diff --git a/README.md b/README.md
index 4f48bce05ee4ff920ab63fe94c7df22e81bad482..91639def3bf70fd17d2e048f2217e5ea3fe377b1 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,7 @@
# Preprocessing package for cleaning and formating data for JASS
This helper package convert heterogeneous GWAS summary statistic format to
-the IMPG input format.
+the JASS input format. Notably, this package realign GWAS summary statistic to a reference panel.
-The package is documented at http://statistical-genetics.pages.pasteur.fr/jass_preprocessing/
\ No newline at end of file
+
+The **full package** documentation is available at http://statistical-genetics.pages.pasteur.fr/jass_preprocessing/
\ No newline at end of file
diff --git a/doc/_build/doctrees/_autosummary/jass_preprocessing.doctree b/doc/_build/doctrees/_autosummary/jass_preprocessing.doctree
index 60825b9ca8e299287ff7e2cf7a82cc7ea7fcd170..a3038fa2363c0c699f791e0db09026635ff6cd53 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 97ce28a38448b98831cdc61717cd5c891c9a44a9..bd7caba23464d99ac6091ad80935f8238a2ba9e0 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 fd9a4b29bf43a3f9fab77f5e84507a48a73297ef..d30175bc9853ee5fd8d403b9b674c3f5ec83c1fe 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 baa64bcc66b50ee5eec7f9081789c4bd60a1c450..c1697f1f00047d0995235d03d9c4dd1378a9b0aa 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 a88da0ec558c867b70dbf4de8cafe571f386e9ec..583cbddff28d0049111dd9f778ddaa4c61d1c7dc 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: 44f0b0a404ac943c811b6f5e7575e3b2
+config: d5740f9f0327be3cbaf9ed1c738013ef
tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/doc/_build/html/_autosummary/jass_preprocessing.html b/doc/_build/html/_autosummary/jass_preprocessing.html
index 887dca5ff19819666f6625195009cced42293a34..1f7f5655e2f24695a2f23e594ee80bce0507e2cf 100644
--- a/doc/_build/html/_autosummary/jass_preprocessing.html
+++ b/doc/_build/html/_autosummary/jass_preprocessing.html
@@ -14,9 +14,7 @@
<script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
<script src="../_static/jquery.js"></script>
<script src="../_static/underscore.js"></script>
- <script src="../_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="../_static/doctools.js"></script>
- <script src="../_static/sphinx_highlight.js"></script>
<script src="../_static/js/theme.js"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
@@ -37,7 +35,17 @@
</form>
</div>
</div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
- <ul>
+ <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../index.html">Welcome to jass_preprocessing’s documentation!</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../index.html#what-is-jass-preprocessing">What is jass preprocessing ?</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../index.html#overview">Overview</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../index.html#installation">Installation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../index.html#input">Input</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../index.html#command-line-usage-example">Command line usage example:</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../index.html#indices-and-tables">Indices and tables</a></li>
+</ul>
+<ul>
<li class="toctree-l1"><a class="reference internal" href="jass_preprocessing.map_gwas.html">jass_preprocessing.map_gwas</a></li>
<li class="toctree-l1"><a class="reference internal" href="jass_preprocessing.dna_utils.html">jass_preprocessing.dna_utils</a></li>
<li class="toctree-l1"><a class="reference internal" href="jass_preprocessing.map_reference.html">jass_preprocessing.map_reference</a></li>
@@ -58,8 +66,8 @@
<div class="rst-content">
<div role="navigation" aria-label="Page navigation">
<ul class="wy-breadcrumbs">
- <li><a href="../index.html" class="icon icon-home"></a></li>
- <li class="breadcrumb-item active">jass_preprocessing package</li>
+ <li><a href="../index.html" class="icon icon-home"></a> »</li>
+ <li>jass_preprocessing package</li>
<li class="wy-breadcrumbs-aside">
<a href="../_sources/_autosummary/jass_preprocessing.rst.txt" rel="nofollow"> View page source</a>
</li>
@@ -70,12 +78,12 @@
<div itemprop="articleBody">
<section id="jass-preprocessing-package">
-<h1>jass_preprocessing package<a class="headerlink" href="#jass-preprocessing-package" title="Permalink to this heading">ïƒ</a></h1>
+<h1>jass_preprocessing package<a class="headerlink" href="#jass-preprocessing-package" title="Permalink to this headline">ïƒ</a></h1>
<section id="submodules">
-<h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this heading">ïƒ</a></h2>
+<h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this headline">ïƒ</a></h2>
</section>
<section id="module-jass_preprocessing.compute_score">
-<span id="jass-preprocessing-compute-score-module"></span><h2>jass_preprocessing.compute_score module<a class="headerlink" href="#module-jass_preprocessing.compute_score" title="Permalink to this heading">ïƒ</a></h2>
+<span id="jass-preprocessing-compute-score-module"></span><h2>jass_preprocessing.compute_score module<a class="headerlink" href="#module-jass_preprocessing.compute_score" title="Permalink to this headline">ïƒ</a></h2>
<dl class="py function">
<dt class="sig sig-object py" id="jass_preprocessing.compute_score.compute_sample_size">
<span class="sig-prename descclassname"><span class="pre">jass_preprocessing.compute_score.</span></span><span class="sig-name descname"><span class="pre">compute_sample_size</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">mgwas</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">diagnostic_folder</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">trait</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">perSS</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.7</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/jass_preprocessing/compute_score.html#compute_sample_size"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#jass_preprocessing.compute_score.compute_sample_size" title="Permalink to this definition">ïƒ</a></dt>
@@ -90,7 +98,7 @@ add the corresponding column to the mgwas dataframe</p>
</section>
<section id="module-jass_preprocessing.dna_utils">
-<span id="jass-preprocessing-dna-utils-module"></span><h2>jass_preprocessing.dna_utils module<a class="headerlink" href="#module-jass_preprocessing.dna_utils" title="Permalink to this heading">ïƒ</a></h2>
+<span id="jass-preprocessing-dna-utils-module"></span><h2>jass_preprocessing.dna_utils module<a class="headerlink" href="#module-jass_preprocessing.dna_utils" title="Permalink to this headline">ïƒ</a></h2>
<p>Few fonction to to compute DNA complement</p>
<dl class="py function">
<dt class="sig sig-object py" id="jass_preprocessing.dna_utils.dna_complement">
@@ -104,7 +112,7 @@ add the corresponding column to the mgwas dataframe</p>
</section>
<section id="module-jass_preprocessing.map_gwas">
-<span id="jass-preprocessing-map-gwas-module"></span><h2>jass_preprocessing.map_gwas module<a class="headerlink" href="#module-jass_preprocessing.map_gwas" title="Permalink to this heading">ïƒ</a></h2>
+<span id="jass-preprocessing-map-gwas-module"></span><h2>jass_preprocessing.map_gwas module<a class="headerlink" href="#module-jass_preprocessing.map_gwas" title="Permalink to this headline">ïƒ</a></h2>
<p>Map GWAS</p>
<p>A set of functions to find GWAS files in subfolder and
to map columns</p>
@@ -192,7 +200,7 @@ column_map and rename columns according to column_map.index</p>
</section>
<section id="module-jass_preprocessing.map_reference">
-<span id="jass-preprocessing-map-reference-module"></span><h2>jass_preprocessing.map_reference module<a class="headerlink" href="#module-jass_preprocessing.map_reference" title="Permalink to this heading">ïƒ</a></h2>
+<span id="jass-preprocessing-map-reference-module"></span><h2>jass_preprocessing.map_reference module<a class="headerlink" href="#module-jass_preprocessing.map_reference" title="Permalink to this headline">ïƒ</a></h2>
<p>Module of function</p>
<dl class="py function">
<dt class="sig sig-object py" id="jass_preprocessing.map_reference.compute_is_aligned">
@@ -283,7 +291,7 @@ Make sure that the same SNPs are in the reference panel and the gwas</p>
</section>
<section id="module-jass_preprocessing.save_output">
-<span id="jass-preprocessing-save-output-module"></span><h2>jass_preprocessing.save_output module<a class="headerlink" href="#module-jass_preprocessing.save_output" title="Permalink to this heading">ïƒ</a></h2>
+<span id="jass-preprocessing-save-output-module"></span><h2>jass_preprocessing.save_output module<a class="headerlink" href="#module-jass_preprocessing.save_output" title="Permalink to this headline">ïƒ</a></h2>
<dl class="py function">
<dt class="sig sig-object py" id="jass_preprocessing.save_output.save_output">
<span class="sig-prename descclassname"><span class="pre">jass_preprocessing.save_output.</span></span><span class="sig-name descname"><span class="pre">save_output</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">mgwas</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ImpG_output_Folder</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">my_study</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/jass_preprocessing/save_output.html#save_output"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#jass_preprocessing.save_output.save_output" title="Permalink to this definition">ïƒ</a></dt>
@@ -298,8 +306,8 @@ Make sure that the same SNPs are in the reference panel and the gwas</p>
</section>
<section id="module-jass_preprocessing">
-<span id="module-contents"></span><h2>Module contents<a class="headerlink" href="#module-jass_preprocessing" title="Permalink to this heading">ïƒ</a></h2>
-<table class="autosummary longtable docutils align-default">
+<span id="module-contents"></span><h2>Module contents<a class="headerlink" href="#module-jass_preprocessing" title="Permalink to this headline">ïƒ</a></h2>
+<table class="longtable docutils align-default">
<colgroup>
<col style="width: 10%" />
<col style="width: 90%" />
diff --git a/doc/_build/html/_autosummary/modules.html b/doc/_build/html/_autosummary/modules.html
index 10c9aaae92ad670adefd2f655f25d6031389b718..07bd8c7d1398eab6a3815cea34b67de0cec6eda3 100644
--- a/doc/_build/html/_autosummary/modules.html
+++ b/doc/_build/html/_autosummary/modules.html
@@ -14,9 +14,7 @@
<script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
<script src="../_static/jquery.js"></script>
<script src="../_static/underscore.js"></script>
- <script src="../_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="../_static/doctools.js"></script>
- <script src="../_static/sphinx_highlight.js"></script>
<script src="../_static/js/theme.js"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
@@ -37,7 +35,17 @@
</form>
</div>
</div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
- <ul>
+ <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../index.html">Welcome to jass_preprocessing’s documentation!</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../index.html#what-is-jass-preprocessing">What is jass preprocessing ?</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../index.html#overview">Overview</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../index.html#installation">Installation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../index.html#input">Input</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../index.html#command-line-usage-example">Command line usage example:</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../index.html#indices-and-tables">Indices and tables</a></li>
+</ul>
+<ul>
<li class="toctree-l1"><a class="reference internal" href="jass_preprocessing.map_gwas.html">jass_preprocessing.map_gwas</a></li>
<li class="toctree-l1"><a class="reference internal" href="jass_preprocessing.dna_utils.html">jass_preprocessing.dna_utils</a></li>
<li class="toctree-l1"><a class="reference internal" href="jass_preprocessing.map_reference.html">jass_preprocessing.map_reference</a></li>
@@ -58,8 +66,8 @@
<div class="rst-content">
<div role="navigation" aria-label="Page navigation">
<ul class="wy-breadcrumbs">
- <li><a href="../index.html" class="icon icon-home"></a></li>
- <li class="breadcrumb-item active">jass_preprocessing</li>
+ <li><a href="../index.html" class="icon icon-home"></a> »</li>
+ <li>jass_preprocessing</li>
<li class="wy-breadcrumbs-aside">
<a href="../_sources/_autosummary/modules.rst.txt" rel="nofollow"> View page source</a>
</li>
@@ -70,42 +78,16 @@
<div itemprop="articleBody">
<section id="jass-preprocessing">
-<h1>jass_preprocessing<a class="headerlink" href="#jass-preprocessing" title="Permalink to this heading">ïƒ</a></h1>
+<h1>jass_preprocessing<a class="headerlink" href="#jass-preprocessing" title="Permalink to this headline">ïƒ</a></h1>
<div class="toctree-wrapper compound">
<ul>
<li class="toctree-l1"><a class="reference internal" href="jass_preprocessing.html">jass_preprocessing package</a><ul>
<li class="toctree-l2"><a class="reference internal" href="jass_preprocessing.html#submodules">Submodules</a></li>
-<li class="toctree-l2"><a class="reference internal" href="jass_preprocessing.html#module-jass_preprocessing.compute_score">jass_preprocessing.compute_score module</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="jass_preprocessing.html#jass_preprocessing.compute_score.compute_sample_size"><code class="docutils literal notranslate"><span class="pre">compute_sample_size()</span></code></a></li>
-<li class="toctree-l3"><a class="reference internal" href="jass_preprocessing.html#jass_preprocessing.compute_score.compute_z_score"><code class="docutils literal notranslate"><span class="pre">compute_z_score()</span></code></a></li>
-</ul>
-</li>
-<li class="toctree-l2"><a class="reference internal" href="jass_preprocessing.html#module-jass_preprocessing.dna_utils">jass_preprocessing.dna_utils module</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="jass_preprocessing.html#jass_preprocessing.dna_utils.dna_complement"><code class="docutils literal notranslate"><span class="pre">dna_complement()</span></code></a></li>
-<li class="toctree-l3"><a class="reference internal" href="jass_preprocessing.html#jass_preprocessing.dna_utils.dna_complement_base"><code class="docutils literal notranslate"><span class="pre">dna_complement_base()</span></code></a></li>
-</ul>
-</li>
