprocessing 1.0 documentation</title> + + + + + + + + + + + + + + + + <link rel="stylesheet" href="../../_static/css/theme.css" type="text/css" /> + <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" /> <link rel="index" title="Index" href="../../genindex.html" /> - <link rel="search" title="Search" href="../../search.html" /> - <meta name="viewport" content="width=device-width,initial-scale=1.0"> - <!--[if lt IE 9]> - <script type="text/javascript" src="_static/css3-mediaqueries.js"></script> - <![endif]--> - </head><body> - <div class="related" role="navigation" aria-label="related navigation"> - <h3>Navigation</h3> - <ul> - <li class="right" style="margin-right: 10px"> - <a href="../../genindex.html" title="General Index" - accesskey="I">index</a></li> - <li class="right" > - <a href="../../py-modindex.html" title="Python Module Index" - >modules</a> |</li> - <li class="nav-item nav-item-0"><a href="../../index.html">jass_preprocessing 1.0 documentation</a> »</li> - <li class="nav-item nav-item-1"><a href="../index.html" accesskey="U">Module code</a> »</li> - </ul> - </div> - <div class="sphinxsidebar" role="navigation" aria-label="main navigation"> - <div class="sphinxsidebarwrapper"> -<div id="searchbox" style="display: none" role="search"> - <h3>Quick search</h3> - <div class="searchformwrapper"> - <form class="search" action="../../search.html" method="get"> - <input type="text" name="q" /> - <input type="submit" value="Go" /> - <input type="hidden" name="check_keywords" value="yes" /> - <input type="hidden" name="area" value="default" /> - </form> - </div> + <link rel="search" title="Search" href="../../search.html" /> + + + <script src="../../_static/js/modernizr.min.js"></script> + +</head> + +<body class="wy-body-for-nav"> + + + <div class="wy-grid-for-nav"> + + + <nav data-toggle="wy-nav-shift" class="wy-nav-side"> + <div class="wy-side-scroll"> + <div class="wy-side-nav-search"> + + + + <a href="../../index.html" class="icon icon-home"> jass_preprocessing + + + + </a> + + + + + + + +<div role="search"> + <form id="rtd-search-form" class="wy-form" action="../../search.html" method="get"> + <input type="text" name="q" placeholder="Search docs" /> + <input type="hidden" name="check_keywords" value="yes" /> + <input type="hidden" name="area" value="default" /> + </form> </div> -<script type="text/javascript">$('#searchbox').show(0);</script> + + + </div> + + <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation"> + + + + + + + <!-- Local TOC --> + <div class="local-toc"></div> + + </div> </div> + </nav> + + <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"> + + + <nav class="wy-nav-top" aria-label="top navigation"> + + <i data-toggle="wy-nav-top" class="fa fa-bars"></i> + <a href="../../index.html">jass_preprocessing</a> + + </nav> + + + <div class="wy-nav-content"> + + <div class="rst-content"> + + + + - <div class="document"> - <div class="documentwrapper"> - <div class="bodywrapper"> - <div class="body" role="main"> + + + + + + + + + + + + +<div role="navigation" aria-label="breadcrumbs navigation"> + + <ul class="wy-breadcrumbs"> + + <li><a href="../../index.html">Docs</a> »</li> + + <li><a href="../index.html">Module code</a> »</li> + + <li>jass_preprocessing.compute_score</li> + + + <li class="wy-breadcrumbs-aside"> + + </li> + + </ul> + + + <hr/> +</div> + <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article"> + <div itemprop="articleBody"> <h1>Source code for jass_preprocessing.compute_score</h1><div class="highlight"><pre> <span></span><span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span> @@ -127,27 +208,52 @@ <span class="k">return</span><span class="p">(</span><span class="n">mgwas</span><span class="p">)</span></div> </pre></div> + </div> + </div> + <footer> + + + <hr/> + + <div role="contentinfo"> + <p> + © Copyright 2018, Hanna Julienne + + </p> + </div> + Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/rtfd/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. + +</footer> + </div> </div> - <div class="clearer"></div> - </div> - <div class="related" role="navigation" aria-label="related navigation"> - <h3>Navigation</h3> - <ul> - <li class="right" style="margin-right: 10px"> - <a href="../../genindex.html" title="General Index" - >index</a></li> - <li class="right" > - <a href="../../py-modindex.html" title="Python Module Index" - >modules</a> |</li> - <li class="nav-item nav-item-0"><a href="../../index.html">jass_preprocessing 1.0 documentation</a> »</li> - <li class="nav-item nav-item-1"><a href="../index.html" >Module code</a> »</li> - </ul> - </div> - <div class="footer" role="contentinfo"> - © Copyright 2018, Hanna Julienne. - Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.7.7. - </div> - </body> + + </section> + + </div> + + + + + + + + <script type="text/javascript" id="documentation_options" data-url_root="../../" src="../../_static/documentation_options.js"></script> + <script type="text/javascript" src="../../_static/jquery.js"></script> + <script type="text/javascript" src="../../_static/underscore.js"></script> + <script type="text/javascript" src="../../_static/doctools.js"></script> + + + + + <script type="text/javascript" src="../../_static/js/theme.js"></script> + + <script type="text/javascript"> + jQuery(function () { + SphinxRtdTheme.Navigation.enable(true); + }); + </script> + +</body> </html> \ No newline at end of file diff --git a/doc/_build/html/_modules/jass_preprocessing/dna_utils.html b/doc/_build/html/_modules/jass_preprocessing/dna_utils.html index 9c9f6c83dabbf019566e5915c0fc8643a31bd957..c30ed3bd95e16da043b8cb7995d4e9210312c35c 100644 --- a/doc/_build/html/_modules/jass_preprocessing/dna_utils.html +++ b/doc/_build/html/_modules/jass_preprocessing/dna_utils.html @@ -1,61 +1,142 @@ -<!doctype html> - -<html xmlns="http://www.w3.org/1999/xhtml"> - <head> - <meta http-equiv="X-UA-Compatible" content="IE=Edge" /> - <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> - <title>jass_preprocessing.dna_utils — jass_preprocessing 1.0 documentation</title> - <link rel="stylesheet" href="../../_static/bizstyle.css" type="text/css" /> - <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" /> - <script type="text/javascript" id="documentation_options" data-url_root="../../" src="../../_static/documentation_options.js"></script> - <script type="text/javascript" src="../../_static/jquery.js"></script> - <script type="text/javascript" src="../../_static/underscore.js"></script> - <script type="text/javascript" src="../../_static/doctools.js"></script> - <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script> - <script type="text/javascript" src="../../_static/bizstyle.js"></script> +<!DOCTYPE html> +<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]--> +<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]--> +<head> + <meta charset="utf-8"> + + <meta name="viewport" content="width=device-width, initial-scale=1.0"> + + <title>jass_preprocessing.dna_utils — jass_preprocessing 1.0 documentation</title> + + + + + + + + + + + + + + + + <link rel="stylesheet" href="../../_static/css/theme.css" type="text/css" /> + <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" /> <link rel="index" title="Index" href="../../genindex.html" /> - <link rel="search" title="Search" href="../../search.html" /> - <meta name="viewport" content="width=device-width,initial-scale=1.0"> - <!--[if lt IE 9]> - <script type="text/javascript" src="_static/css3-mediaqueries.js"></script> - <![endif]--> - </head><body> - <div class="related" role="navigation" aria-label="related navigation"> - <h3>Navigation</h3> - <ul> - <li class="right" style="margin-right: 10px"> - <a href="../../genindex.html" title="General Index" - accesskey="I">index</a></li> - <li class="right" > - <a href="../../py-modindex.html" title="Python Module Index" - >modules</a> |</li> - <li class="nav-item nav-item-0"><a href="../../index.html">jass_preprocessing 1.0 documentation</a> »</li> - <li class="nav-item nav-item-1"><a href="../index.html" accesskey="U">Module code</a> »</li> - </ul> - </div> - <div class="sphinxsidebar" role="navigation" aria-label="main navigation"> - <div class="sphinxsidebarwrapper"> -<div id="searchbox" style="display: none" role="search"> - <h3>Quick search</h3> - <div class="searchformwrapper"> - <form class="search" action="../../search.html" method="get"> - <input type="text" name="q" /> - <input type="submit" value="Go" /> - <input type="hidden" name="check_keywords" value="yes" /> - <input type="hidden" name="area" value="default" /> - </form> - </div> + <link rel="search" title="Search" href="../../search.html" /> + + + <script src="../../_static/js/modernizr.min.js"></script> + +</head> + +<body class="wy-body-for-nav"> + + + <div class="wy-grid-for-nav"> + + + <nav data-toggle="wy-nav-shift" class="wy-nav-side"> + <div class="wy-side-scroll"> + <div class="wy-side-nav-search"> + + + + <a href="../../index.html" class="icon icon-home"> jass_preprocessing + + + + </a> + + + + + + + +<div role="search"> + <form id="rtd-search-form" class="wy-form" action="../../search.html" method="get"> + <input type="text" name="q" placeholder="Search docs" /> + <input type="hidden" name="check_keywords" value="yes" /> + <input type="hidden" name="area" value="default" /> + </form> </div> -<script type="text/javascript">$('#searchbox').show(0);</script> + + + </div> + + <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation"> + + + + + + + <!-- Local TOC --> + <div class="local-toc"></div> + + </div> </div> + </nav> + + <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"> + + + <nav class="wy-nav-top" aria-label="top navigation"> + + <i data-toggle="wy-nav-top" class="fa fa-bars"></i> + <a href="../../index.html">jass_preprocessing</a> + + </nav> + + + <div class="wy-nav-content"> + + <div class="rst-content"> + + + + - <div class="document"> - <div class="documentwrapper"> - <div class="bodywrapper"> - <div class="body" role="main"> + + + + + + + + + + + + +<div role="navigation" aria-label="breadcrumbs navigation"> + + <ul class="wy-breadcrumbs"> + + <li><a href="../../index.html">Docs</a> »</li> + + <li><a href="../index.html">Module code</a> »</li> + + <li>jass_preprocessing.dna_utils</li> + + + <li class="wy-breadcrumbs-aside"> + + </li> + + </ul> + + + <hr/> +</div> + <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article"> + <div itemprop="articleBody"> <h1>Source code for jass_preprocessing.dna_utils</h1><div class="highlight"><pre> <span></span><span class="sd">"""</span> @@ -75,27 +156,52 @@ <span class="k">return</span><span class="p">([</span><span class="n">dna_complement_base</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="nb">input</span><span class="p">])</span></div> </pre></div> + </div> + </div> + <footer> + + + <hr/> + + <div role="contentinfo"> + <p> + © Copyright 2018, Hanna Julienne + + </p> + </div> + Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/rtfd/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. + +</footer> + </div> </div> - <div class="clearer"></div> - </div> - <div class="related" role="navigation" aria-label="related navigation"> - <h3>Navigation</h3> - <ul> - <li class="right" style="margin-right: 10px"> - <a href="../../genindex.html" title="General Index" - >index</a></li> - <li class="right" > - <a href="../../py-modindex.html" title="Python Module Index" - >modules</a> |</li> - <li class="nav-item nav-item-0"><a href="../../index.html">jass_preprocessing 1.0 documentation</a> »</li> - <li class="nav-item nav-item-1"><a href="../index.html" >Module code</a> »</li> - </ul> - </div> - <div class="footer" role="contentinfo"> - © Copyright 2018, Hanna Julienne. - Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.7.7. - </div> - </body> + + </section> + + </div> + + + + + + + + <script type="text/javascript" id="documentation_options" data-url_root="../../" src="../../_static/documentation_options.js"></script> + <script type="text/javascript" src="../../_static/jquery.js"></script> + <script type="text/javascript" src="../../_static/underscore.js"></script> + <script type="text/javascript" src="../../_static/doctools.js"></script> + + + + + <script type="text/javascript" src="../../_static/js/theme.js"></script> + + <script type="text/javascript"> + jQuery(function () { + SphinxRtdTheme.Navigation.enable(true); + }); + </script> + +</body> </html> \ No newline at end of file diff --git a/doc/_build/html/_modules/jass_preprocessing/map_gwas.html b/doc/_build/html/_modules/jass_preprocessing/map_gwas.html index 3712dee7914b60ada2037e8981d1d61ddb524d3f..ec7b4140ecbad83c62ed14a47c3a91bc98dd442b 100644 --- a/doc/_build/html/_modules/jass_preprocessing/map_gwas.html +++ b/doc/_build/html/_modules/jass_preprocessing/map_gwas.html @@ -1,61 +1,142 @@ -<!doctype html> - -<html xmlns="http://www.w3.org/1999/xhtml"> - <head> - <meta http-equiv="X-UA-Compatible" content="IE=Edge" /> - <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> - <title>jass_preprocessing.map_gwas — jass_preprocessing 1.0 documentation</title> - <link rel="stylesheet" href="../../_static/bizstyle.css" type="text/css" /> - <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" /> - <script type="text/javascript" id="documentation_options" data-url_root="../../" src="../../_static/documentation_options.js"></script> - <script type="text/javascript" src="../../_static/jquery.js"></script> - <script type="text/javascript" src="../../_static/underscore.js"></script> - <script type="text/javascript" src="../../_static/doctools.js"></script> - <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script> - <script type="text/javascript" src="../../_static/bizstyle.js"></script> +<!DOCTYPE html> +<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]--> +<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]--> +<head> + <meta charset="utf-8"> + + <meta name="viewport" content="width=device-width, initial-scale=1.0"> + + <title>jass_preprocessing.map_gwas — jass_preprocessing 1.0 documentation</title> + + + + + + + + + + + + + + + + <link rel="stylesheet" href="../../_static/css/theme.css" type="text/css" /> + <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" /> <link rel="index" title="Index" href="../../genindex.html" /> - <link rel="search" title="Search" href="../../search.html" /> - <meta name="viewport" content="width=device-width,initial-scale=1.0"> - <!--[if lt IE 9]> - <script type="text/javascript" src="_static/css3-mediaqueries.js"></script> - <![endif]--> - </head><body> - <div class="related" role="navigation" aria-label="related navigation"> - <h3>Navigation</h3> - <ul> - <li class="right" style="margin-right: 10px"> - <a href="../../genindex.html" title="General Index" - accesskey="I">index</a></li> - <li class="right" > - <a href="../../py-modindex.html" title="Python Module Index" - >modules</a> |</li> - <li class="nav-item nav-item-0"><a href="../../index.html">jass_preprocessing 1.0 documentation</a> »</li> - <li class="nav-item nav-item-1"><a href="../index.html" accesskey="U">Module code</a> »</li> - </ul> - </div> - <div class="sphinxsidebar" role="navigation" aria-label="main navigation"> - <div class="sphinxsidebarwrapper"> -<div id="searchbox" style="display: none" role="search"> - <h3>Quick search</h3> - <div class="searchformwrapper"> - <form class="search" action="../../search.html" method="get"> - <input type="text" name="q" /> - <input type="submit" value="Go" /> - <input type="hidden" name="check_keywords" value="yes" /> - <input type="hidden" name="area" value="default" /> - </form> - </div> + <link rel="search" title="Search" href="../../search.html" /> + + + <script src="../../_static/js/modernizr.min.js"></script> + +</head> + +<body class="wy-body-for-nav"> + + + <div class="wy-grid-for-nav"> + + + <nav data-toggle="wy-nav-shift" class="wy-nav-side"> + <div class="wy-side-scroll"> + <div class="wy-side-nav-search"> + + + + <a href="../../index.html" class="icon icon-home"> jass_preprocessing + + + + </a> + + + + + + + +<div role="search"> + <form id="rtd-search-form" class="wy-form" action="../../search.html" method="get"> + <input type="text" name="q" placeholder="Search docs" /> + <input type="hidden" name="check_keywords" value="yes" /> + <input type="hidden" name="area" value="default" /> + </form> </div> -<script type="text/javascript">$('#searchbox').show(0);</script> + + + </div> + + <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation"> + + + + + + + <!