-<li class="toctree-l2"><a class="reference internal" href="jass_preprocessing.html#module-jass_preprocessing.map_gwas">jass_preprocessing.map_gwas module</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="jass_preprocessing.html#jass_preprocessing.map_gwas.convert_missing_values"><code class="docutils literal notranslate"><span class="pre">convert_missing_values()</span></code></a></li>
-<li class="toctree-l3"><a class="reference internal" href="jass_preprocessing.html#jass_preprocessing.map_gwas.gwas_internal_link"><code class="docutils literal notranslate"><span class="pre">gwas_internal_link()</span></code></a></li>
-<li class="toctree-l3"><a class="reference internal" href="jass_preprocessing.html#jass_preprocessing.map_gwas.map_columns_position"><code class="docutils literal notranslate"><span class="pre">map_columns_position()</span></code></a></li>
-<li class="toctree-l3"><a class="reference internal" href="jass_preprocessing.html#jass_preprocessing.map_gwas.read_gwas"><code class="docutils literal notranslate"><span class="pre">read_gwas()</span></code></a></li>
-<li class="toctree-l3"><a class="reference internal" href="jass_preprocessing.html#jass_preprocessing.map_gwas.walkfs"><code class="docutils literal notranslate"><span class="pre">walkfs()</span></code></a></li>
-</ul>
-</li>
-<li class="toctree-l2"><a class="reference internal" href="jass_preprocessing.html#module-jass_preprocessing.map_reference">jass_preprocessing.map_reference module</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="jass_preprocessing.html#jass_preprocessing.map_reference.compute_is_aligned"><code class="docutils literal notranslate"><span class="pre">compute_is_aligned()</span></code></a></li>
-<li class="toctree-l3"><a class="reference internal" href="jass_preprocessing.html#jass_preprocessing.map_reference.compute_is_flipped"><code class="docutils literal notranslate"><span class="pre">compute_is_flipped()</span></code></a></li>
-<li class="toctree-l3"><a class="reference internal" href="jass_preprocessing.html#jass_preprocessing.map_reference.compute_snp_alignement"><code class="docutils literal notranslate"><span class="pre">compute_snp_alignement()</span></code></a></li>
-<li class="toctree-l3"><a class="reference internal" href="jass_preprocessing.html#jass_preprocessing.map_reference.map_on_ref_panel"><code class="docutils literal notranslate"><span class="pre">map_on_ref_panel()</span></code></a></li>
-<li class="toctree-l3"><a class="reference internal" href="jass_preprocessing.html#jass_preprocessing.map_reference.read_reference"><code class="docutils literal notranslate"><span class="pre">read_reference()</span></code></a></li>
-</ul>
-</li>
-<li class="toctree-l2"><a class="reference internal" href="jass_preprocessing.html#module-jass_preprocessing.save_output">jass_preprocessing.save_output module</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="jass_preprocessing.html#jass_preprocessing.save_output.save_output"><code class="docutils literal notranslate"><span class="pre">save_output()</span></code></a></li>
-<li class="toctree-l3"><a class="reference internal" href="jass_preprocessing.html#jass_preprocessing.save_output.save_output_by_chromosome"><code class="docutils literal notranslate"><span class="pre">save_output_by_chromosome()</span></code></a></li>
-</ul>
-</li>
+<li class="toctree-l2"><a class="reference internal" href="jass_preprocessing.html#module-jass_preprocessing.compute_score">jass_preprocessing.compute_score module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="jass_preprocessing.html#module-jass_preprocessing.dna_utils">jass_preprocessing.dna_utils module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="jass_preprocessing.html#module-jass_preprocessing.map_gwas">jass_preprocessing.map_gwas module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="jass_preprocessing.html#module-jass_preprocessing.map_reference">jass_preprocessing.map_reference module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="jass_preprocessing.html#module-jass_preprocessing.save_output">jass_preprocessing.save_output module</a></li>
<li class="toctree-l2"><a class="reference internal" href="jass_preprocessing.html#module-jass_preprocessing">Module contents</a><ul>
<li class="toctree-l3"><a class="reference internal" href="_autosummary/jass_preprocessing.map_gwas.html">jass_preprocessing.map_gwas</a></li>
<li class="toctree-l3"><a class="reference internal" href="_autosummary/jass_preprocessing.dna_utils.html">jass_preprocessing.dna_utils</a></li>
diff --git a/doc/_build/html/_modules/index.html b/doc/_build/html/_modules/index.html
index d3bad4d577f9ea89a338f06581abc6d395d6bbae..d15b04eb25a67771bcd2118f0cc0192c7c7d755f 100644
--- a/doc/_build/html/_modules/index.html
+++ b/doc/_build/html/_modules/index.html
@@ -13,9 +13,7 @@
<script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
<script src="../_static/jquery.js"></script>
<script src="../_static/underscore.js"></script>
- <script src="../_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="../_static/doctools.js"></script>
- <script src="../_static/sphinx_highlight.js"></script>
<script src="../_static/js/theme.js"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
@@ -67,8 +65,8 @@
<div class="rst-content">
<div role="navigation" aria-label="Page navigation">
<ul class="wy-breadcrumbs">
- <li><a href="../index.html" class="icon icon-home"></a></li>
- <li class="breadcrumb-item active">Overview: module code</li>
+ <li><a href="../index.html" class="icon icon-home"></a> »</li>
+ <li>Overview: module code</li>
<li class="wy-breadcrumbs-aside">
</li>
</ul>
diff --git a/doc/_build/html/_modules/jass_preprocessing/compute_score.html b/doc/_build/html/_modules/jass_preprocessing/compute_score.html
index 75dd0d9212397f1f75714a27c7075b1612a3e31d..80696cb5fe1e51af72a43ae47ab6b10e53f0ef19 100644
--- a/doc/_build/html/_modules/jass_preprocessing/compute_score.html
+++ b/doc/_build/html/_modules/jass_preprocessing/compute_score.html
@@ -13,9 +13,7 @@
<script data-url_root="../../" id="documentation_options" src="../../_static/documentation_options.js"></script>
<script src="../../_static/jquery.js"></script>
<script src="../../_static/underscore.js"></script>
- <script src="../../_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="../../_static/doctools.js"></script>
- <script src="../../_static/sphinx_highlight.js"></script>
<script src="../../_static/js/theme.js"></script>
<link rel="index" title="Index" href="../../genindex.html" />
<link rel="search" title="Search" href="../../search.html" />
@@ -36,7 +34,17 @@
</form>
</div>
</div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
- <ul>
+ <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../../index.html">Welcome to jass_preprocessing’s documentation!</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../index.html#what-is-jass-preprocessing">What is jass preprocessing ?</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../index.html#overview">Overview</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../index.html#installation">Installation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../index.html#input">Input</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../index.html#command-line-usage-example">Command line usage example:</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../index.html#indices-and-tables">Indices and tables</a></li>
+</ul>
+<ul>
<li class="toctree-l1"><a class="reference internal" href="../../_autosummary/jass_preprocessing.map_gwas.html">jass_preprocessing.map_gwas</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../_autosummary/jass_preprocessing.dna_utils.html">jass_preprocessing.dna_utils</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../_autosummary/jass_preprocessing.map_reference.html">jass_preprocessing.map_reference</a></li>
@@ -57,9 +65,9 @@
<div class="rst-content">
<div role="navigation" aria-label="Page navigation">
<ul class="wy-breadcrumbs">
- <li><a href="../../index.html" class="icon icon-home"></a></li>
- <li class="breadcrumb-item"><a href="../index.html">Module code</a></li>
- <li class="breadcrumb-item active">jass_preprocessing.compute_score</li>
+ <li><a href="../../index.html" class="icon icon-home"></a> »</li>
+ <li><a href="../index.html">Module code</a> »</li>
+ <li>jass_preprocessing.compute_score</li>
<li class="wy-breadcrumbs-aside">
</li>
</ul>
@@ -122,7 +130,7 @@
<span class="n">warnings</span><span class="o">.</span><span class="n">warn</span><span class="p">(</span><span class="s2">"Some snp had an infinite sample size"</span><span class="p">)</span>
<span class="n">myW_thres</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">percentile</span><span class="p">(</span><span class="n">myN</span><span class="o">.</span><span class="n">dropna</span><span class="p">(),</span> <span class="mi">90</span><span class="p">)</span>
- <span class="n">ss_thres</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">perSS</span><span class="p">)</span> <span class="o">*</span> <span class="n">myW_thres</span>
+ <span class="n">ss_thres</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">double</span><span class="p">(</span><span class="n">perSS</span><span class="p">)</span> <span class="o">*</span> <span class="n">myW_thres</span>
<span class="n">mgwas</span><span class="p">[</span><span class="s2">"computed_N"</span><span class="p">]</span> <span class="o">=</span> <span class="n">myN</span>
<span class="n">plt</span><span class="o">.</span><span class="n">clf</span><span class="p">()</span>
<span class="n">p1</span> <span class="o">=</span> <span class="n">sns</span><span class="o">.</span><span class="n">distplot</span><span class="p">(</span><span class="n">mgwas</span><span class="o">.</span><span class="n">computed_N</span><span class="p">[</span><span class="o">~</span><span class="n">mgwas</span><span class="o">.</span><span class="n">computed_N</span><span class="o">.</span><span class="n">isna</span><span class="p">()])</span>
diff --git a/doc/_build/html/_modules/jass_preprocessing/map_gwas.html b/doc/_build/html/_modules/jass_preprocessing/map_gwas.html
index 79620a57f06c2e054af970d900e1b5826f0c6281..d190e89ddfec8f95bf0f72cea5a729a1ddeb02ff 100644
--- a/doc/_build/html/_modules/jass_preprocessing/map_gwas.html
+++ b/doc/_build/html/_modules/jass_preprocessing/map_gwas.html
@@ -13,9 +13,7 @@
<script data-url_root="../../" id="documentation_options" src="../../_static/documentation_options.js"></script>
<script src="../../_static/jquery.js"></script>
<script src="../../_static/underscore.js"></script>
- <script src="../../_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="../../_static/doctools.js"></script>
- <script src="../../_static/sphinx_highlight.js"></script>
<script src="../../_static/js/theme.js"></script>
<link rel="index" title="Index" href="../../genindex.html" />
<link rel="search" title="Search" href="../../search.html" />
@@ -36,7 +34,17 @@
</form>
</div>
</div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
- <ul>
+ <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../../index.html">Welcome to jass_preprocessing’s documentation!</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../index.html#what-is-jass-preprocessing">What is jass preprocessing ?</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../index.html#overview">Overview</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../index.html#installation">Installation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../index.html#input">Input</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../index.html#command-line-usage-example">Command line usage example:</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../index.html#indices-and-tables">Indices and tables</a></li>
+</ul>
+<ul>
<li class="toctree-l1"><a class="reference internal" href="../../_autosummary/jass_preprocessing.map_gwas.html">jass_preprocessing.map_gwas</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../_autosummary/jass_preprocessing.dna_utils.html">jass_preprocessing.dna_utils</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../_autosummary/jass_preprocessing.map_reference.html">jass_preprocessing.map_reference</a></li>
@@ -57,9 +65,9 @@
<div class="rst-content">
<div role="navigation" aria-label="Page navigation">
<ul class="wy-breadcrumbs">
- <li><a href="../../index.html" class="icon icon-home"></a></li>
- <li class="breadcrumb-item"><a href="../index.html">Module code</a></li>
- <li class="breadcrumb-item active">jass_preprocessing.map_gwas</li>
+ <li><a href="../../index.html" class="icon icon-home"></a> »</li>
+ <li><a href="../index.html">Module code</a> »</li>
+ <li>jass_preprocessing.map_gwas</li>
<li class="wy-breadcrumbs-aside">
</li>
</ul>
@@ -217,12 +225,13 @@
<span class="n">fullGWAS</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span><span class="n">gwas_internal_link</span><span class="p">,</span> <span class="n">delim_whitespace</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
<span class="n">usecols</span> <span class="o">=</span> <span class="n">column_map</span><span class="o">.</span><span class="n">values</span><span class="p">,</span>
<span class="n">compression</span><span class="o">=</span><span class="n">compression</span><span class="p">,</span>
- <span class="c1">#column_dict['label_position'].keys(),</span>
- <span class="n">names</span><span class="o">=</span> <span class="n">column_map</span><span class="o">.</span><span class="n">index</span><span class="p">,</span>
- <span class="n">header</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">na_values</span><span class="o">=</span> <span class="p">[</span><span class="s1">''</span><span class="p">,</span> <span class="s1">'#N/A'</span><span class="p">,</span> <span class="s1">'#N/A'</span><span class="p">,</span> <span class="s1">'N/A'</span><span class="p">,</span><span class="s1">'#NA'</span><span class="p">,</span> <span class="s1">'-1.#IND'</span><span class="p">,</span> <span class="s1">'-1.#QNAN'</span><span class="p">,</span>
- <span class="s1">'-NaN'</span><span class="p">,</span> <span class="s1">'-nan'</span><span class="p">,</span> <span class="s1">'1.#IND'</span><span class="p">,</span> <span class="s1">'1.#QNAN'</span><span class="p">,</span> <span class="s1">'N/A'</span><span class="p">,</span>
- <span class="s1">'NA'</span><span class="p">,</span> <span class="s1">'NULL'</span><span class="p">,</span> <span class="s1">'NaN'</span><span class="p">,</span>