-- Local TOC --> + <div class="local-toc"></div> + + </div> </div> + </nav> + + <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"> + + + <nav class="wy-nav-top" aria-label="top navigation"> + + <i data-toggle="wy-nav-top" class="fa fa-bars"></i> + <a href="../../index.html">jass_preprocessing</a> + + </nav> + + + <div class="wy-nav-content"> + + <div class="rst-content"> + + + + + + + - <div class="document"> - <div class="documentwrapper"> - <div class="bodywrapper"> - <div class="body" role="main"> + + + + + + + + + +<div role="navigation" aria-label="breadcrumbs navigation"> + + <ul class="wy-breadcrumbs"> + + <li><a href="../../index.html">Docs</a> »</li> + + <li><a href="../index.html">Module code</a> »</li> + + <li>jass_preprocessing.map_gwas</li> + + + <li class="wy-breadcrumbs-aside"> + + </li> + + </ul> + + + <hr/> +</div> + <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article"> + <div itemprop="articleBody"> <h1>Source code for jass_preprocessing.map_gwas</h1><div class="highlight"><pre> <span></span><span class="sd">"""</span> @@ -206,27 +287,52 @@ <span class="k">return</span> <span class="n">fullGWAS</span></div> </pre></div> + </div> + </div> + <footer> + + + <hr/> + + <div role="contentinfo"> + <p> + © Copyright 2018, Hanna Julienne + + </p> + </div> + Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/rtfd/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. + +</footer> + </div> </div> - <div class="clearer"></div> - </div> - <div class="related" role="navigation" aria-label="related navigation"> - <h3>Navigation</h3> - <ul> - <li class="right" style="margin-right: 10px"> - <a href="../../genindex.html" title="General Index" - >index</a></li> - <li class="right" > - <a href="../../py-modindex.html" title="Python Module Index" - >modules</a> |</li> - <li class="nav-item nav-item-0"><a href="../../index.html">jass_preprocessing 1.0 documentation</a> »</li> - <li class="nav-item nav-item-1"><a href="../index.html" >Module code</a> »</li> - </ul> - </div> - <div class="footer" role="contentinfo"> - © Copyright 2018, Hanna Julienne. - Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.7.7. - </div> - </body> + + </section> + + </div> + + + + + + + + <script type="text/javascript" id="documentation_options" data-url_root="../../" src="../../_static/documentation_options.js"></script> + <script type="text/javascript" src="../../_static/jquery.js"></script> + <script type="text/javascript" src="../../_static/underscore.js"></script> + <script type="text/javascript" src="../../_static/doctools.js"></script> + + + + + <script type="text/javascript" src="../../_static/js/theme.js"></script> + + <script type="text/javascript"> + jQuery(function () { + SphinxRtdTheme.Navigation.enable(true); + }); + </script> + +</body> </html> \ No newline at end of file diff --git a/doc/_build/html/_modules/jass_preprocessing/map_reference.html b/doc/_build/html/_modules/jass_preprocessing/map_reference.html index 93f2563d2da8f234e7901800afb16e955d12e6e1..336b4d01f6c1864fbccce43fdeec165919dcf4ea 100644 --- a/doc/_build/html/_modules/jass_preprocessing/map_reference.html +++ b/doc/_build/html/_modules/jass_preprocessing/map_reference.html @@ -1,61 +1,142 @@ -<!doctype html> - -<html xmlns="http://www.w3.org/1999/xhtml"> - <head> - <meta http-equiv="X-UA-Compatible" content="IE=Edge" /> - <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> - <title>jass_preprocessing.map_reference — jass_preprocessing 1.0 documentation</title> - <link rel="stylesheet" href="../../_static/bizstyle.css" type="text/css" /> - <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" /> - <script type="text/javascript" id="documentation_options" data-url_root="../../" src="../../_static/documentation_options.js"></script> - <script type="text/javascript" src="../../_static/jquery.js"></script> - <script type="text/javascript" src="../../_static/underscore.js"></script> - <script type="text/javascript" src="../../_static/doctools.js"></script> - <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script> - <script type="text/javascript" src="../../_static/bizstyle.js"></script> +<!DOCTYPE html> +<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]--> +<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]--> +<head> + <meta charset="utf-8"> + + <meta name="viewport" content="width=device-width, initial-scale=1.0"> + + <title>jass_preprocessing.map_reference — jass_preprocessing 1.0 documentation</title> + + + + + + + + + + + + + + + + <link rel="stylesheet" href="../../_static/css/theme.css" type="text/css" /> + <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" /> <link rel="index" title="Index" href="../../genindex.html" /> - <link rel="search" title="Search" href="../../search.html" /> - <meta name="viewport" content="width=device-width,initial-scale=1.0"> - <!--[if lt IE 9]> - <script type="text/javascript" src="_static/css3-mediaqueries.js"></script> - <![endif]--> - </head><body> - <div class="related" role="navigation" aria-label="related navigation"> - <h3>Navigation</h3> - <ul> - <li class="right" style="margin-right: 10px"> - <a href="../../genindex.html" title="General Index" - accesskey="I">index</a></li> - <li class="right" > - <a href="../../py-modindex.html" title="Python Module Index" - >modules</a> |</li> - <li class="nav-item nav-item-0"><a href="../../index.html">jass_preprocessing 1.0 documentation</a> »</li> - <li class="nav-item nav-item-1"><a href="../index.html" accesskey="U">Module code</a> »</li> - </ul> - </div> - <div class="sphinxsidebar" role="navigation" aria-label="main navigation"> - <div class="sphinxsidebarwrapper"> -<div id="searchbox" style="display: none" role="search"> - <h3>Quick search</h3> - <div class="searchformwrapper"> - <form class="search" action="../../search.html" method="get"> - <input type="text" name="q" /> - <input type="submit" value="Go" /> - <input type="hidden" name="check_keywords" value="yes" /> - <input type="hidden" name="area" value="default" /> - </form> - </div> + <link rel="search" title="Search" href="../../search.html" /> + + + <script src="../../_static/js/modernizr.min.js"></script> + +</head> + +<body class="wy-body-for-nav"> + + + <div class="wy-grid-for-nav"> + + + <nav data-toggle="wy-nav-shift" class="wy-nav-side"> + <div class="wy-side-scroll"> + <div class="wy-side-nav-search"> + + + + <a href="../../index.html" class="icon icon-home"> jass_preprocessing + + + + </a> + + + + + + + +<div role="search"> + <form id="rtd-search-form" class="wy-form" action="../../search.html" method="get"> + <input type="text" name="q" placeholder="Search docs" /> + <input type="hidden" name="check_keywords" value="yes" /> + <input type="hidden" name="area" value="default" /> + </form> </div> -<script type="text/javascript">$('#searchbox').show(0);</script> + + + </div> + + <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation"> + + + + + + + <!-- Local TOC --> + <div class="local-toc"></div> + + </div> </div> + </nav> + + <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"> + + + <nav class="wy-nav-top" aria-label="top navigation"> + + <i data-toggle="wy-nav-top" class="fa fa-bars"></i> + <a href="../../index.html">jass_preprocessing</a> + + </nav> + + + <div class="wy-nav-content"> + + <div class="rst-content"> + + + + + + + - <div class="document"> - <div class="documentwrapper"> - <div class="bodywrapper"> - <div class="body" role="main"> + + + + + + + + + +<div role="navigation" aria-label="breadcrumbs navigation"> + + <ul class="wy-breadcrumbs"> + + <li><a href="../../index.html">Docs</a> »</li> + + <li><a href="../index.html">Module code</a> »</li> + + <li>jass_preprocessing.map_reference</li> + + + <li class="wy-breadcrumbs-aside"> + + </li> + + </ul> + + + <hr/> +</div> + <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article"> + <div itemprop="articleBody"> <h1>Source code for jass_preprocessing.map_reference</h1><div class="highlight"><pre> <span></span><span class="sd">"""</span> @@ -186,27 +267,52 @@ <span class="k">return</span><span class="p">(</span><span class="n">mgwas</span><span class="p">)</span></div> </pre></div> + </div> + </div> + <footer> + + + <hr/> + + <div role="contentinfo"> + <p> + © Copyright 2018, Hanna Julienne + + </p> + </div> + Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/rtfd/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. + +</footer> + </div> </div> - <div class="clearer"></div> - </div> - <div class="related" role="navigation" aria-label="related navigation"> - <h3>Navigation</h3> - <ul> - <li class="right" style="margin-right: 10px"> - <a href="../../genindex.html" title="General Index" - >index</a></li> - <li class="right" > - <a href="../../py-modindex.html" title="Python Module Index" - >modules</a> |</li> - <li class="nav-item nav-item-0"><a href="../../index.html">jass_preprocessing 1.0 documentation</a> »</li> - <li class="nav-item nav-item-1"><a href="../index.html" >Module code</a> »</li> - </ul> - </div> - <div class="footer" role="contentinfo"> - © Copyright 2018, Hanna Julienne. - Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.7.7. - </div> - </body> + + </section> + + </div> + + + + + + + + <script