- <span class="s1">'nan'</span><span class="p">,</span> <span class="s1">'na'</span><span class="p">,</span> <span class="s1">'.'</span><span class="p">,</span> <span class="s1">'-'</span><span class="p">],</span> <span class="n">dtype</span><span class="o">=</span><span class="p">{</span><span class="s2">"snpid"</span><span class="p">:</span><span class="nb">str</span><span class="p">,</span> <span class="s2">"a1"</span><span class="p">:</span><span class="nb">str</span><span class="p">,</span><span class="s2">"a2"</span><span class="p">:</span><span class="nb">str</span><span class="p">,</span><span class="s2">"freq"</span><span class="p">:</span><span class="nb">float</span><span class="p">,</span> <span class="s2">"z"</span><span class="p">:</span><span class="nb">float</span><span class="p">,</span><span class="s2">"se"</span><span class="p">:</span><span class="nb">float</span><span class="p">,</span> <span class="s2">"pval"</span><span class="p">:</span><span class="nb">float</span><span class="p">})</span>
+ <span class="c1">#column_dict['label_position'].keys(),</span>
+ <span class="n">names</span><span class="o">=</span> <span class="n">column_map</span><span class="o">.</span><span class="n">index</span><span class="p">,</span>
+ <span class="n">header</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">na_values</span><span class="o">=</span> <span class="p">[</span><span class="s1">''</span><span class="p">,</span> <span class="s1">'#N/A'</span><span class="p">,</span> <span class="s1">'#N/A'</span><span class="p">,</span> <span class="s1">'N/A'</span><span class="p">,</span><span class="s1">'#NA'</span><span class="p">,</span> <span class="s1">'-1.#IND'</span><span class="p">,</span> <span class="s1">'-1.#QNAN'</span><span class="p">,</span>
+ <span class="s1">'-NaN'</span><span class="p">,</span> <span class="s1">'-nan'</span><span class="p">,</span> <span class="s1">'1.#IND'</span><span class="p">,</span> <span class="s1">'1.#QNAN'</span><span class="p">,</span> <span class="s1">'N/A'</span><span class="p">,</span>
+ <span class="s1">'NA'</span><span class="p">,</span> <span class="s1">'NULL'</span><span class="p">,</span> <span class="s1">'NaN'</span><span class="p">,</span>
+ <span class="s1">'nan'</span><span class="p">,</span> <span class="s1">'na'</span><span class="p">,</span> <span class="s1">'.'</span><span class="p">,</span> <span class="s1">'-'</span><span class="p">],</span>
+ <span class="n">dtype</span><span class="o">=</span><span class="p">{</span><span class="s2">"snpid"</span><span class="p">:</span><span class="nb">str</span><span class="p">,</span> <span class="s2">"a1"</span><span class="p">:</span><span class="nb">str</span><span class="p">,</span><span class="s2">"a2"</span><span class="p">:</span><span class="nb">str</span><span class="p">,</span><span class="s2">"freq"</span><span class="p">:</span><span class="n">np</span><span class="o">.</span><span class="n">double</span><span class="p">,</span> <span class="s2">"z"</span><span class="p">:</span><span class="n">np</span><span class="o">.</span><span class="n">double</span><span class="p">,</span><span class="s2">"se"</span><span class="p">:</span><span class="n">np</span><span class="o">.</span><span class="n">double</span><span class="p">,</span> <span class="s2">"pval"</span><span class="p">:</span><span class="n">np</span><span class="o">.</span><span class="n">double</span><span class="p">})</span>
<span class="nb">print</span><span class="p">(</span><span class="n">fullGWAS</span><span class="o">.</span><span class="n">head</span><span class="p">())</span>
<span class="c1">#Ensure that allele are written in upper cases:</span>
diff --git a/doc/_build/html/_modules/jass_preprocessing/map_reference.html b/doc/_build/html/_modules/jass_preprocessing/map_reference.html
index 7abe24dfa0ded9729542a99b437e68786af034f3..f4ea68f09e8bfed5c8bcf91f7a8506d115d2e260 100644
--- a/doc/_build/html/_modules/jass_preprocessing/map_reference.html
+++ b/doc/_build/html/_modules/jass_preprocessing/map_reference.html
@@ -13,9 +13,7 @@
<script data-url_root="../../" id="documentation_options" src="../../_static/documentation_options.js"></script>
<script src="../../_static/jquery.js"></script>
<script src="../../_static/underscore.js"></script>
- <script src="../../_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="../../_static/doctools.js"></script>
- <script src="../../_static/sphinx_highlight.js"></script>
<script src="../../_static/js/theme.js"></script>
<link rel="index" title="Index" href="../../genindex.html" />
<link rel="search" title="Search" href="../../search.html" />
@@ -36,7 +34,17 @@
</form>
</div>
</div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
- <ul>
+ <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../../index.html">Welcome to jass_preprocessing’s documentation!</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../index.html#what-is-jass-preprocessing">What is jass preprocessing ?</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../index.html#overview">Overview</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../index.html#installation">Installation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../index.html#input">Input</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../index.html#command-line-usage-example">Command line usage example:</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../index.html#indices-and-tables">Indices and tables</a></li>
+</ul>
+<ul>
<li class="toctree-l1"><a class="reference internal" href="../../_autosummary/jass_preprocessing.map_gwas.html">jass_preprocessing.map_gwas</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../_autosummary/jass_preprocessing.dna_utils.html">jass_preprocessing.dna_utils</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../_autosummary/jass_preprocessing.map_reference.html">jass_preprocessing.map_reference</a></li>
@@ -57,9 +65,9 @@
<div class="rst-content">
<div role="navigation" aria-label="Page navigation">
<ul class="wy-breadcrumbs">
- <li><a href="../../index.html" class="icon icon-home"></a></li>
- <li class="breadcrumb-item"><a href="../index.html">Module code</a></li>
- <li class="breadcrumb-item active">jass_preprocessing.map_reference</li>
+ <li><a href="../../index.html" class="icon icon-home"></a> »</li>
+ <li><a href="../index.html">Module code</a> »</li>
+ <li>jass_preprocessing.map_reference</li>
<li class="wy-breadcrumbs-aside">
</li>
</ul>
@@ -92,14 +100,17 @@
<span class="sd"> """</span>
<span class="n">ref</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span><span class="n">gwas_reference_panel</span><span class="p">,</span> <span class="n">header</span><span class="o">=</span><span class="kc">None</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">names</span> <span class="o">=</span><span class="p">[</span> <span class="s1">'chr'</span><span class="p">,</span> <span class="s2">"snp_id"</span><span class="p">,</span> <span class="s2">"MAF"</span><span class="p">,</span><span class="s2">"pos"</span><span class="p">,</span> <span class="s2">"ref"</span><span class="p">,</span> <span class="s2">"alt"</span><span class="p">],</span>
- <span class="n">dtype</span> <span class="o">=</span> <span class="p">{</span><span class="s2">"chr"</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="s2">"snp_id"</span><span class="p">:</span><span class="nb">str</span><span class="p">,</span> <span class="s2">"MAF"</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">float</span><span class="p">,</span> <span class="s2">"pos"</span><span class="p">:</span><span class="n">np</span><span class="o">.</span><span class="n">int</span><span class="p">,</span> <span class="s2">"ref"</span><span class="p">:</span><span class="nb">str</span><span class="p">,</span> <span class="s2">"alt"</span><span class="p">:</span><span class="nb">str</span><span class="p">},</span>
+ <span class="n">dtype</span> <span class="o">=</span> <span class="p">{</span><span class="s2">"chr"</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="s2">"snp_id"</span><span class="p">:</span><span class="nb">str</span><span class="p">,</span> <span class="s2">"MAF"</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">double</span><span class="p">,</span> <span class="s2">"pos"</span><span class="p">:</span><span class="n">np</span><span class="o">.</span><span class="n">double</span><span class="p">,</span> <span class="s2">"ref"</span><span class="p">:</span><span class="nb">str</span><span class="p">,</span> <span class="s2">"alt"</span><span class="p">:</span><span class="nb">str</span><span class="p">},</span>
<span class="n">index_col</span><span class="o">=</span><span class="s2">"snp_id"</span><span class="p">)</span>
+ <span class="n">ref</span> <span class="o">=</span> <span class="n">ref</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="o">~</span><span class="n">ref</span><span class="o">.</span><span class="n">pos</span><span class="o">.</span><span class="n">isnull</span><span class="p">()]</span>
+ <span class="n">ref</span><span class="o">.</span><span class="n">pos</span> <span class="o">=</span> <span class="n">ref</span><span class="o">.</span><span class="n">pos</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="s1">'int'</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">sorted_alleles</span><span class="p">(</span><span class="n">x</span><span class="p">):</span>
<span class="k">return</span> <span class="s2">""</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="nb">sorted</span><span class="p">(</span><span class="n">x</span><span class="p">))</span>
<span class="c1">#Filter Strand ambiguous if biallelic</span>
<span class="n">ref</span> <span class="o">=</span> <span class="n">ref</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="o">~</span><span class="p">(</span><span class="n">ref</span><span class="o">.</span><span class="n">ref</span><span class="o">+</span><span class="n">ref</span><span class="o">.</span><span class="n">alt</span><span class="p">)</span><span class="o">.</span><span class="n">isin</span><span class="p">([</span><span class="s2">"AT"</span><span class="p">,</span> <span class="s2">"TA"</span><span class="p">,</span> <span class="s1">'CG'</span><span class="p">,</span><span class="s1">'GC'</span><span class="p">])]</span>
-
+ <span class="nb">print</span><span class="p">(</span><span class="s2">"REFERENCE"</span><span class="p">)</span>
+ <span class="nb">print</span><span class="p">(</span><span class="n">ref</span><span class="o">.</span><span class="n">head</span><span class="p">())</span>
<span class="n">ref</span><span class="p">[</span><span class="s2">"positional_index"</span><span class="p">]</span> <span class="o">=</span> <span class="n">ref</span><span class="o">.</span><span class="n">chr</span><span class="o">.</span><span class="n">apply</span><span class="p">(</span><span class="nb">str</span><span class="p">)</span><span class="o">+</span><span class="n">ref</span><span class="o">.</span><span class="n">pos</span><span class="o">.</span><span class="n">apply</span><span class="p">(</span><span class="nb">str</span><span class="p">)</span><span class="o">+</span><span class="p">(</span><span class="n">ref</span><span class="o">.</span><span class="n">ref</span><span class="o">+</span><span class="n">ref</span><span class="o">.</span><span class="n">alt</span><span class="p">)</span><span class="o">.</span><span class="n">apply</span><span class="p">(</span><span class="n">sorted_alleles</span><span class="p">)</span>
<span class="k">if</span> <span class="n">mask_MHC</span><span class="p">:</span>
diff --git a/doc/_build/html/_modules/jass_preprocessing/save_output.html b/doc/_build/html/_modules/jass_preprocessing/save_output.html
index 93894fbb3c27d2277c958b7123cb7672d84e8807..cbb5d6d35bb286d343119d11db35cb56102d73af 100644
--- a/doc/_build/html/_modules/jass_preprocessing/save_output.html
+++ b/doc/_build/html/_modules/jass_preprocessing/save_output.html
@@ -13,9 +13,7 @@
<script data-url_root="../../" id="documentation_options" src="../../_static/documentation_options.js"></script>
<script src="../../_static/jquery.js"></script>
<script src="../../_static/underscore.js"></script>
- <script src="../../_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="../../_static/doctools.js"></script>
- <script src="../../_static/sphinx_highlight.js"></script>
<script src="../../_static/js/theme.js"></script>
<link rel="index" title="Index" href="../../genindex.html" />
<link rel="search" title="Search" href="../../search.html" />
@@ -36,7 +34,17 @@
</form>
</div>
</div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
- <ul>
+ <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../../index.html">Welcome to jass_preprocessing’s documentation!</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../index.html#what-is-jass-preprocessing">What is jass preprocessing ?</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../index.html#overview">Overview</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../index.html#installation">Installation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../index.html#input">Input</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../index.html#command-line-usage-example">Command line usage example:</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../index.html#indices-and-tables">Indices and tables</a></li>
+</ul>
+<ul>
<li class="toctree-l1"><a class="reference internal" href="../../_autosummary/jass_preprocessing.map_gwas.html">jass_preprocessing.map_gwas</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../_autosummary/jass_preprocessing.dna_utils.html">jass_preprocessing.dna_utils</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../_autosummary/jass_preprocessing.map_reference.html">jass_preprocessing.map_reference</a></li>
@@ -57,9 +65,9 @@
<div class="rst-content">
<div role="navigation" aria-label="Page navigation">
<ul class="wy-breadcrumbs">
- <li><a href="../../index.html" class="icon icon-home"></a></li>
- <li class="breadcrumb-item"><a href="../index.html">Module code</a></li>
- <li class="breadcrumb-item active">jass_preprocessing.save_output</li>
+ <li><a href="../../index.html" class="icon icon-home"></a> »</li>
+ <li><a href="../index.html">Module code</a> »</li>
+ <li>jass_preprocessing.save_output</li>
<li class="wy-breadcrumbs-aside">
</li>
</ul>
diff --git a/doc/_build/html/_sources/index.rst.txt b/doc/_build/html/_sources/index.rst.txt
index 1998c87266db096afb055e1ca8b7f5200aa3aabb..297fd70bed6913d9af16cbaacb6d6067651f7a6b 100644
--- a/doc/_build/html/_sources/index.rst.txt
+++ b/doc/_build/html/_sources/index.rst.txt
@@ -14,7 +14,7 @@ Welcome to jass_preprocessing's documentation!
What is jass preprocessing ?
============================
-Jass preprocessing is a tool that takes in input
+Jass preprocessing is a command line tool that takes in input
heterogeneous GWAS summary statistics and performs standardization and quality checks to output standardized summary statistic files that can be used as input in the JASS python package and the RAISS imputation package.
@@ -22,13 +22,13 @@ Overview
========
The QC and preprocessing step goes as follow:
-* map column from of a specific GWAS to standardize names
-* 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:
+#. Map column from of a heterogeneous GWAS entry file to standardize names
+#. Select GWAS SNPs that are in the input reference panel
+#. Align coded allele of the GWASs data with the reference panel
+#. Infer the sample size by SNPs if not present in input data (from MAF, standard deviation and genetic effect)
+#. Filter SNPs with an heterogeneous sample size (as JASS and RAISS packages assume sample size to be constant across SNPs)
+#. Normalize the effect size to Z-scores
+#. Save the output by chromosome as the following example:
+----------+-------+------+-----+--------+
| rsID | pos | A0 | A1 | Z |
@@ -36,14 +36,15 @@ The QC and preprocessing step goes as follow:
| rs6548219| 30762 | A | G | -1.133 |
+----------+-------+------+-----+--------+
-* (Optional) Save the output to one file with a chromosome column
-(input format needed to perform LD-score)
+* (Optional step) Save the output to one file with a chromosome column
+(input format needed to perform LD-score). The additional output correspond to: P, the p-value; N_effective (Effective sample size estimated/retrieved from the data).
+Effective sample size refers to the total sample size for continuous trait and to 1 / ( 1/Ncases + 1/Ncontrol ) for binary traits.
-+-------+-----------+--------+----+----+-----+-----+
-| chrom | rsID | pos | A0 | A1 | Z | P |
-+-------+-----------+--------+----+----+-----+-----+
-| 1 | rs4075116 |1003629 | C | T | 0.3 | 0.76|
-+-------+-----------+--------+----+----+-----+-----+
++-------+-----------+--------+----+----+-----+-----+------------------+
+| chrom | rsID | pos | A0 | A1 | Z | P | N_effective |
++-------+-----------+--------+----+----+-----+-----+------------------+
+| 1 | rs4075116 |1003629 | C | T | 0.3 | 0.76| 10220.98 |
++-------+-----------+--------+----+----+-----+-----+------------------+
Installation
@@ -58,14 +59,13 @@ In a terminal, execute the following lines:
Input
======
-* A reference panel (1000 genome format). The user is expected to provide a reference panel
- in tsv format with the following columns in the following order, without header:
+* **A reference panel** to the format below. The user is expected to provide a reference panel
+ in tsv format with the following columns in the following order (chromosome, rsID, Minor Allele
+ Frequency, Position, reference, Alternative allele), **without header**.
+-----+------------+---------+-------+-----+-----+
-| chr | snp_id | MAF | pos | ref | alt |
-+=====+============+=========+=======+=====+=====+
| 1 | rs62635286 |0.0970447| 13116 | T | G |
-+-----+------------+---------+-------+-----+-----+
++=====+============+=========+=======+=====+=====+
| 1 | rs63125786 |0.0970447| 15116 | T | A |
+-----+------------+---------+-------+-----+-----+
| 1 | rs5686 |0.1970447| 17116 | A | G |
@@ -74,40 +74,58 @@ Input
+-----+------------+---------+-------+-----+-----+
-* Folder containing all raw gwas data : (all chromosomes in one file) (minimal conditions?? tab separated?)
-* a list containing the name of GWAS file to the string format.
-* A descriptor csv files that will described each GWAS summary statistic files:
-
+* The **GWAS Folder** containing all raw gwas data (correspond to the --gwas-info command line parameter): all chromosomes in one file, compressed or uncompressed
+* A descriptor csv files (see example below and `here <https://gitlab.pasteur.fr/statistical-genetics/jass_suite_pipeline/-/blob/master/input_files/Data_test_EAS.csv>`_)that will described each GWAS summary statistic files (correspond to the --input-folder command line parameter):
* a header
* 1 line per study
- * the fields are:
-
+ * the fields categories are:
+-------------------------------------------+---------------------------------------------------------------+
| category | field name |
+===========================================+===============================================================+
| path to the data | filename |
+-------------------------------------------+---------------------------------------------------------------+
-| study info fields | Consortium,Outcome,fullName,type,Nsample,Ncase,Ncontrol,Nsnp |
+| study info fields | Consortium,Outcome,fullName,Nsample,Ncase,Ncontrol,Nsnp |
+-------------------------------------------+---------------------------------------------------------------+
| names of the header in the GWAS file | snpid,a1,a2,freq,pval,n,z,OR,se,code,imp,ncas,ncont |
+-------------------------------------------+---------------------------------------------------------------+
-.. Give an example
-.. | I don't know | altNcas,altNcont|
-
-Note that the combination of Consortium and outcome must be unique because it will be used as an index in the cleaning process.
-
-Here is an example of descriptor field, the field irrelevant (for example odd ratio for continuous trait) for the study must be filled with na.
-Some fields are optional like the imputation_quality. If not used they can be filled with na.
+**Study field definition**:
+
+* filename: gwas summary statistic name as it appear in the **GWAS folder**
+* Consortium : the Consortium of the study (can also be the category of the trait) in **upper case and without _ characters**
+* Outcome: a short tag for the Outcome of the study in **upper case and without _ characters**
+* FullName: full description of the trait (for your own information not used in the cleaning process)
+* Nsample: Number of sample in the study
+* Ncase: Number of cases in the study (left empty if trait is continuous)
+* Ncontrol: Number of control in the study (left empty if trait is continuous)
+
+**Field corresping to column names in the summary statistic**
+
+* snpid: name of the column storing rsid in the gwas file
+* POS: name of the column storing the position in the gwas file
+* CHR: name of the column storing the chromosome in the gwas file
+* a1: effect allele
+* a2: Other allele
+* freq: name of the column storing the minor allele frequence in the gwas file
+* pval: name of the column storing the pvalue in the gwas file
+* n: name of the column storing the sample size by variants (optional, will be inferred from the MAF, genetic effect and standard deviation if absent)
+* z: name of the column storing the genetic effect (beta) in the gwas file
+* index-type: precise the type of index
+* imputation_quality: (Optional) column containing individual-based imputation quality. Will be used to filter low quality imputation data from GWASs if the option --imputation-quality-treshold is used
+
+.. warning::
+ Note that the concatenation of Consortium and Outcome must be **unique** because as it will be used as an index in the cleaning process.
+ Both Outcome and Consortium must be in **uppercase and with no _ characters**
+
+Here is an example of descriptor field (downloadable example `here <https://gitlab.pasteur.fr/statistical-genetics/jass_suite_pipeline/-/blob/master/input_files/Data_test_EAS.csv>`_), the field irrelevant (for example odd ratio for continuous trait) for the study must be filled with na or left empty.
+Some fields are optional like the imputation_quality. If not used they can be filled with na.
.. csv-table:: GWAS information table
:header-rows: 1
- "filename","consortia","outcome","fullName","type","Nsample","Ncase","Ncontrol","Nsnp","snpid","a1","a2","freq","pval","n","z","OR","se","code","imp","ncas","ncont","imputation_quality","index_type"
- "GIANT_HEIGHT_Wood_et_al.txt","GIANT","HEIGHT","Height","Anthropometry",253288, na, na, 2550858, "MarkerName", "Allele1", "Allele2", "Freq.Allele1.HapMapCEU","p","N","b",na,"SE",na,na,na,na, "imputationInfo","rsID"
-
-
+ "filename","Consortium","Outcome","FullName","Type","Nsample","Ncase","Ncontrol","Nsnp","snpid", "POS", "a1","a2","freq","pval","n","z","OR","se","code","imp","ncas","ncont","imputation_quality","index_type"
+ "GIANT_HEIGHT_Wood_et_al.txt","GIANT","HEIGHT","Height","Anthropometry",253288, na, na, 2550858, "MarkerName", "position","Allele1", "Allele2", "Freq.Allele1.HapMapCEU","p","N","b",na,"SE",na,na,na,na, "imputationInfo","rs-number"
Command line usage example:
diff --git a/doc/_build/html/_static/basic.css b/doc/_build/html/_static/basic.css
index eeb0519a69bacca5e0d1dc516e93d845743dabf0..912859b55d96750bff001bb79037a83a6c02332c 100644
--- a/doc/_build/html/_static/basic.css
+++ b/doc/_build/html/_static/basic.css
@@ -4,7 +4,7 @@
*
* Sphinx stylesheet -- basic theme.
*
- * :copyright: Copyright 2007-2022 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2021 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
@@ -222,7 +222,7 @@ table.modindextable td {
/* -- general body styles --------------------------------------------------- */
div.body {
- min-width: 360px;
+ min-width: 450px;
max-width: 800px;
}
@@ -236,6 +236,7 @@ div.body p, div.body dd, div.body li, div.body blockquote {
a.headerlink {
visibility: hidden;
}
+
a.brackets:before,
span.brackets > a:before{
content: "[";
@@ -246,7 +247,6 @@ span.brackets > a:after {
content: "]";
}
-
h1:hover > a.headerlink,
h2:hover > a.headerlink,
h3:hover > a.headerlink,
@@ -334,11 +334,13 @@ aside.sidebar {
p.sidebar-title {
font-weight: bold;
}
+
div.admonition, div.topic, blockquote {
clear: left;
}
/* -- topics ---------------------------------------------------------------- */
+
div.topic {
border: 1px solid #ccc;
padding: 7px;
@@ -426,6 +428,10 @@ table.docutils td, table.docutils th {
border-bottom: 1px solid #aaa;
}
+table.footnote td, table.footnote th {
+ border: 0 !important;
+}
+
th {
text-align: left;
padding-right: 5px;
@@ -608,6 +614,7 @@ ol.simple p,
ul.simple p {
margin-bottom: 0;
}
+
dl.footnote > dt,
dl.citation > dt {
float: left;
@@ -636,11 +643,11 @@ dl.field-list > dt {
padding-left: 0.5em;
padding-right: 5px;
}
+
dl.field-list > dt:after {
content: ":";
}
-
dl.field-list > dd {
padding-left: 0.5em;
margin-top: 0em;
@@ -724,9 +731,8 @@ dl.glossary dt {
.classifier:before {
font-style: normal;
- margin: 0 0.5em;
+ margin: 0.5em;
content: ":";
- display: inline-block;
}
abbr, acronym {
@@ -750,7 +756,6 @@ span.pre {
-ms-hyphens: none;
-webkit-hyphens: none;
hyphens: none;
- white-space: nowrap;
}
div[class*="highlight-"] {
diff --git a/doc/_build/html/_static/doctools.js b/doc/_build/html/_static/doctools.js
index 527b876ca636d9a23d0cb3cc73ff6355b94fd7da..8cbf1b161a6527c8c6ad1c4f1fdc156e065ab262 100644
--- a/doc/_build/html/_static/doctools.js
+++ b/doc/_build/html/_static/doctools.js
@@ -2,155 +2,322 @@
* doctools.js
* ~~~~~~~~~~~
*
- * Base JavaScript utilities for all Sphinx HTML documentation.