type="text/javascript" id="documentation_options" data-url_root="../../" src="../../_static/documentation_options.js"></script> + <script type="text/javascript" src="../../_static/jquery.js"></script> + <script type="text/javascript" src="../../_static/underscore.js"></script> + <script type="text/javascript" src="../../_static/doctools.js"></script> + + + + + <script type="text/javascript" src="../../_static/js/theme.js"></script> + + <script type="text/javascript"> + jQuery(function () { + SphinxRtdTheme.Navigation.enable(true); + }); + </script> + +</body> </html> \ No newline at end of file diff --git a/doc/_build/html/_modules/jass_preprocessing/save_output.html b/doc/_build/html/_modules/jass_preprocessing/save_output.html index 4eeb238ce9e9fbea0756066c96f4e7e7f56e8750..f9a906ee2fd0c0b6f3ed3d759fc0f70f5463714e 100644 --- a/doc/_build/html/_modules/jass_preprocessing/save_output.html +++ b/doc/_build/html/_modules/jass_preprocessing/save_output.html @@ -1,61 +1,142 @@ -<!doctype html> - -<html xmlns="http://www.w3.org/1999/xhtml"> - <head> - <meta http-equiv="X-UA-Compatible" content="IE=Edge" /> - <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> - <title>jass_preprocessing.save_output — jass_preprocessing 1.0 documentation</title> - <link rel="stylesheet" href="../../_static/bizstyle.css" type="text/css" /> - <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" /> - <script type="text/javascript" id="documentation_options" data-url_root="../../" src="../../_static/documentation_options.js"></script> - <script type="text/javascript" src="../../_static/jquery.js"></script> - <script type="text/javascript" src="../../_static/underscore.js"></script> - <script type="text/javascript" src="../../_static/doctools.js"></script> - <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script> - <script type="text/javascript" src="../../_static/bizstyle.js"></script> +<!DOCTYPE html> +<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]--> +<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]--> +<head> + <meta charset="utf-8"> + + <meta name="viewport" content="width=device-width, initial-scale=1.0"> + + <title>jass_preprocessing.save_output — jass_preprocessing 1.0 documentation</title> + + + + + + + + + + + + + + + + <link rel="stylesheet" href="../../_static/css/theme.css" type="text/css" /> + <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" /> <link rel="index" title="Index" href="../../genindex.html" /> - <link rel="search" title="Search" href="../../search.html" /> - <meta name="viewport" content="width=device-width,initial-scale=1.0"> - <!--[if lt IE 9]> - <script type="text/javascript" src="_static/css3-mediaqueries.js"></script> - <![endif]--> - </head><body> - <div class="related" role="navigation" aria-label="related navigation"> - <h3>Navigation</h3> - <ul> - <li class="right" style="margin-right: 10px"> - <a href="../../genindex.html" title="General Index" - accesskey="I">index</a></li> - <li class="right" > - <a href="../../py-modindex.html" title="Python Module Index" - >modules</a> |</li> - <li class="nav-item nav-item-0"><a href="../../index.html">jass_preprocessing 1.0 documentation</a> »</li> - <li class="nav-item nav-item-1"><a href="../index.html" accesskey="U">Module code</a> »</li> - </ul> - </div> - <div class="sphinxsidebar" role="navigation" aria-label="main navigation"> - <div class="sphinxsidebarwrapper"> -<div id="searchbox" style="display: none" role="search"> - <h3>Quick search</h3> - <div class="searchformwrapper"> - <form class="search" action="../../search.html" method="get"> - <input type="text" name="q" /> - <input type="submit" value="Go" /> - <input type="hidden" name="check_keywords" value="yes" /> - <input type="hidden" name="area" value="default" /> - </form> - </div> + <link rel="search" title="Search" href="../../search.html" /> + + + <script src="../../_static/js/modernizr.min.js"></script> + +</head> + +<body class="wy-body-for-nav"> + + + <div class="wy-grid-for-nav"> + + + <nav data-toggle="wy-nav-shift" class="wy-nav-side"> + <div class="wy-side-scroll"> + <div class="wy-side-nav-search"> + + + + <a href="../../index.html" class="icon icon-home"> jass_preprocessing + + + + </a> + + + + + + + +<div role="search"> + <form id="rtd-search-form" class="wy-form" action="../../search.html" method="get"> + <input type="text" name="q" placeholder="Search docs" /> + <input type="hidden" name="check_keywords" value="yes" /> + <input type="hidden" name="area" value="default" /> + </form> </div> -<script type="text/javascript">$('#searchbox').show(0);</script> + + + </div> + + <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation"> + + + + + + + <!-- Local TOC --> + <div class="local-toc"></div> + + </div> </div> + </nav> + + <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"> + + + <nav class="wy-nav-top" aria-label="top navigation"> + + <i data-toggle="wy-nav-top" class="fa fa-bars"></i> + <a href="../../index.html">jass_preprocessing</a> + + </nav> + + + <div class="wy-nav-content"> + + <div class="rst-content"> + + + + - <div class="document"> - <div class="documentwrapper"> - <div class="bodywrapper"> - <div class="body" role="main"> + + + + + + + + + + + + +<div role="navigation" aria-label="breadcrumbs navigation"> + + <ul class="wy-breadcrumbs"> + + <li><a href="../../index.html">Docs</a> »</li> + + <li><a href="../index.html">Module code</a> »</li> + + <li>jass_preprocessing.save_output</li> + + + <li class="wy-breadcrumbs-aside"> + + </li> + + </ul> + + + <hr/> +</div> + <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article"> + <div itemprop="articleBody"> <h1>Source code for jass_preprocessing.save_output</h1><div class="highlight"><pre> <span></span><span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span> @@ -109,27 +190,52 @@ <span class="n">mgwas_copy</span><span class="o">.</span><span class="n">sort_values</span><span class="p">([</span><span class="s1">'chrom'</span><span class="p">,</span><span class="s1">'pos'</span><span class="p">])</span><span class="o">.</span><span class="n">to_csv</span><span class="p">(</span><span class="n">impg_output_file</span><span class="p">,</span> <span class="n">sep</span><span class="o">=</span><span class="s2">"</span><span class="se">\t</span><span class="s2">"</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span></div> </pre></div> + </div> + </div> + <footer> + + + <hr/> + + <div role="contentinfo"> + <p> + © Copyright 2018, Hanna Julienne + + </p> + </div> + Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/rtfd/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. + +</footer> + </div> </div> - <div class="clearer"></div> - </div> - <div class="related" role="navigation" aria-label="related navigation"> - <h3>Navigation</h3> - <ul> - <li class="right" style="margin-right: 10px"> - <a href="../../genindex.html" title="General Index" - >index</a></li> - <li class="right" > - <a href="../../py-modindex.html" title="Python Module Index" - >modules</a> |</li> - <li class="nav-item nav-item-0"><a href="../../index.html">jass_preprocessing 1.0 documentation</a> »</li> - <li class="nav-item nav-item-1"><a href="../index.html" >Module code</a> »</li> - </ul> - </div> - <div class="footer" role="contentinfo"> - © Copyright 2018, Hanna Julienne. - Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.7.7. - </div> - </body> + + </section> + + </div> + + + + + + + + <script type="text/javascript" id="documentation_options" data-url_root="../../" src="../../_static/documentation_options.js"></script> + <script type="text/javascript" src="../../_static/jquery.js"></script> + <script type="text/javascript" src="../../_static/underscore.js"></script> + <script type="text/javascript" src="../../_static/doctools.js"></script> + + + + + <script type="text/javascript" src="../../_static/js/theme.js"></script> + + <script type="text/javascript"> + jQuery(function () { + SphinxRtdTheme.Navigation.enable(true); + }); + </script> + +</body> </html> \ No newline at end of file diff --git a/doc/_build/html/_sources/index.rst.txt b/doc/_build/html/_sources/index.rst.txt index e424cf390f160df460033869f157f95fa2c19b27..7136a4067686fa41a885c328bacf6133ea3bde08 100644 --- a/doc/_build/html/_sources/index.rst.txt +++ b/doc/_build/html/_sources/index.rst.txt @@ -24,6 +24,8 @@ The QC and preprocessing step goes as follow: * Select GWAS SNPs that are in the input reference panel * Align coded allele of the GWAS with the reference panel * Infer Number of sample by SNPs if not present in input data +* Filter SNPs with a small sample size +* Normalize the effect size by sample size to have Z-scores * Save the output by chromosome as the following example: +----------+-------+------+-----+--------+ @@ -93,11 +95,15 @@ Hard coded path (l.20-29 of JASS_Pre-processing/main_preprocessing.py) Command line usage example: ============================ -The file : "/JASS_Pre-processing/main_preprocessing.py" gives a complete example on how to use this package. +It is possible to launch the complete preprocessing from the command line: + +.. argparse:: + :ref: jass_preprocessing.