+ * Sphinx JavaScript utilities for all documentation.
*
- * :copyright: Copyright 2007-2022 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2021 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
-"use strict";
-
-const BLACKLISTED_KEY_CONTROL_ELEMENTS = new Set([
- "TEXTAREA",
- "INPUT",
- "SELECT",
- "BUTTON",
-]);
-
-const _ready = (callback) => {
- if (document.readyState !== "loading") {
- callback();
- } else {
- document.addEventListener("DOMContentLoaded", callback);
+
+/**
+ * select a different prefix for underscore
+ */
+$u = _.noConflict();
+
+/**
+ * make the code below compatible with browsers without
+ * an installed firebug like debugger
+if (!window.console || !console.firebug) {
+ var names = ["log", "debug", "info", "warn", "error", "assert", "dir",
+ "dirxml", "group", "groupEnd", "time", "timeEnd", "count", "trace",
+ "profile", "profileEnd"];
+ window.console = {};
+ for (var i = 0; i < names.length; ++i)
+ window.console[names[i]] = function() {};
+}
+ */
+
+/**
+ * small helper function to urldecode strings
+ *
+ * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL
+ */
+jQuery.urldecode = function(x) {
+ if (!x) {
+ return x
+ }
+ return decodeURIComponent(x.replace(/\+/g, ' '));
+};
+
+/**
+ * small helper function to urlencode strings
+ */
+jQuery.urlencode = encodeURIComponent;
+
+/**
+ * This function returns the parsed url parameters of the
+ * current request. Multiple values per key are supported,
+ * it will always return arrays of strings for the value parts.
+ */
+jQuery.getQueryParameters = function(s) {
+ if (typeof s === 'undefined')
+ s = document.location.search;
+ var parts = s.substr(s.indexOf('?') + 1).split('&');
+ var result = {};
+ for (var i = 0; i < parts.length; i++) {
+ var tmp = parts[i].split('=', 2);
+ var key = jQuery.urldecode(tmp[0]);
+ var value = jQuery.urldecode(tmp[1]);
+ if (key in result)
+ result[key].push(value);
+ else
+ result[key] = [value];
}
+ return result;
};
+/**
+ * highlight a given string on a jquery object by wrapping it in
+ * span elements with the given class name.
+ */
+jQuery.fn.highlightText = function(text, className) {
+ function highlight(node, addItems) {
+ if (node.nodeType === 3) {
+ var val = node.nodeValue;
+ var pos = val.toLowerCase().indexOf(text);
+ if (pos >= 0 &&
+ !jQuery(node.parentNode).hasClass(className) &&
+ !jQuery(node.parentNode).hasClass("nohighlight")) {
+ var span;
+ var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg");
+ if (isInSVG) {
+ span = document.createElementNS("http://www.w3.org/2000/svg", "tspan");
+ } else {
+ span = document.createElement("span");
+ span.className = className;
+ }
+ span.appendChild(document.createTextNode(val.substr(pos, text.length)));
+ node.parentNode.insertBefore(span, node.parentNode.insertBefore(
+ document.createTextNode(val.substr(pos + text.length)),
+ node.nextSibling));
+ node.nodeValue = val.substr(0, pos);
+ if (isInSVG) {
+ var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect");
+ var bbox = node.parentElement.getBBox();
+ rect.x.baseVal.value = bbox.x;
+ rect.y.baseVal.value = bbox.y;
+ rect.width.baseVal.value = bbox.width;
+ rect.height.baseVal.value = bbox.height;
+ rect.setAttribute('class', className);
+ addItems.push({
+ "parent": node.parentNode,
+ "target": rect});
+ }
+ }
+ }
+ else if (!jQuery(node).is("button, select, textarea")) {
+ jQuery.each(node.childNodes, function() {
+ highlight(this, addItems);
+ });
+ }
+ }
+ var addItems = [];
+ var result = this.each(function() {
+ highlight(this, addItems);
+ });
+ for (var i = 0; i < addItems.length; ++i) {
+ jQuery(addItems[i].parent).before(addItems[i].target);
+ }
+ return result;
+};
+
+/*
+ * backward compatibility for jQuery.browser
+ * This will be supported until firefox bug is fixed.
+ */
+if (!jQuery.browser) {
+ jQuery.uaMatch = function(ua) {
+ ua = ua.toLowerCase();
+
+ var match = /(chrome)[ \/]([\w.]+)/.exec(ua) ||
+ /(webkit)[ \/]([\w.]+)/.exec(ua) ||
+ /(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) ||
+ /(msie) ([\w.]+)/.exec(ua) ||
+ ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) ||
+ [];
+
+ return {
+ browser: match[ 1 ] || "",
+ version: match[ 2 ] || "0"
+ };
+ };
+ jQuery.browser = {};
+ jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true;
+}
+
/**
* Small JavaScript module for the documentation.
*/
-const Documentation = {
- init: () => {
- Documentation.initDomainIndexTable();
- Documentation.initOnKeyListeners();
+var Documentation = {
+
+ init : function() {
+ this.fixFirefoxAnchorBug();
+ this.highlightSearchWords();
+ this.initIndexTable();
+ if (DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) {
+ this.initOnKeyListeners();
+ }
},
/**
* i18n support
*/
- TRANSLATIONS: {},
- PLURAL_EXPR: (n) => (n === 1 ? 0 : 1),
- LOCALE: "unknown",
+ TRANSLATIONS : {},
+ PLURAL_EXPR : function(n) { return n === 1 ? 0 : 1; },
+ LOCALE : 'unknown',
// gettext and ngettext don't access this so that the functions
// can safely bound to a different name (_ = Documentation.gettext)
- gettext: (string) => {
- const translated = Documentation.TRANSLATIONS[string];
- switch (typeof translated) {
- case "undefined":
- return string; // no translation
- case "string":
- return translated; // translation exists
- default:
- return translated[0]; // (singular, plural) translation tuple exists
- }
+ gettext : function(string) {
+ var translated = Documentation.TRANSLATIONS[string];
+ if (typeof translated === 'undefined')
+ return string;
+ return (typeof translated === 'string') ? translated : translated[0];
},
- ngettext: (singular, plural, n) => {
- const translated = Documentation.TRANSLATIONS[singular];
- if (typeof translated !== "undefined")
- return translated[Documentation.PLURAL_EXPR(n)];
- return n === 1 ? singular : plural;
+ ngettext : function(singular, plural, n) {
+ var translated = Documentation.TRANSLATIONS[singular];
+ if (typeof translated === 'undefined')
+ return (n == 1) ? singular : plural;
+ return translated[Documentation.PLURALEXPR(n)];
},
- addTranslations: (catalog) => {
- Object.assign(Documentation.TRANSLATIONS, catalog.messages);
- Documentation.PLURAL_EXPR = new Function(
- "n",
- `return (${catalog.plural_expr})`
- );
- Documentation.LOCALE = catalog.locale;
+ addTranslations : function(catalog) {
+ for (var key in catalog.messages)
+ this.TRANSLATIONS[key] = catalog.messages[key];
+ this.PLURAL_EXPR = new Function('n', 'return +(' + catalog.plural_expr + ')');
+ this.LOCALE = catalog.locale;
},
/**
- * helper function to focus on search bar
+ * add context elements like header anchor links
*/
- focusSearchBar: () => {
- document.querySelectorAll("input[name=q]")[0]?.focus();
+ addContextElements : function() {
+ $('div[id] > :header:first').each(function() {
+ $('<a class="headerlink">\u00B6</a>').
+ attr('href', '#' + this.id).
+ attr('title', _('Permalink to this headline')).
+ appendTo(this);
+ });
+ $('dt[id]').each(function() {
+ $('<a class="headerlink">\u00B6</a>').
+ attr('href', '#' + this.id).
+ attr('title', _('Permalink to this definition')).
+ appendTo(this);
+ });
},
/**
- * Initialise the domain index toggle buttons
+ * workaround a firefox stupidity
+ * see: https://bugzilla.mozilla.org/show_bug.cgi?id=645075
*/
- initDomainIndexTable: () => {
- const toggler = (el) => {
- const idNumber = el.id.substr(7);
- const toggledRows = document.querySelectorAll(`tr.cg-${idNumber}`);
- if (el.src.substr(-9) === "minus.png") {
- el.src = `${el.src.substr(0, el.src.length - 9)}plus.png`;
- toggledRows.forEach((el) => (el.style.display = "none"));
- } else {
- el.src = `${el.src.substr(0, el.src.length - 8)}minus.png`;
- toggledRows.forEach((el) => (el.style.display = ""));
+ fixFirefoxAnchorBug : function() {
+ if (document.location.hash && $.browser.mozilla)
+ window.setTimeout(function() {
+ document.location.href += '';
+ }, 10);
+ },
+
+ /**
+ * highlight the search words provided in the url in the text
+ */
+ highlightSearchWords : function() {
+ var params = $.getQueryParameters();
+ var terms = (params.highlight) ? params.highlight[0].split(/\s+/) : [];
+ if (terms.length) {
+ var body = $('div.body');
+ if (!body.length) {
+ body = $('body');
}
- };
+ window.setTimeout(function() {
+ $.each(terms, function() {
+ body.highlightText(this.toLowerCase(), 'highlighted');
+ });
+ }, 10);
+ $('<p class="highlight-link"><a href="javascript:Documentation.' +
+ 'hideSearchWords()">' + _('Hide Search Matches') + '</a></p>')
+ .appendTo($('#searchbox'));
+ }
+ },
+
+ /**
+ * init the domain index toggle buttons
+ */
+ initIndexTable : function() {
+ var togglers = $('img.toggler').click(function() {
+ var src = $(this).attr('src');
+ var idnum = $(this).attr('id').substr(7);
+ $('tr.cg-' + idnum).toggle();
+ if (src.substr(-9) === 'minus.png')
+ $(this).attr('src', src.substr(0, src.length-9) + 'plus.png');
+ else
+ $(this).attr('src', src.substr(0, src.length-8) + 'minus.png');
+ }).css('display', '');
+ if (DOCUMENTATION_OPTIONS.COLLAPSE_INDEX) {
+ togglers.click();
+ }
+ },
- const togglerElements = document.querySelectorAll("img.toggler");
- togglerElements.forEach((el) =>
- el.addEventListener("click", (event) => toggler(event.currentTarget))
- );
- togglerElements.forEach((el) => (el.style.display = ""));
- if (DOCUMENTATION_OPTIONS.COLLAPSE_INDEX) togglerElements.forEach(toggler);
+ /**
+ * helper function to hide the search marks again
+ */
+ hideSearchWords : function() {
+ $('#searchbox .highlight-link').fadeOut(300);
+ $('span.highlighted').removeClass('highlighted');
},
- initOnKeyListeners: () => {
- // only install a listener if it is really needed
- if (
- !DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS &&
- !DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS
- )
- return;
-
- document.addEventListener("keydown", (event) => {
- // bail for input elements
- if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return;
- // bail with special keys
- if (event.altKey || event.ctrlKey || event.metaKey) return;
-
- if (!event.shiftKey) {
- switch (event.key) {
- case "ArrowLeft":
- if (!DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) break;
-
- const prevLink = document.querySelector('link[rel="prev"]');
- if (prevLink && prevLink.href) {
- window.location.href = prevLink.href;
- event.preventDefault();
+ /**
+ * make the url absolute
+ */
+ makeURL : function(relativeURL) {
+ return DOCUMENTATION_OPTIONS.URL_ROOT + '/' + relativeURL;
+ },
+
+ /**
+ * get the current relative url
+ */
+ getCurrentURL : function() {
+ var path = document.location.pathname;
+ var parts = path.split(/\//);
+ $.each(DOCUMENTATION_OPTIONS.URL_ROOT.split(/\//), function() {
+ if (this === '..')