__main__.add_preprocessing_argument Indices and tables ================== + * :ref:`genindex` * :ref:`modindex` * :ref:`search` diff --git a/doc/_build/html/_static/basic.css b/doc/_build/html/_static/basic.css index 19ced1057aebf39d3dac6f6a5d864491231a3e33..104f076ae8ae5d6118dc13db6cb16e2ae9de1bda 100644 --- a/doc/_build/html/_static/basic.css +++ b/doc/_build/html/_static/basic.css @@ -81,6 +81,10 @@ div.sphinxsidebar input { font-size: 1em; } +div.sphinxsidebar #searchbox form.search { + overflow: hidden; +} + div.sphinxsidebar #searchbox input[type="text"] { float: left; width: 80%; @@ -427,6 +431,13 @@ table.field-list td, table.field-list th { hyphens: manual; } +/* -- hlist styles ---------------------------------------------------------- */ + +table.hlist td { + vertical-align: top; +} + + /* -- other body styles ----------------------------------------------------- */ ol.arabic { diff --git a/doc/_build/html/_static/doctools.js b/doc/_build/html/_static/doctools.js index d8928926bf24bb081d91a12f7b92e1b2d8b142b6..ffadbec11f71c338696d5c014de9b64afe31a516 100644 --- a/doc/_build/html/_static/doctools.js +++ b/doc/_build/html/_static/doctools.js @@ -150,7 +150,9 @@ var Documentation = { this.fixFirefoxAnchorBug(); this.highlightSearchWords(); this.initIndexTable(); - + if (DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) { + this.initOnKeyListeners(); + } }, /** @@ -310,4 +312,4 @@ _ = Documentation.gettext; $(document).ready(function() { Documentation.init(); -}); \ No newline at end of file +}); diff --git a/doc/_build/html/_static/documentation_options.js b/doc/_build/html/_static/documentation_options.js index 9b69b42bcd98b555324995d9afee402ad1b09250..837eacf30de116b6aff70d9761453e9c93abb1b5 100644 --- a/doc/_build/html/_static/documentation_options.js +++ b/doc/_build/html/_static/documentation_options.js @@ -5,5 +5,292 @@ var DOCUMENTATION_OPTIONS = { COLLAPSE_INDEX: false, FILE_SUFFIX: '.html', HAS_SOURCE: true, - SOURCELINK_SUFFIX: '.txt' -}; \ No newline at end of file + SOURCELINK_SUFFIX: '.txt', + NAVIGATION_WITH_KEYS: false, + SEARCH_LANGUAGE_STOP_WORDS: ["a","and","are","as","at","be","but","by","for","if","in","into","is","it","near","no","not","of","on","or","such","that","the","their","then","there","these","they","this","to","was","will","with"] +}; + + + +/* Non-minified version JS is _stemmer.js if file is provided */ +/** + * Porter Stemmer + */ +var Stemmer = function() { + + var step2list = { + ational: 'ate', + tional: 'tion', + enci: 'ence', + anci: 'ance', + izer: 'ize', + bli: 'ble', + alli: 'al', + entli: 'ent', + eli: 'e', + ousli: 'ous', + ization: 'ize', + ation: 'ate', + ator: 'ate', + alism: 'al', + iveness: 'ive', + fulness: 'ful', + ousness: 'ous', + aliti: 'al', + iviti: 'ive', + biliti: 'ble', + logi: 'log' + }; + + var step3list = { + icate: 'ic', + ative: '', + alize: 'al', + iciti: 'ic', + ical: 'ic', + ful: '', + ness: '' + }; + + var c = "[^aeiou]"; // consonant + var v = "[aeiouy]"; // vowel + var C = c + "[^aeiouy]*"; // consonant sequence + var V = v + "[aeiou]*"; // vowel sequence + + var mgr0 = "^(" + C + ")?" + V + C; // [C]VC... is m>0 + var meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$"; // [C]VC[V] is m=1 + var mgr1 = "^(" + C + ")?" + V + C + V + C; // [C]VCVC... is m>1 + var s_v = "^(" + C + ")?" + v; // vowel in stem + + this.stemWord = function (w) { + var stem; + var suffix; + var firstch; + var origword = w; + + if (w.length < 3) + return w; + + var re; + var re2; + var re3; + var re4; + + firstch = w.substr(0,1); + if (firstch == "y") + w = firstch.toUpperCase() + w.substr(1); + + // Step 1a + re = /^(.+?)(ss|i)es$/; + re2 = /^(.+?)([^s])s$/; + + if (re.test(w)) + w = w.replace(re,"$1$2"); + else if (re2.test(w)) + w = w.replace(re2,"$1$2"); + + // Step 1b + re = /^(.+?)eed$/; + re2 = /^(.+?)(ed|ing)$/; + if (re.test(w)) { + var fp = re.exec(w); + re = new RegExp(mgr0); + if (re.test(fp[1])) { + re = /.$/; + w = w.replace(re,""); + } + } + else if (re2.test(w)) { + var fp = re2.exec(w); + stem = fp[1]; + re2 = new RegExp(s_v); + if (re2.test(stem)) { + w = stem; + re2 = /(at|bl|iz)$/; + re3 = new RegExp("([^aeiouylsz])\\1$"); + re4 = new RegExp("^" + C + v + "[^aeiouwxy]$"); + if (re2.test(w)) + w = w + "e"; + else if (re3.test(w)) { + re = /.$/; + w = w.replace(re,""); + } + else if (re4.test(w)) + w = w + "e"; + } + } + + // Step 1c + re = /^(.+?)y$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(s_v); + if (re.test(stem)) + w = stem + "i"; + } + + // Step 2 + re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + suffix = fp[2]; + re = new RegExp(mgr0); + if (re.test(stem)) + w = stem + step2list[suffix]; + } + + // Step 3 + re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + suffix = fp[2]; + re = new RegExp(mgr0); + if (re.test(stem)) + w = stem + step3list[suffix]; + } + + // Step 4 + re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/; + re2 = /^(.+?)(s|t)(ion)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(mgr1); + if (re.test(stem)) + w = stem; + } + else if (re2.test(w)) { + var fp = re2.exec(w); + stem = fp[1] + fp[2]; + re2 = new RegExp(mgr1); + if (re2.test(stem)) + w = stem; + } + + // Step 5 + re = /^(.+?)e$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(mgr1); + re2 = new RegExp(meq1); + re3 = new RegExp("^" + C + v + "[^aeiouwxy]$"); + if (re.test(stem) || (re2.test(stem) && !(re3.test(stem)))) + w = stem; + } + re = /ll$/; + re2 = new RegExp(mgr1); + if (re.test(w) && re2.test(w)) { + re = /.$/; + w = w.replace(re,""); + } + + // and turn initial Y back to y + if (firstch == "y") + w = firstch.toLowerCase() + w.substr(1); + return w; + } +} + + + + + +var splitChars = (function() { + var result = {}; + var singles = [96, 180, 187, 191, 215, 247, 749, 885, 903, 907, 909, 930, 1014, 1648, + 1748, 1809, 2416, 2473, 2481, 2526, 2601, 2609, 2612, 2615, 2653, 2702, + 2706, 2729, 2737, 2740, 2857, 2865, 2868, 2910, 2928, 2948, 2961, 2971, + 2973, 3085, 3089, 3113, 3124, 3213, 3217, 3241, 3252, 3295, 3341, 3345, + 3369, 3506, 3516, 3633, 3715, 3721, 3736, 3744, 3748, 3750, 3756, 3761, + 3781, 3912, 4239, 4347, 4681, 4695, 4697, 4745, 4785, 4799, 4801, 4823, + 4881, 5760, 5901, 5997, 6313, 7405, 8024, 8026, 8028, 8030, 8117, 8125, + 8133, 8181, 8468, 8485, 8487, 8489, 8494, 8527, 11311, 11359, 11687, 11695, + 11703, 11711, 11719, 11727, 11735, 12448, 12539, 43010, 43014, 43019, 43587, + 43696, 43713, 64286, 64297, 64311, 64317, 64319, 64322, 64325, 65141]; + var i, j, start, end; + for (i = 0; i < singles.length; i++) { + result[singles[i]] = true; + } + var ranges = [[0, 47], [58, 64], [91, 94], [123, 169], [171, 177], [182, 184], [706, 709], + [722, 735], [741, 747], [751, 879], [888, 889], [894, 901], [1154, 1161], + [1318, 1328], [1367, 1368], [1370, 1376], [1416, 1487], [1515, 1519], [1523, 1568], + [1611, 1631], [1642, 1645], [1750, 1764], [1767, 1773], [1789, 1790], [1792, 1807], + [1840, 1868], [1958, 1968], [1970, 1983], [2027, 2035], [2038, 2041], [2043, 2047], + [2070, 2073], [2075, 2083], [2085, 2087], [2089, 2307], [2362, 2364], [2366, 2383], + [2385, 2391], [2402, 2405], [2419, 2424], [2432, 2436], [2445, 2446], [2449, 2450], + [2483, 2485], [2490, 2492], [2494, 2509], [2511, 2523], [2530, 2533], [2546, 2547], + [2554, 2564], [2571, 2574], [2577, 2578], [2618, 2648], [2655, 2661], [2672, 2673], + [2677, 2692], [2746, 2748], [2750, 2767], [2769, 2783], [2786, 2789], [2800, 2820], + [2829, 2830], [2833, 2834], [2874, 2876], [2878, 2907], [2914, 2917], [2930, 2946], + [2955, 2957], [2966, 2968], [2976, 2978], [2981, 2983], [2987, 2989], [3002, 3023], + [3025, 3045], [3059, 3076], [3130, 3132], [3134, 3159], [3162, 3167], [3170, 3173], + [3184, 3191], [3199, 3204], [3258, 3260], [3262, 3293], [3298, 3301], [3312, 3332], + [3386, 3388], [3390, 3423], [3426, 3429], [3446, 3449], [3456, 3460], [3479, 3481], + [3518, 3519], [3527, 3584], [3636, 3647], [3655, 3663], [3674, 3712], [3717, 3718], + [3723, 3724], [3726, 3731], [3752, 3753], [3764, 3772], [3774, 