+ parts.pop();
+ });
+ var url = parts.join('/');
+ return path.substring(url.lastIndexOf('/') + 1, path.length - 1);
+ },
+
+ initOnKeyListeners: function() {
+ $(document).keydown(function(event) {
+ var activeElementType = document.activeElement.tagName;
+ // don't navigate when in search box, textarea, dropdown or button
+ if (activeElementType !== 'TEXTAREA' && activeElementType !== 'INPUT' && activeElementType !== 'SELECT'
+ && activeElementType !== 'BUTTON' && !event.altKey && !event.ctrlKey && !event.metaKey
+ && !event.shiftKey) {
+ switch (event.keyCode) {
+ case 37: // left
+ var prevHref = $('link[rel="prev"]').prop('href');
+ if (prevHref) {
+ window.location.href = prevHref;
+ return false;
}
break;
- case "ArrowRight":
- if (!DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) break;
-
- const nextLink = document.querySelector('link[rel="next"]');
- if (nextLink && nextLink.href) {
- window.location.href = nextLink.href;
- event.preventDefault();
+ case 39: // right
+ var nextHref = $('link[rel="next"]').prop('href');
+ if (nextHref) {
+ window.location.href = nextHref;
+ return false;
}
break;
}
}
-
- // some keyboard layouts may need Shift to get /
- switch (event.key) {
- case "/":
- if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) break;
- Documentation.focusSearchBar();
- event.preventDefault();
- }
});
- },
+ }
};
// quick alias for translations
-const _ = Documentation.gettext;
+_ = Documentation.gettext;
-_ready(Documentation.init);
+$(document).ready(function() {
+ Documentation.init();
+});
diff --git a/doc/_build/html/_static/documentation_options.js b/doc/_build/html/_static/documentation_options.js
index a7f754b66f245c8342c8dfc42de1b439f620054f..07966ec63146bb6f2a1abcec249abdcac88c9822 100644
--- a/doc/_build/html/_static/documentation_options.js
+++ b/doc/_build/html/_static/documentation_options.js
@@ -1,14 +1,12 @@
var DOCUMENTATION_OPTIONS = {
URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
VERSION: '1.0',
- LANGUAGE: 'en',
+ LANGUAGE: 'None',
COLLAPSE_INDEX: false,
BUILDER: 'html',
FILE_SUFFIX: '.html',
LINK_SUFFIX: '.html',
HAS_SOURCE: true,
SOURCELINK_SUFFIX: '.txt',
- NAVIGATION_WITH_KEYS: false,
- SHOW_SEARCH_SUMMARY: true,
- ENABLE_SEARCH_SHORTCUTS: true,
+ NAVIGATION_WITH_KEYS: false
};
\ No newline at end of file
diff --git a/doc/_build/html/_static/jquery.js b/doc/_build/html/_static/jquery.js
index c4c6022f2982e8dae64cebd6b9a2b59f2547faad..b0614034ad3a95e4ae9f53c2b015eeb3e8d68bde 100644
--- a/doc/_build/html/_static/jquery.js
+++ b/doc/_build/html/_static/jquery.js
@@ -1,2 +1,2 @@
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diff --git a/doc/_build/html/_static/pygments.css b/doc/_build/html/_static/pygments.css
index 691aeb82d0057a353637453f168872571a8e5328..d14395efc33a7370ec510acfc36ea481590f98eb 100644
--- a/doc/_build/html/_static/pygments.css
+++ b/doc/_build/html/_static/pygments.css
@@ -1,8 +1,8 @@
-pre { line-height: 125%; }
-td.linenos .normal { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; }
-span.linenos { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; }
-td.linenos .special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }
-span.linenos.special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }
+pre { line-height: 125%; margin: 0; }
+td.linenos pre { color: #000000; background-color: #f0f0f0; padding: 0 5px 0 5px; }
+span.linenos { color: #000000; background-color: #f0f0f0; padding: 0 5px 0 5px; }
+td.linenos pre.special { color: #000000; background-color: #ffffc0; padding: 0 5px 0 5px; }
+span.linenos.special { color: #000000; background-color: #ffffc0; padding: 0 5px 0 5px; }
.highlight .hll { background-color: #ffffcc }
.highlight { background: #eeffcc; }
.highlight .c { color: #408090; font-style: italic } /* Comment */
diff --git a/doc/_build/html/_static/searchtools.js b/doc/_build/html/_static/searchtools.js
index e89e34d4e7729c9cf60e90e97ecc0507ebc398ec..58ff35c4345d19830352048b89abc8e7c06e4f20 100644
--- a/doc/_build/html/_static/searchtools.js
+++ b/doc/_build/html/_static/searchtools.js
@@ -4,24 +4,22 @@
*
* Sphinx JavaScript utilities for the full-text search.
*
- * :copyright: Copyright 2007-2022 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2021 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
-"use strict";
-/**
- * Simple result scoring code.
- */
-if (typeof Scorer === "undefined") {
+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 [docname, title, anchor, descr, score, filename]
+ // The function takes a result array [filename, title, anchor, descr, score]
// and returns the new score.
/*
- score: result => {
- const [docname, title, anchor, descr, score, filename] = result
- return score
+ score: function(result) {
+ return result[4];
},
*/
@@ -30,11 +28,9 @@ if (typeof Scorer === "undefined") {
// 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
- },
+ 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,
@@ -43,495 +39,455 @@ if (typeof Scorer === "undefined") {
partialTitle: 7,
// query found in terms
term: 5,
- partialTerm: 2,
+ partialTerm: 2
};
}
-const _removeChildren = (element) => {
- while (element && element.lastChild) element.removeChild(element.lastChild);
-};
-
-/**
- * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping
- */
-const _escapeRegExp = (string) =>
- string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string
-
-const _displayItem = (item, searchTerms) => {
- const docBuilder = DOCUMENTATION_OPTIONS.BUILDER;
- const docUrlRoot = DOCUMENTATION_OPTIONS.URL_ROOT;
- const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX;
- const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX;
- const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY;
-
- const [docName, title, anchor, descr, score, _filename] = item;
-
- let listItem = document.createElement("li");
- let requestUrl;
- let linkUrl;
- if (docBuilder === "dirhtml") {
- // dirhtml builder
- let dirname = docName + "/";
- if (dirname.match(/\/index\/$/))
- dirname = dirname.substring(0, dirname.length - 6);
- else if (dirname === "index/") dirname = "";
- requestUrl = docUrlRoot + dirname;
- linkUrl = requestUrl;
- } else {
- // normal html builders
- requestUrl = docUrlRoot + docName + docFileSuffix;
- linkUrl = docName + docLinkSuffix;
+if (!splitQuery) {
+ function splitQuery(query) {
+ return query.split(/\s+/);
}
- let linkEl = listItem.appendChild(document.createElement("a"));
- linkEl.href = linkUrl + anchor;
- linkEl.dataset.score = score;
- linkEl.innerHTML = title;
- if (descr)
- listItem.appendChild(document.createElement("span")).innerHTML =
- " (" + descr + ")";
- else if (showSearchSummary)
- fetch(requestUrl)
- .then((responseData) => responseData.text())
- .then((data) => {
- if (data)
- listItem.appendChild(
- Search.makeSearchSummary(data, searchTerms)
- );
- });
- Search.output.appendChild(listItem);
-};
-const _finishSearch = (resultCount) => {
- Search.stopPulse();
- Search.title.innerText = _("Search Results");
- if (!resultCount)
- Search.status.innerText = Documentation.gettext(
- "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories."
- );
- else
- Search.status.innerText = _(
- `Search finished, found ${resultCount} page(s) matching the search query.`
- );
-};
-const _displayNextItem = (
- results,
- resultCount,
- searchTerms
-) => {
- // results left, load the summary and display it
- // this is intended to be dynamic (don't sub resultsCount)
- if (results.length) {
- _displayItem(results.pop(), searchTerms);
- setTimeout(
- () => _displayNextItem(results, resultCount, searchTerms),
- 5
- );
- }
- // search finished, update title and status message
- else _finishSearch(resultCount);
-};
-
-/**
- * Default splitQuery function. Can be overridden in ``sphinx.search`` with a
- * custom function per language.
- *
- * The regular expression works by splitting the string on consecutive characters
- * that are not Unicode letters, numbers, underscores, or emoji characters.
- * This is the same as ``\W+`` in Python, preserving the surrogate pair area.
- */
-if (typeof splitQuery === "undefined") {
- var splitQuery = (query) => query
- .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu)
- .filter(term => term) // remove remaining empty strings
}
/**
* Search Module
*/
-const Search = {
- _index: null,
- _queued_query: null,
- _pulse_status: -1,
-
- htmlToText: (htmlString) => {
- const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html');
- htmlElement.querySelectorAll(".headerlink").forEach((el) => { el.remove() });
- const docContent = htmlElement.querySelector('[role="main"]');
- if (docContent !== undefined) return docContent.textContent;
- console.warn(
- "Content block not found. Sphinx search tries to obtain it via '[role=main]'. Could you check your theme or template."
- );
- return "";
+var Search = {
+
+ _index : null,
+ _queued_query : null,
+ _pulse_status : -1,
+
+ htmlToText : function(htmlString) {
+ var virtualDocument = document.implementation.createHTMLDocument('virtual');
+ var htmlElement = $(htmlString, virtualDocument);
+ htmlElement.find('.headerlink').remove();
+ docContent = htmlElement.find('[role=main]')[0];
+ if(docContent === undefined) {
+ console.warn("Content block not found. Sphinx search tries to obtain it " +
+ "via '[role=main]'. Could you check your theme or template.");
+ return "";
+ }
+ return docContent.textContent || docContent.innerText;
},
- init: () => {
- const query = new URLSearchParams(window.location.search).get("q");
- document
- .querySelectorAll('input[name="q"]')
- .forEach((el) => (el.value = query));
- if (query) Search.performSearch(query);
+ init : function() {
+ var params = $.getQueryParameters();
+ if (params.q) {
+ var query = params.q[0];
+ $('input[name="q"]')[0].value = query;
+ this.performSearch(query);
+ }
},
- loadIndex: (url) =>
- (document.body.appendChild(document.createElement("script")).src = url),
+ loadIndex : function(url) {
+ $.ajax({type: "GET", url: url, data: null,
+ dataType: "script", cache: true,
+ complete: function(jqxhr, textstatus) {
+ if (textstatus != "success") {
+ document.getElementById("searchindexloader").src = url;
+ }
+ }});
+ },
- setIndex: (index) => {
- Search._index = index;
- if (Search._queued_query !== null) {
- const query = Search._queued_query;
- Search._queued_query = null;
- Search.query(query);
+ setIndex : function(index) {
+ var q;
+ this._index = index;
+ if ((q = this._queued_query) !== null) {
+ this._queued_query = null;
+ Search.query(q);
}
},
- hasIndex: () => Search._index !== null,
-
- deferQuery: (query) => (Search._queued_query = query),
+ hasIndex : function() {
+ return this._index !== null;
+ },
- stopPulse: () => (Search._pulse_status = -1),
+ deferQuery : function(query) {
+ this._queued_query = query;
+ },
- startPulse: () => {
- if (Search._pulse_status >= 0) return;
+ stopPulse : function() {
+ this._pulse_status = 0;
+ },
- const pulse = () => {
+ startPulse : function() {
+ if (this._pulse_status >= 0)
+ return;
+ function pulse() {
+ var i;
Search._pulse_status = (Search._pulse_status + 1) % 4;
- Search.dots.innerText = ".".repeat(Search._pulse_status);
- if (Search._pulse_status >= 0) window.setTimeout(pulse, 500);
- };
+ var dotString = '';
+ for (i = 0; i < Search._pulse_status; i++)
+ dotString += '.';
+ Search.dots.text(dotString);
+ if (Search._pulse_status > -1)
+ window.setTimeout(pulse, 500);
+ }
pulse();
},
/**
* perform a search for something (or wait until index is loaded)
*/
- performSearch: (query) => {
+ performSearch : function(query) {
// create the required interface elements
- const searchText = document.createElement("h2");
- searchText.textContent = _("Searching");
- const searchSummary = document.createElement("p");
- searchSummary.classList.add("search-summary");
- searchSummary.innerText = "";
- const searchList = document.createElement("ul");
- searchList.classList.add("search");
-
- const out = document.getElementById("search-results");
- Search.title = out.appendChild(searchText);
- Search.dots = Search.title.appendChild(document.createElement("span"));
- Search.status = out.appendChild(searchSummary);
- Search.output = out.appendChild(searchList);
-
- const searchProgress = document.getElementById("search-progress");
- // Some themes don't use the search progress node
- if (searchProgress) {
- searchProgress.innerText = _("Preparing search...");
- }
- Search.startPulse();
+ this.out = $('#search-results');
+ this.title = $('<h2>' + _('Searching') + '</h2>').appendTo(this.out);
+ this.dots = $('<span></span>').appendTo(this.title);
+ this.status = $('<p class="search-summary"> </p>').appendTo(this.out);
+ this.output = $('<ul class="search"/>').appendTo(this.out);
+
+ $('#search-progress').text(_('Preparing search...'));
+ this.startPulse();
// index already loaded, the browser was quick!
- if (Search.hasIndex()) Search.query(query);
- else Search.deferQuery(query);
+ if (this.hasIndex())
+ this.query(query);
+ else
+ this.deferQuery(query);
},
/**
* execute search (requires search index to be loaded)
*/
- query: (query) => {
- const filenames = Search._index.filenames;
- const docNames = Search._index.docnames;
- const titles = Search._index.titles;
- const allTitles = Search._index.alltitles;
- const indexEntries = Search._index.indexentries;
-
- // stem the search terms and add them to the correct list
- const stemmer = new Stemmer();
- const searchTerms = new Set();
- const excludedTerms = new Set();
- const highlightTerms = new Set();
- const objectTerms = new Set(splitQuery(query.toLowerCase().trim()));
- splitQuery(query.trim()).forEach((queryTerm) => {
- const queryTermLower = queryTerm.toLowerCase();
-
- // maybe skip this "word"
- // stopwords array is from language_data.js
- if (
- stopwords.indexOf(queryTermLower) !== -1 ||
- queryTerm.match(/^\d+$/)
- )
- return;
+ query : function(query) {
+ var i;
+
+ // stem the searchterms and add them to the correct list
+ var stemmer = new Stemmer();
+ var searchterms = [];
+ var excluded = [];
+ var hlterms = [];
+ var tmp = splitQuery(query);
+ var objectterms = [];
+ for (i = 0; i < tmp.length; i++) {
+ if (tmp[i] !== "") {
+ objectterms.push(tmp[i].toLowerCase());
+ }
+ if ($u.indexOf(stopwords, tmp[i].toLowerCase()) != -1 || tmp[i] === "") {
+ // skip this "word"
+ continue;
+ }
// stem the word
- let word = stemmer.stemWord(queryTermLower);
+ var word = stemmer.stemWord(tmp[i].toLowerCase());
+ // prevent stemmer from cutting word smaller than two chars
+ if(word.length < 3 && tmp[i].length >= 3) {
+ word = tmp[i];
+ }
+ var toAppend;
// select the correct list
- if (word[0] === "-") excludedTerms.add(word.substr(1));
+ if (word[0] == '-') {
+ toAppend = excluded;
+ word = word.substr(1);
+ }
else {
- searchTerms.add(word);
- highlightTerms.add(queryTermLower);
+ toAppend = searchterms;
+ hlterms.push(tmp[i].toLowerCase());
}
- });
-
- if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js
- localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" "))
+ // only add if not already in the list
+ if (!$u.contains(toAppend, word))
+ toAppend.push(word);
}
+ var highlightstring = '?highlight=' + $.urlencode(hlterms.join(" "));
- // console.debug("SEARCH: searching for:");
- // console.info("required: ", [...searchTerms]);
- // console.info("excluded: ", [...excludedTerms]);
-
- // array of [docname, title, anchor, descr, score, filename]
- let results = [];
- _removeChildren(document.getElementById("search-progress"));
-
- const queryLower = query.toLowerCase();
- for (const [title, foundTitles] of Object.entries(allTitles)) {
- if (title.toLowerCase().includes(queryLower) && (queryLower.length >= title.length/2)) {
- for (const [file, id] of foundTitles) {
- let score = Math.round(100 * queryLower.length / title.length)
- results.push([
- docNames[file],
- titles[file] !== title ? `${titles[file]} > ${title}` : title,
- id !== null ? "#" + id : "",
- null,
- score,
- filenames[file],
- ]);
- }
- }
- }
+ // console.debug('SEARCH: searching for:');
+ // console.info('required: ', searchterms);
+ // console.info('excluded: ', excluded);
- // search for explicit entries in index directives
- for (const [entry, foundEntries] of Object.entries(indexEntries)) {
- if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) {
- for (const [file, id] of foundEntries) {
- let score = Math.round(100 * queryLower.length / entry.length)
- results.push([
- docNames[file],
- titles[file],
- id ? "#" + id : "",
- null,
- score,
- filenames[file],
- ]);
- }
- }
- }
+ // prepare search
+ var terms = this._index.terms;
+ var titleterms = this._index.titleterms;
+
+ // array of [filename, title, anchor, descr, score]
+ var results = [];
+ $('#search-progress').empty();
// lookup as object
- objectTerms.forEach((term) =>
- results.push(...Search.performObjectSearch(term, objectTerms))
- );
+ for (i = 0; i < objectterms.length; i++) {
+ var others = [].concat(objectterms.slice(0, i),
+ objectterms.slice(i+1, objectterms.length));
+ results = results.concat(this.performObjectSearch(objectterms[i], others));
+ }
// lookup as search terms in fulltext
- results.push(...Search.performTermsSearch(searchTerms, excludedTerms));
+ results = results.concat(this.performTermsSearch(searchterms, excluded, terms, titleterms));
// let the scorer override scores with a custom scoring function
- if (Scorer.score) results.forEach((item) => (item[4] = Scorer.score(item)));
+ if (Scorer.score) {
+ for (i = 0; i < results.length; i++)
+ results[i][4] = Scorer.score(results[i]);
+ }
// now sort the results by score (in opposite order of appearance, since the
// display function below uses pop() to retrieve items) and then
// alphabetically
- results.sort((a, b) => {
- const leftScore = a[4];
- const rightScore = b[4];
- if (leftScore === rightScore) {
+ results.sort(function(a, b) {
+ var left = a[4];
+ var right = b[4];
+ if (left > right) {
+ return 1;
+ } else if (left < right) {
+ return -1;
+ } else {
// same score: sort alphabetically
- const leftTitle = a[1].toLowerCase();
- const rightTitle = b[1].toLowerCase();
- if (leftTitle === rightTitle) return 0;
- return leftTitle > rightTitle ? -1 : 1; // inverted is intentional
+ left = a[1].toLowerCase();
+ right = b[1].toLowerCase();
+ return (left > right) ? -1 : ((left < right) ? 1 : 0);
}
- return leftScore > rightScore ? 1 : -1;
});
- // remove duplicate search results
- // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept
- let seen = new Set();
- results = results.reverse().reduce((acc, result) => {
- let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(',');
- if (!seen.has(resultStr)) {
- acc.push(result);
- seen.add(resultStr);
- }
- return acc;
- }, []);
-
- results = results.reverse();
-
// for debugging
//Search.lastresults = results.slice(); // a copy
- // console.info("search results:", Search.lastresults);
+ //console.info('search results:', Search.lastresults);
// print the results
- _displayNextItem(results, results.length, searchTerms);
+ var resultCount = results.length;
+ function displayNextItem() {
+ // results left, load the summary and display it
+ if (results.length) {
+ var item = results.pop();
+ var listItem = $('<li></li>');
+ var requestUrl = "";
+ var linkUrl = "";
+ if (DOCUMENTATION_OPTIONS.BUILDER === 'dirhtml') {
+ // dirhtml builder
+ var dirname = item[0] + '/';
+ if (dirname.match(/\/index\/$/)) {
+ dirname = dirname.substring(0, dirname.length-6);
+ } else if (dirname == 'index/') {
+ dirname = '';
+ }
+ requestUrl = DOCUMENTATION_OPTIONS.URL_ROOT + dirname;
+ linkUrl = requestUrl;
+
+ } else {
+ // normal html builders
+ requestUrl = DOCUMENTATION_OPTIONS.URL_ROOT + item[0] + DOCUMENTATION_OPTIONS.FILE_SUFFIX;
+ linkUrl = item[0] + DOCUMENTATION_OPTIONS.LINK_SUFFIX;
+ }
+ listItem.append($('<a/>').attr('href',
+ linkUrl +
+ highlightstring + item[2]).html(item[1]));
+ if (item[3]) {
+ listItem.append($('<span> (' + item[3] + ')</span>'));
+ Search.output.append(listItem);
+ setTimeout(function() {
+ displayNextItem();
+ }, 5);
+ } else if (DOCUMENTATION_OPTIONS.HAS_SOURCE) {
+ $.ajax({url: requestUrl,
+ dataType: "text",
+ complete: function(jqxhr, textstatus) {
+ var data = jqxhr.responseText;
+ if (data !== '' && data !== undefined) {
+ var summary = Search.makeSearchSummary(data, searchterms, hlterms);
+ if (summary) {
+ listItem.append(summary);
+ }
+ }
+ Search.output.append(listItem);
+ setTimeout(function() {
+ displayNextItem();
+ }, 5);
+ }});
+ } else {
+ // no source available, just display title
+ Search.output.append(listItem);
+ setTimeout(function() {
+ displayNextItem();
+ }, 5);
+ }
+ }
+ // search finished, update title and status message
+ else {
+ Search.stopPulse();
+ Search.title.text(_('Search Results'));
+ if (!resultCount)
+ Search.status.text(_('Your search did not match any documents. Please make sure that all words are spelled correctly and that you\'ve selected enough categories.'));
+ else
+ Search.status.text(_('Search finished, found %s page(s) matching the search query.').replace('%s', resultCount));
+ Search.status.fadeIn(500);
+ }
+ }
+ displayNextItem();
},
/**
* search for object names
*/
- performObjectSearch: (object, objectTerms) => {
- const filenames = Search._index.filenames;
- const docNames = Search._index.docnames;
- const objects = Search._index.objects;
- const objNames = Search._index.objnames;
- const titles = Search._index.titles;
-
- const results = [];
-
- const objectSearchCallback = (prefix, match) => {
- const name = match[4]
- const fullname = (prefix ? prefix + "." : "") + name;
- const fullnameLower = fullname.toLowerCase();
- if (fullnameLower.indexOf(object) < 0) return;
-
- let score = 0;
- const parts = fullnameLower.split(".");
-
- // check for different match types: exact matches of full name or
- // "last name" (i.e. last dotted part)
- if (fullnameLower === object || parts.slice(-1)[0] === object)
- score += Scorer.objNameMatch;
- else if (parts.slice(-1)[0].indexOf(object) > -1)
- score += Scorer.objPartialMatch; // matches in last name
-
- const objName = objNames[match[1]][2];
- const title = titles[match[0]];
-
- // If more than one term searched for, we require other words to be
- // found in the name/title/description
- const otherTerms = new Set(objectTerms);
- otherTerms.delete(object);
- if (otherTerms.size > 0) {
- const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase();
- if (
- [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0)
- )
- return;
+ performObjectSearch : function(object, otherterms) {
+ var filenames = this._index.filenames;
+ var docnames = this._index.docnames;
+ var objects = this._index.objects;
+ var objnames = this._index.objnames;
+ var titles = this._index.titles;
+
+ var i;
+ var results = [];
+
+ for (var prefix in objects) {
+ for (var name in objects[prefix]) {
+ var fullname = (prefix ? prefix + '.' : '') + name;
+ var fullnameLower = fullname.toLowerCase()
+ if (fullnameLower.indexOf(object) > -1) {
+ var score = 0;
+ var parts = fullnameLower.split('.');
+ // check for different match types: exact matches of full name or
+ // "last name" (i.e. last dotted part)
+ if (fullnameLower == object || parts[parts.length - 1] == object) {
+ score += Scorer.objNameMatch;
+ // matches in last name
+ } else if (parts[parts.length - 1].indexOf(object) > -1) {
+ score += Scorer.objPartialMatch;
+ }
+ var match = objects[prefix][name];
+ var objname = objnames[match[1]][2];
+ var title = titles[match[0]];
+ // If more than one term searched for, we require other words to be
+ // found in the name/title/description
+ if (otherterms.length > 0) {
+ var haystack = (prefix + ' ' + name + ' ' +
+ objname + ' ' + title).toLowerCase();
+ var allfound = true;
+ for (i = 0; i < otherterms.length; i++) {
+ if (haystack.indexOf(otherterms[i]) == -1) {
+ allfound = false;
+ break;
+ }
+ }
+ if (!allfound) {
+ continue;
+ }
+ }
+ var descr = objname + _(', in ') + title;
+
+ var anchor = match[3];
+ if (anchor === '')
+ anchor = fullname;
+ else if (anchor == '-')
+ anchor = objnames[match[1]][1] + '-' + fullname;
+ // add custom score for some objects according to scorer
+ if (Scorer.objPrio.hasOwnProperty(match[2])) {
+ score += Scorer.objPrio[match[2]];
+ } else {
+ score += Scorer.objPrioDefault;
+ }
+ results.push([docnames[match[0]], fullname, '#'+anchor, descr, score, filenames[match[0]]]);
+ }
}
+ }
- let anchor = match[3];
- if (anchor === "") anchor = fullname;
- else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname;
-
- const descr = objName + _(", in ") + title;
-
- // add custom score for some objects according to scorer
- if (Scorer.objPrio.hasOwnProperty(match[2]))
- score += Scorer.objPrio[match[2]];
- else score += Scorer.objPrioDefault;
-
- results.push([
- docNames[match[0]],
- fullname,
- "#" + anchor,
- descr,
- score,
- filenames[match[0]],
- ]);
- };
- Object.keys(objects).forEach((prefix) =>
- objects[prefix].forEach((array) =>