3775], [3783, 3791], + [3802, 3803], [3806, 3839], [3841, 3871], [3892, 3903], [3949, 3975], [3980, 4095], + [4139, 4158], [4170, 4175], [4182, 4185], [4190, 4192], [4194, 4196], [4199, 4205], + [4209, 4212], [4226, 4237], [4250, 4255], [4294, 4303], [4349, 4351], [4686, 4687], + [4702, 4703], [4750, 4751], [4790, 4791], [4806, 4807], [4886, 4887], [4955, 4968], + [4989, 4991], [5008, 5023], [5109, 5120], [5741, 5742], [5787, 5791], [5867, 5869], + [5873, 5887], [5906, 5919], [5938, 5951], [5970, 5983], [6001, 6015], [6068, 6102], + [6104, 6107], [6109, 6111], [6122, 6127], [6138, 6159], [6170, 6175], [6264, 6271], + [6315, 6319], [6390, 6399], [6429, 6469], [6510, 6511], [6517, 6527], [6572, 6592], + [6600, 6607], [6619, 6655], [6679, 6687], [6741, 6783], [6794, 6799], [6810, 6822], + [6824, 6916], [6964, 6980], [6988, 6991], [7002, 7042], [7073, 7085], [7098, 7167], + [7204, 7231], [7242, 7244], [7294, 7400], [7410, 7423], [7616, 7679], [7958, 7959], + [7966, 7967], [8006, 8007], [8014, 8015], [8062, 8063], [8127, 8129], [8141, 8143], + [8148, 8149], [8156, 8159], [8173, 8177], [8189, 8303], [8306, 8307], [8314, 8318], + [8330, 8335], [8341, 8449], [8451, 8454], [8456, 8457], [8470, 8472], [8478, 8483], + [8506, 8507], [8512, 8516], [8522, 8525], [8586, 9311], [9372, 9449], [9472, 10101], + [10132, 11263], [11493, 11498], [11503, 11516], [11518, 11519], [11558, 11567], + [11622, 11630], [11632, 11647], [11671, 11679], [11743, 11822], [11824, 12292], + [12296, 12320], [12330, 12336], [12342, 12343], [12349, 12352], [12439, 12444], + [12544, 12548], [12590, 12592], [12687, 12689], [12694, 12703], [12728, 12783], + [12800, 12831], [12842, 12880], [12896, 12927], [12938, 12976], [12992, 13311], + [19894, 19967], [40908, 40959], [42125, 42191], [42238, 42239], [42509, 42511], + [42540, 42559], [42592, 42593], [42607, 42622], [42648, 42655], [42736, 42774], + [42784, 42785], [42889, 42890], [42893, 43002], [43043, 43055], [43062, 43071], + [43124, 43137], [43188, 43215], [43226, 43249], [43256, 43258], [43260, 43263], + [43302, 43311], [43335, 43359], [43389, 43395], [43443, 43470], [43482, 43519], + [43561, 43583], [43596, 43599], [43610, 43615], [43639, 43641], [43643, 43647], + [43698, 43700], [43703, 43704], [43710, 43711], [43715, 43738], [43742, 43967], + [44003, 44015], [44026, 44031], [55204, 55215], [55239, 55242], [55292, 55295], + [57344, 63743], [64046, 64047], [64110, 64111], [64218, 64255], [64263, 64274], + [64280, 64284], [64434, 64466], [64830, 64847], [64912, 64913], [64968, 65007], + [65020, 65135], [65277, 65295], [65306, 65312], [65339, 65344], [65371, 65381], + [65471, 65473], [65480, 65481], [65488, 65489], [65496, 65497]]; + for (i = 0; i < ranges.length; i++) { + start = ranges[i][0]; + end = ranges[i][1]; + for (j = start; j <= end; j++) { + result[j] = true; + } + } + return result; +})(); + +function splitQuery(query) { + var result = []; + var start = -1; + for (var i = 0; i < query.length; i++) { + if (splitChars[query.charCodeAt(i)]) { + if (start !== -1) { + result.push(query.slice(start, i)); + start = -1; + } + } else if (start === -1) { + start = i; + } + } + if (start !== -1) { + result.push(query.slice(start)); + } + return result; +} + + diff --git a/doc/_build/html/_static/searchtools.js b/doc/_build/html/_static/searchtools.js index 41b8336776442fbc64332ffbd3d2c1ddd8b3b9c2..7473859b245fa63f5d8812e2249c8d1ae67425fd 100644 --- a/doc/_build/html/_static/searchtools.js +++ b/doc/_build/html/_static/searchtools.js @@ -1,5 +1,5 @@ /* - * searchtools.js_t + * searchtools.js * ~~~~~~~~~~~~~~~~ * * Sphinx JavaScript utilities for the full-text search. @@ -9,323 +9,44 @@ * */ - -/* Non-minified version JS is _stemmer.js if file is provided */ -/** - * Porter Stemmer - */ -var Stemmer = function() { - - var step2list = { - ational: 'ate', - tional: 'tion', - enci: 'ence', - anci: 'ance', - izer: 'ize', - bli: 'ble', - alli: 'al', - entli: 'ent', - eli: 'e', - ousli: 'ous', - ization: 'ize', - ation: 'ate', - ator: 'ate', - alism: 'al', - iveness: 'ive', - fulness: 'ful', - ousness: 'ous', - aliti: 'al', - iviti: 'ive', - biliti: 'ble', - logi: 'log' - }; - - var step3list = { - icate: 'ic', - ative: '', - alize: 'al', - iciti: 'ic', - ical: 'ic', - ful: '', - ness: '' +if (!Scorer) { + /** + * Simple result scoring code. + */ + var Scorer = { + // Implement the following function to further tweak the score for each result + // The function takes a result array [filename, title, anchor, descr, score] + // and returns the new score. + /* + score: function(result) { + return result[4]; + }, + */ + + // query matches the full name of an object + objNameMatch: 11, + // or matches in the last dotted part of the object name + objPartialMatch: 6, + // Additive scores depending on the priority of the object + objPrio: {0: 15, // used to be importantResults + 1: 5, // used to be objectResults + 2: -5}, // used to be unimportantResults + // Used when the priority is not in the mapping. + objPrioDefault: 0, + + // query found in title + title: 15, + // query found in terms + term: 5 }; - - var c = "[^aeiou]"; // consonant - var v = "[aeiouy]"; // vowel - var C = c + "[^aeiouy]*"; // consonant sequence - var V = v + "[aeiou]*"; // vowel sequence - - var mgr0 = "^(" + C + ")?" + V + C; // [C]VC... is m>0 - var meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$"; // [C]VC[V] is m=1 - var mgr1 = "^(" + C + ")?" + V + C + V + C; // [C]VCVC... is m>1 - var s_v = "^(" + C + ")?" + v; // vowel in stem - - this.stemWord = function (w) { - var stem; - var suffix; - var firstch; - var origword = w; - - if (w.length < 3) - return w; - - var re; - var re2; - var re3; - var re4; - - firstch = w.substr(0,1); - if (firstch == "y") - w = firstch.toUpperCase() + w.substr(1); - - // Step 1a - re = /^(.+?)(ss|i)es$/; - re2 = /^(.+?)([^s])s$/; - - if (re.test(w)) - w = w.replace(re,"$1$2"); - else if (re2.test(w)) - w = w.replace(re2,"$1$2"); - - // Step 1b - re = /^(.+?)eed$/; - re2 = /^(.+?)(ed|ing)$/; - if (re.test(w)) { - var fp = re.exec(w); - re = new RegExp(mgr0); - if (re.test(fp[1])) { - re = /.$/; - w = w.replace(re,""); - } - } - else if (re2.test(w)) { - var fp = re2.exec(w); - stem = fp[1]; - re2 = new RegExp(s_v); - if (re2.test(stem)) { - w = stem; - re2 = /(at|bl|iz)$/; - re3 = new RegExp("([^aeiouylsz])\\1$"); - re4 = new RegExp("^" + C + v + "[^aeiouwxy]$"); - if (re2.test(w)) - w = w + "e"; - else if (re3.test(w)) { - re = /.$/; - w = w.replace(re,""); - } - else if (re4.test(w)) - w = w + "e"; - } - } - - // Step 1c - re = /^(.+?)y$/; - if (re.test(w)) { - var fp = re.exec(w); - stem = fp[1]; - re = new RegExp(s_v); - if (re.test(stem)) - w = stem + "i"; - } - - // Step 2 - re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/; - if (re.test(w)) { - var fp = re.exec(w); - stem = fp[1]; - suffix = fp[2]; - re = new RegExp(mgr0); - if (re.test(stem)) - w = stem + step2list[suffix]; - } - - // Step 3 - re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/; - if (re.test(w)) { - var fp = re.exec(w); - stem = fp[1]; - suffix = fp[2]; - re = new RegExp(mgr0); - if (re.test(stem)) - w = stem + step3list[suffix]; - } - - // Step 4 - re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/; - re2 = /^(.+?)(s|t)(ion)$/; - if (re.test(w)) { - var fp = re.exec(w); - stem = fp[1]; - re = new RegExp(mgr1); - if (re.test(stem)) - w = stem; - } - else if (re2.test(w)) { - var fp = re2.exec(w); - stem = fp[1] + fp[2]; - re2 = new RegExp(mgr1); - if (re2.test(stem)) - w = stem; - } - - // Step 5 - re = /^(.+?)e$/; - if (re.test(w)) { - var fp = re.exec(w); - stem = fp[1]; - re = new RegExp(mgr1); - re2 = new RegExp(meq1); - re3 = new RegExp("^" + C + v + "[^aeiouwxy]$"); - if (re.test(stem) || (re2.test(stem) && !(re3.test(stem)))) - w = stem; - } - re = /ll$/; - re2 = new RegExp(mgr1); - if (re.test(w) && re2.test(w)) { - re = /.$/; - w = w.replace(re,""); - } - - // and turn initial Y back to y - if (firstch == "y") - w = firstch.toLowerCase() + w.substr(1); - return w; - } } - - -/** - * Simple result scoring code. - */ -var Scorer = { - // Implement the following function to further tweak the score for each result - // The function takes a result array [filename, title, anchor, descr, score] - // and returns the new score. - /* - score: function(result) { - return result[4]; - }, - */ - - // query matches the full name of an object - objNameMatch: 11, - // or matches in the last dotted part of the object name - objPartialMatch: 6, - // Additive scores depending on the priority of the object - objPrio: {0: 15, // used to be importantResults - 1: 5, // used to be objectResults - 2: -5}, // used to be unimportantResults - // Used when the priority is not in the mapping. - objPrioDefault: 0, - - // query found in title - title: 15, - // query found in terms - term: 5 -}; - - - - - -var splitChars = (function() { - var result = {}; - var singles = [96, 180, 187, 191, 215, 247, 749, 885, 903, 907, 909, 930, 1014, 1648, - 1748, 1809, 2416, 2473, 2481, 2526, 2601, 2609, 2612, 2615, 2653, 2702, - 2706, 2729, 2737, 2740, 2857, 2865, 2868, 2910, 2928, 2948, 2961, 2971, - 2973, 3085, 3089, 3113, 3124, 3213, 3217, 3241, 3252, 3295, 3341, 3345, - 3369, 3506, 3516, 3633, 3715, 3721, 3736, 3744, 3748, 3750, 3756, 3761, - 3781, 3912, 4239, 4347, 4681, 4695, 4697, 4745, 4785, 4799, 4801, 4823, - 4881, 5760, 5901, 5997, 6313, 7405, 8024, 8026, 8028, 8030, 8117, 8125, - 8133, 8181, 8468, 8485, 8487, 8489, 8494, 8527, 11311, 11359, 11687, 11695, - 11703, 11711, 11719, 11727, 11735, 12448, 12539, 43010, 43014, 43019, 43587, - 43696, 43713, 64286, 64297, 64311, 64317, 64319, 64322, 64325, 65141]; - var i, j, start, end; - for (i = 0; i < singles.length; i++) { - result[singles[i]] = true; - } - var ranges = [[0, 47], [58, 64], [91, 94], [123, 169], [171, 177], [182, 184], [706, 709], - [722, 735], [741, 747], [751, 879], [888, 889], [894, 901], [1154, 1161], - [1318, 1328], [1367, 1368], [1370, 1376], [1416, 1487], [1515, 1519], [1523, 1568], - [1611, 1631], [1642, 1645], [1750, 1764], [1767, 1773], [1789, 1790], [1792, 1807], - [1840, 1868], [1958, 1968], [1970, 1983], [2027, 2035], [2038, 2041], [2043, 2047], - [2070, 2073], [2075, 2083], [2085, 2087], [2089, 2307], [2362, 2364], [2366, 2383], - [2385, 2391], [2402, 2405], [2419, 2424], [2432, 2436], [2445, 2446], [2449, 2450], - [2483, 2485], [2490, 2492], [2494, 2509], [2511, 2523], [2530, 2533], [2546, 2547], - [2554, 2564], [2571, 2574], [2577, 2578], [2618, 2648], [2655, 2661], [2672, 2673], - [2677, 2692], [2746, 2748], [2750, 2767], [2769, 2783], [2786, 2789], [2800, 2820], - [2829, 2830], [2833, 2834], [2874, 2876], [2878, 2907], [2914, 2917], [2930, 2946], - [2955, 2957], [2966, 2968], [2976, 2978], [2981, 2983], [2987, 2989], [3002, 3023], - [3025, 3045], [3059, 3076], [3130, 3132], [3134, 3159], [3162, 3167], [3170, 3173], - [3184, 3191], [3199, 3204], [3258, 3260], [3262, 3293], [3298, 3301], [3312, 3332], - [3386, 3388], [3390, 3423], [3426, 3429], [3446, 3449], [3456, 3460], [3479, 3481], - [3518, 3519], [3527, 3584], [3636, 3647], [3655, 3663], [3674, 3712], [3717, 3718], - [3723, 3724], [3726, 3731], [3752, 3753], [3764, 3772], [3774, 3775], [3783, 3791], - [3802, 3803], [3806, 3839], [3841, 3871], [3892, 3903], [3949, 3975], [3980, 4095], - [4139, 4158], [4170, 4175], [4182, 4185], [4190, 4192], [4194, 4196], [4199, 4205], - [4209, 4212], [4226, 4237], [4250, 4255], [4294, 4303], [4349, 4351], [4686, 4687], - [4702, 4703], [4750, 4751], [4790, 4791], [4806, 4807], [4886, 4887], [4955, 4968], - [4989, 4991], [5008, 5023], [5109, 5120], [5741, 5742], [5787, 5791], [5867, 5869], - [5873, 5887], [5906, 5919], [5938, 5951], [5970, 5983], [6001, 6015], [6068, 6102], - [6104, 6107], [6109, 6111], [6122, 6127], [6138, 6159], [6170, 6175], [6264, 6271], - [6315, 6319], [6390, 6399], [6429, 6469], [6510, 6511], [6517, 6527], [6572, 6592], - [6600, 6607], [6619, 6655], [6679, 6687], [6741, 6783], [6794, 6799], [6810, 6822], - [6824, 6916], [6964, 6980], [6988, 6991], [7002, 7042], [7073, 7085], [7098, 7167], - [7204, 7231], [7242, 7244], [7294, 7400], [7410, 7423], [7616, 7679], [7958, 7959], - [7966, 7967], [8006, 8007], [8014, 8015], [8062, 8063], [8127, 8129], [8141, 8143], - [8148, 8149], [8156, 8159], [8173, 8177], [8189, 8303], [8306, 8307], [8314, 8318], - [8330, 8335], [8341, 8449], [8451, 8454], [8456, 8457], [8470, 8472], [8478, 8483], - [8506, 8507], [8512, 8516], [8522, 8525], [8586, 9311], [9372, 9449], [9472, 10101], - [10132, 11263], [11493, 11498], [11503, 11516], [11518, 11519], [11558, 11567], - [11622, 11630], [11632, 11647], [11671, 11679], [11743, 11822], [11824, 12292], - [12296, 12320], [12330, 12336], [12342, 12343], [12349, 12352], [12439, 12444], - [12544, 12548], [12590, 12592], [12687, 12689], [12694, 12703], [12728, 12783], - [12800, 12831], [12842, 12880], [12896, 12927], [12938, 12976], [12992, 13311], - [19894, 19967], [40908, 40959], [42125, 42191], [42238, 42239], [42509, 42511], - [42540, 42559], [42592, 42593], [42607, 42622], [42648, 42655], [42736, 42774], - [42784, 42785], [42889, 42890], [42893, 43002], [43043, 43055], [43062, 43071], - [43124, 43137], [43188, 43215], [43226, 43249], [43256, 43258], [43260, 43263], - [43302, 43311], [43335, 43359], [43389, 43395], [43443, 43470], [43482, 43519], - [43561, 43583], [43596, 43599], [43610, 43615], [43639, 43641], [43643, 43647], - [43698, 43700], [43703, 43704], [43710, 43711], [43715, 43738], [43742, 43967], - [44003, 44015], [44026, 44031], [55204, 55215], [55239, 55242], [55292, 55295], - [57344, 63743], [64046, 64047], [64110, 64111], [64218, 64255], [64263, 64274], - [64280, 64284], [64434, 64466], [64830, 64847], [64912, 64913], [64968, 65007], - [65020, 65135], [65277, 65295], [65306, 65312], [65339, 65344], [65371, 65381], - [65471, 65473], [65480, 65481], [65488, 65489], [65496, 65497]]; - for (i = 0; i < ranges.length; i++) { - start = ranges[i][0]; - end = ranges[i][1]; - for (j = start; j <= end; j++) { - result[j] = true; - } - } - return result; -})(); - -function splitQuery(query) { - var result = []; - var start = -1; - for (var i = 0; i < query.length; i++) { - if (splitChars[query.charCodeAt(i)]) { - if (start !== -1) { - result.push(query.slice(start, i)); - start = -1; - } - } else if (start === -1) { - start = i; - } - } - if (start !== -1) { - result.push(query.slice(start)); - } - return result; +if (!splitQuery) { + function splitQuery(query) { + return query.split(/\s+/); + } } - - - /** * Search Module */ @@ -417,7 +138,7 @@ var Search = { */ query : function(query) { var i; - var stopwords = ["a","and","are","as","at","be","but","by","for","if","in","into","is","it","near","no","not","of","on","or","such","that","the","their","then","there","these","they","this","to","was","will","with"]; + var stopwords = DOCUMENTATION_OPTIONS.SEARCH_LANGUAGE_STOP_WORDS; // stem the searchterms and add them to the correct list var stemmer = new Stemmer(); @@ -758,4 +479,4 @@ var Search = { $(document).ready(function() { Search.init(); -}); \ No newline at end of file +}); diff --git a/doc/_build/html/genindex.html b/doc/_build/html/genindex.html index 61624f3fb0c2325e247a74c62f4991b43835854b..d087160a11e743638e35b4cd4154d466406ea6ad 100644 --- a/doc/_build/html/genindex.html +++ b/doc/_build/html/genindex.html @@ -1,61 +1,143 @@ -<!doctype html> - -<html xmlns="http://www.w3.org/1999/xhtml"> - <head> - <meta http-equiv="X-UA-Compatible" content="IE=Edge" /> - <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> - 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class="wy-side-nav-search"> + + + + <a href="#" class="icon icon-home"> jass_preprocessing + + + + </a> + + + + + + + +<div role="search"> + <form id="rtd-search-form" class="wy-form" action="search.html" method="get"> + <input type="text" name="q" placeholder="Search docs" /> + <input type="hidden" name="check_keywords" value="yes" /> + <input type="hidden" name="area" value="default" /> + </form> +</div> + + + </div> + + <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation"> + + + + + + + <!-- Local TOC --> + <div class="local-toc"><ul> <li><a class="reference internal" href="#">Welcome to jass_preprocessing’s documentation!</a></li> <li><a class="reference internal" href="#what-is-jass-preprocessing">What is jass preprocessing ?</a></li> <li><a class="reference internal" href="#overview">Overview</a></li> <li><a class="reference internal" href="#installation">Installation</a></li> <li><a class="reference internal" href="#input">Input</a></li> -<li><a class="reference internal" href="#command-line-usage-example">Command line usage example:</a></li> +<li><a class="reference internal" href="#command-line-usage-example">Command line usage example:</a><ul> +<li><a class="reference internal" href="#Named Arguments">Named Arguments</a></li> +</ul> +</li> <li><a class="reference internal" href="#indices-and-tables">Indices and tables</a></li> </ul> - - <div role="note" aria-label="source link"> - <h3>This Page</h3> - <ul class="this-page-menu"> - <li><a href="_sources/index.rst.txt" - rel="nofollow">Show Source</a></li> - </ul> - </div> -<div id="searchbox" style="display: none" role="search"> - <h3>Quick search</h3> - <div class="searchformwrapper"> - <form class="search" action="search.html" method="get"> - <input type="text" name="q" /> - <input type="submit" value="Go" /> - <input type="hidden" name="check_keywords" value="yes" /> - <input type="hidden" name="area" value="default" /> - </form> - </div> </div> -<script type="text/javascript">$('#searchbox').show(0);</script> + + </div> </div> + </nav> + + <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"> + + + <nav class="wy-nav-top" aria-label="top navigation"> + + <i data-toggle="wy-nav-top" class="fa fa-bars"></i> + <a href="#">jass_preprocessing</a> + + </nav> + + + <div class="wy-nav-content"> + + <div class="rst-content"> + + + + + + + - <div class="document"> - <div class="documentwrapper"> - <div class="bodywrapper"> - <div class="body" role="main"> + + + + + + + + + +<div role="navigation" aria-label="breadcrumbs navigation"> + + <ul class="wy-breadcrumbs"> + + <li><a href="#">Docs</a> »</li> + + <li>Welcome to jass_preprocessing’s documentation!</li> + + + <li class="wy-breadcrumbs-aside"> + + + <a href="_sources/index.rst.txt" rel="nofollow"> View page source</a> + + + </li> + + </ul> + + + <hr/> +</div> + <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article"> + <div itemprop="articleBody"> <div class="section" id="welcome-to-jass-preprocessing-s-documentation"> <h1>Welcome to jass_preprocessing’s documentation!<a class="headerlink" href="#welcome-to-jass-preprocessing-s-documentation" title="Permalink to this headline">¶</a></h1> @@ -92,6 +170,8 @@ heterogeneous GWAS summary statistics and performs standardization and quality c <li>Select GWAS SNPs that are in the input reference panel</li> <li>Align coded allele of the GWAS with the reference panel</li> <li>Infer Number of sample by SNPs if not present in input data</li> +<li>Filter SNPs with a small sample size</li> +<li>Normalize the effect size by sample size to have Z-scores</li> <li>Save the output by chromosome as the following example:</li> </ul> <table border="1" class="docutils"> @@ -221,7 +301,45 @@ execute the following lines:</p> </div> <div class="section" id="command-line-usage-example"> <h1>Command line usage example:<a class="headerlink" href="#command-line-usage-example" title="Permalink to this headline">¶</a></h1> -<p>The file : “/JASS_Pre-processing/main_preprocessing.py†gives a complete example on how to use this package.</p> +<p>It is possible to launch the complete preprocessing from the command line:</p> +<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">usage</span><span class="p">:</span> <span class="n">sphinx</span><span class="o">-</span><span class="n">build</span> <span class="p">[</span><span class="o">-</span><span class="n">h</span><span class="p">]</span> <span class="o">--</span><span class="n">percent</span><span class="o">-</span><span class="n">sample</span><span class="o">-</span><span class="n">size</span> <span class="n">PERCENT_SAMPLE_SIZE</span> <span class="o">--</span><span class="n">gwas</span><span class="o">-</span><span class="n">info</span> + <span class="n">GWAS_INFO</span> <span class="o">--</span><span class="n">ref</span><span class="o">-</span><span class="n">folder</span> <span class="n">REF_FOLDER</span> <span class="o">--</span><span class="n">gwas</span><span class="o">-</span><span class="n">folder</span> + <span class="n">GWAS_FOLDER</span> <span class="o">--</span><span class="n">output</span><span class="o">-</span><span class="n">folder</span> <span class="n">OUTPUT_FOLDER</span> + <span class="p">[</span><span class="o">--</span><span class="n">output</span><span class="o">-</span><span class="n">folder</span><span class="o">-</span><span class="mi">1</span><span class="o">-</span><span class="n">file</span> <span class="n">OUTPUT_FOLDER_1_FILE</span><span class="p">]</span> +</pre></div> +</div> +<div class="section" id="Named Arguments"> +<h2>Named Arguments<a class="headerlink" href="#Named Arguments" title="Permalink to this headline">¶</a></h2> +<table class="docutils option-list" frame="void" rules="none"> +<col class="option" /> +<col class="description" /> +<tbody valign="top"> +<tr><td class="option-group" colspan="2"> +<kbd>--percent-sample-size</kbd></td> +</tr> +<tr><td> </td><td>the proportion of the 90th percentile of the sample size used to filter the SNPs</td></tr> +<tr><td class="option-group"> +<kbd>--gwas-info</kbd></td> +<td>Path to the file describing the format of the individual GWASs files</td></tr> +<tr><td class="option-group"> +<kbd>--ref-folder</kbd></td> +<td>reference panel location (used to determine which snp to impute)</td></tr> +<tr><td class="option-group"> +<kbd>--gwas-folder</kbd></td> +<td><blockquote class="first last"> +<div>Path to the folder containing the GWASs summ stat files, must end by ‘/’</div></blockquote> +</td></tr> +<tr><td class="option-group" colspan="2"> +<kbd>--output-folder</kbd></td> +</tr> +<tr><td> </td><td>Location of main ouput folder for preprocessed GWAS files (splitted by chromosome)</td></tr> +<tr><td class="option-group" colspan="2"> +<kbd>--output-folder-1-file</kbd></td> +</tr> +<tr><td> </td><td>optional location to store the preprocessing in one tabular file with one chromosome columns</td></tr> +</tbody> +</table> +</div> </div> <div class="section" id="indices-and-tables"> <h1>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Permalink to this headline">¶</a></h1> @@ -233,26 +351,52 @@ execute the following lines:</p> </div> + </div> + </div> + <footer> + + + <hr/> + + <div role="contentinfo"> + <p> + © Copyright 2018, Hanna Julienne + + </p> + </div> + Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/rtfd/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. + +</footer> + </div> </div> - <div class="clearer"></div> - </div> - <div class="related" role="navigation" aria-label="related navigation"> - <h3>Navigation</h3> - <ul> - <li class="right" style="margin-right: 10px"> - <a href="genindex.html" title="General Index" - >index</a></li> - <li class="right" > - <a href="py-modindex.html" 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See the documentation for # a list of builtin themes. # -html_theme = 'bizstyle' - +#html_theme = 'bizstyle' +html_theme = 'sphinx_rtd_theme' # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the # documentation. diff --git a/doc/source/index.rst b/doc/source/index.rst index ac94d8f10cb7c99ea17b97c2ab2f8d7027b7264e..8a554cc7528d0462e33804feee04116856cd27b0 100644 --- a/doc/source/index.rst +++ b/doc/source/index.rst @@ -95,11 +95,17 @@ Hard coded path (l.20-29 of JASS_Pre-processing/main_preprocessing.py) Command line usage example: ============================ -The file : "/JASS_Pre-processing/main_preprocessing.py" gives a complete example on how to use this package. +It is possible to launch the complete preprocessing (all steps described in section Overview section) from the command line: + +.. argparse:: + :ref: jass_preprocessing.__main__.add_preprocessing_argument Indices and tables ================== + * :ref:`genindex` * :ref:`modindex` +.. automodule:: impute_jass + :members: * :ref:`search` diff --git a/jass_preprocessing/__main__.py b/jass_preprocessing/__main__.py index fe698cc57a2f26eb4f6542f3912dada4df7cf1e8..46943b83500480753a4898623f6e22447fe7fbe1 100644 --- a/jass_preprocessing/__main__.py +++ b/jass_preprocessing/__main__.py @@ -59,6 +59,7 @@ def launch_preprocessing(args): def add_preprocessing_argument(): + parser = argparse.ArgumentParser() parser.add_argument('--percent-sample-size', required=True, help= "the proportion of the 90th percentile of the sample size used to filter the SNPs") parser.add_argument('--gwas-info', required=True, help= "Path to the file describing the format of the individual GWASs files") @@ -70,11 +71,12 @@ def add_preprocessing_argument(): parser.set_defaults(func=launch_preprocessing) + return parser def main(): - parser = argparse.ArgumentParser()#prog='impute_jass') - parser = add_preprocessing_argument(parser) + + parser = add_preprocessing_argument() args = parser.parse_args() args.func(args) diff --git a/jass_preprocessing/__pycache__/compute_score.cpython-35.pyc b/jass_preprocessing/__pycache__/compute_score.cpython-35.pyc index 8061951fbd3e205cc5542110f65e84ea39a857f5..b2269fda3bde8364ba13e9146007998e0f9aa6cb 100644 Binary files a/jass_preprocessing/__pycache__/compute_score.cpython-35.pyc and b/jass_preprocessing/__pycache__/compute_score.cpython-35.pyc differ