- objectSearchCallback(prefix, array)
- )
- );
return results;
},
+ /**
+ * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions
+ */
+ escapeRegExp : function(string) {
+ return string.replace(/[.*+\-?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string
+ },
+
/**
* search for full-text terms in the index
*/
- performTermsSearch: (searchTerms, excludedTerms) => {
- // prepare search
- const terms = Search._index.terms;
- const titleTerms = Search._index.titleterms;
- const filenames = Search._index.filenames;
- const docNames = Search._index.docnames;
- const titles = Search._index.titles;
+ performTermsSearch : function(searchterms, excluded, terms, titleterms) {
+ var docnames = this._index.docnames;
+ var filenames = this._index.filenames;
+ var titles = this._index.titles;
- const scoreMap = new Map();
- const fileMap = new Map();
+ var i, j, file;
+ var fileMap = {};
+ var scoreMap = {};
+ var results = [];
// perform the search on the required terms
- searchTerms.forEach((word) => {
- const files = [];
- const arr = [
- { files: terms[word], score: Scorer.term },
- { files: titleTerms[word], score: Scorer.title },
+ for (i = 0; i < searchterms.length; i++) {
+ var word = searchterms[i];
+ var files = [];
+ var _o = [
+ {files: terms[word], score: Scorer.term},
+ {files: titleterms[word], score: Scorer.title}
];
// add support for partial matches
if (word.length > 2) {
- const escapedWord = _escapeRegExp(word);
- Object.keys(terms).forEach((term) => {
- if (term.match(escapedWord) && !terms[word])
- arr.push({ files: terms[term], score: Scorer.partialTerm });
- });
- Object.keys(titleTerms).forEach((term) => {
- if (term.match(escapedWord) && !titleTerms[word])
- arr.push({ files: titleTerms[word], score: Scorer.partialTitle });
- });
+ var word_regex = this.escapeRegExp(word);
+ for (var w in terms) {
+ if (w.match(word_regex) && !terms[word]) {
+ _o.push({files: terms[w], score: Scorer.partialTerm})
+ }
+ }
+ for (var w in titleterms) {
+ if (w.match(word_regex) && !titleterms[word]) {
+ _o.push({files: titleterms[w], score: Scorer.partialTitle})
+ }
+ }
}
// no match but word was a required one
- if (arr.every((record) => record.files === undefined)) return;
-
+ if ($u.every(_o, function(o){return o.files === undefined;})) {
+ break;
+ }
// found search word in contents
- arr.forEach((record) => {
- if (record.files === undefined) return;
-
- let recordFiles = record.files;
- if (recordFiles.length === undefined) recordFiles = [recordFiles];
- files.push(...recordFiles);
-
- // set score for the word in each file
- recordFiles.forEach((file) => {
- if (!scoreMap.has(file)) scoreMap.set(file, {});
- scoreMap.get(file)[word] = record.score;
- });
+ $u.each(_o, function(o) {
+ var _files = o.files;
+ if (_files === undefined)
+ return
+
+ if (_files.length === undefined)
+ _files = [_files];
+ files = files.concat(_files);
+
+ // set score for the word in each file to Scorer.term
+ for (j = 0; j < _files.length; j++) {
+ file = _files[j];
+ if (!(file in scoreMap))
+ scoreMap[file] = {};
+ scoreMap[file][word] = o.score;
+ }
});
// create the mapping
- files.forEach((file) => {
- if (fileMap.has(file) && fileMap.get(file).indexOf(word) === -1)
- fileMap.get(file).push(word);
- else fileMap.set(file, [word]);
- });
- });
+ for (j = 0; j < files.length; j++) {
+ file = files[j];
+ if (file in fileMap && fileMap[file].indexOf(word) === -1)
+ fileMap[file].push(word);
+ else
+ fileMap[file] = [word];
+ }
+ }
// now check if the files don't contain excluded terms
- const results = [];
- for (const [file, wordList] of fileMap) {
- // check if all requirements are matched
+ for (file in fileMap) {
+ var valid = true;
- // as search terms with length < 3 are discarded
- const filteredTermCount = [...searchTerms].filter(
- (term) => term.length > 2
- ).length;
+ // check if all requirements are matched
+ var filteredTermCount = // as search terms with length < 3 are discarded: ignore
+ searchterms.filter(function(term){return term.length > 2}).length
if (
- wordList.length !== searchTerms.size &&
- wordList.length !== filteredTermCount
- )
- continue;
+ fileMap[file].length != searchterms.length &&
+ fileMap[file].length != filteredTermCount
+ ) continue;
// ensure that none of the excluded terms is in the search result
- if (
- [...excludedTerms].some(
- (term) =>
- terms[term] === file ||
- titleTerms[term] === file ||
- (terms[term] || []).includes(file) ||
- (titleTerms[term] || []).includes(file)
- )
- )
- break;
+ for (i = 0; i < excluded.length; i++) {
+ if (terms[excluded[i]] == file ||
+ titleterms[excluded[i]] == file ||
+ $u.contains(terms[excluded[i]] || [], file) ||
+ $u.contains(titleterms[excluded[i]] || [], file)) {
+ valid = false;
+ break;
+ }
+ }
- // select one (max) score for the file.
- const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w]));
- // add result to the result list
- results.push([
- docNames[file],
- titles[file],
- "",
- null,
- score,
- filenames[file],
- ]);
+ // if we have still a valid result we can add it to the result list
+ if (valid) {
+ // select one (max) score for the file.
+ // for better ranking, we should calculate ranking by using words statistics like basic tf-idf...
+ var score = $u.max($u.map(fileMap[file], function(w){return scoreMap[file][w]}));
+ results.push([docnames[file], titles[file], '', null, score, filenames[file]]);
+ }
}
return results;
},
@@ -539,28 +495,34 @@ const Search = {
/**
* helper function to return a node containing the
* search summary for a given text. keywords is a list
- * of stemmed words.
+ * of stemmed words, hlwords is the list of normal, unstemmed
+ * words. the first one is used to find the occurrence, the
+ * latter for highlighting it.
*/
- makeSearchSummary: (htmlText, keywords) => {
- const text = Search.htmlToText(htmlText);
- if (text === "") return null;
-
- const textLower = text.toLowerCase();
- const actualStartPosition = [...keywords]
- .map((k) => textLower.indexOf(k.toLowerCase()))
- .filter((i) => i > -1)
- .slice(-1)[0];
- const startWithContext = Math.max(actualStartPosition - 120, 0);
-
- const top = startWithContext === 0 ? "" : "...";
- const tail = startWithContext + 240 < text.length ? "..." : "";
-
- let summary = document.createElement("p");
- summary.classList.add("context");
- summary.textContent = top + text.substr(startWithContext, 240).trim() + tail;
-
- return summary;
- },
+ makeSearchSummary : function(htmlText, keywords, hlwords) {
+ var text = Search.htmlToText(htmlText);
+ if (text == "") {
+ return null;
+ }
+ var textLower = text.toLowerCase();
+ var start = 0;
+ $.each(keywords, function() {
+ var i = textLower.indexOf(this.toLowerCase());
+ if (i > -1)
+ start = i;
+ });
+ start = Math.max(start - 120, 0);
+ var excerpt = ((start > 0) ? '...' : '') +
+ $.trim(text.substr(start, 240)) +
+ ((start + 240 - text.length) ? '...' : '');
+ var rv = $('<p class="context"></p>').text(excerpt);
+ $.each(hlwords, function() {
+ rv = rv.highlightText(this, 'highlighted');
+ });
+ return rv;
+ }
};
-_ready(Search.init);
+$(document).ready(function() {
+ Search.init();
+});
diff --git a/doc/_build/html/genindex.html b/doc/_build/html/genindex.html
index 69d0f2eac6760389230ca770364e8cd16d4fcfae..a27dbbeb52e9195d781f7d69364229fc1bdfb862 100644
--- a/doc/_build/html/genindex.html
+++ b/doc/_build/html/genindex.html
@@ -13,9 +13,7 @@
<script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
<script src="_static/jquery.js"></script>
<script src="_static/underscore.js"></script>
- <script src="_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="_static/doctools.js"></script>
- <script src="_static/sphinx_highlight.js"></script>
<script src="_static/js/theme.js"></script>
<link rel="index" title="Index" href="#" />
<link rel="search" title="Search" href="search.html" />
@@ -67,8 +65,8 @@
<div class="rst-content">
<div role="navigation" aria-label="Page navigation">
<ul class="wy-breadcrumbs">
- <li><a href="index.html" class="icon icon-home"></a></li>
- <li class="breadcrumb-item active">Index</li>
+ <li><a href="index.html" class="icon icon-home"></a> »</li>
+ <li>Index</li>
<li class="wy-breadcrumbs-aside">
</li>
</ul>
diff --git a/doc/_build/html/index.html b/doc/_build/html/index.html
index 59f8bac8780ced67ee1f4e9c68650c790b869523..3c7e568ac79098bf71843bcfd8d88e0e049bdd93 100644
--- a/doc/_build/html/index.html
+++ b/doc/_build/html/index.html
@@ -14,9 +14,7 @@
<script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
<script src="_static/jquery.js"></script>
<script src="_static/underscore.js"></script>
- <script src="_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="_static/doctools.js"></script>
- <script src="_static/sphinx_highlight.js"></script>
<script src="_static/js/theme.js"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
@@ -48,7 +46,7 @@
<li class="toctree-l1"><a class="reference internal" href="#installation">Installation</a></li>
<li class="toctree-l1"><a class="reference internal" href="#input">Input</a></li>
<li class="toctree-l1"><a class="reference internal" href="#command-line-usage-example">Command line usage example:</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="#named-arguments">Named Arguments</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#Named Arguments">Named Arguments</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="#indices-and-tables">Indices and tables</a><ul>
@@ -81,8 +79,8 @@
<div class="rst-content">
<div role="navigation" aria-label="Page navigation">
<ul class="wy-breadcrumbs">
- <li><a href="#" class="icon icon-home"></a></li>
- <li class="breadcrumb-item active">Welcome to jass_preprocessing’s documentation!</li>
+ <li><a href="#" class="icon icon-home"></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>
@@ -93,7 +91,7 @@
<div itemprop="articleBody">
<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 heading">ïƒ</a></h1>
+<h1>Welcome to jass_preprocessing’s documentation!<a class="headerlink" href="#welcome-to-jass-preprocessing-s-documentation" title="Permalink to this headline">ïƒ</a></h1>
<div class="toctree-wrapper compound">
<p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
<ul class="current">
@@ -105,7 +103,7 @@
<li class="toctree-l1"><a class="reference internal" href="#installation">Installation</a></li>
<li class="toctree-l1"><a class="reference internal" href="#input">Input</a></li>
<li class="toctree-l1"><a class="reference internal" href="#command-line-usage-example">Command line usage example:</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="#named-arguments">Named Arguments</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#Named Arguments">Named Arguments</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="#indices-and-tables">Indices and tables</a><ul>
@@ -120,22 +118,22 @@
</div>
</section>
<section id="what-is-jass-preprocessing">
-<h1>What is jass preprocessing ?<a class="headerlink" href="#what-is-jass-preprocessing" title="Permalink to this heading">ïƒ</a></h1>
-<p>Jass preprocessing is a tool that takes in input
+<h1>What is jass preprocessing ?<a class="headerlink" href="#what-is-jass-preprocessing" title="Permalink to this headline">ïƒ</a></h1>
+<p>Jass preprocessing is a command line tool that takes in input
heterogeneous GWAS summary statistics and performs standardization and quality checks to output standardized summary statistic files that can be used as input in the JASS python package and the RAISS imputation package.</p>
</section>
<section id="overview">
-<h1>Overview<a class="headerlink" href="#overview" title="Permalink to this heading">ïƒ</a></h1>
+<h1>Overview<a class="headerlink" href="#overview" title="Permalink to this headline">ïƒ</a></h1>
<p>The QC and preprocessing step goes as follow:</p>
-<ul class="simple">
-<li><p>map column from of a specific GWAS to standardize names</p></li>
+<ol class="arabic simple">
+<li><p>Map column from of a heterogeneous GWAS entry file to standardize names</p></li>
<li><p>Select GWAS SNPs that are in the input reference panel</p></li>
-<li><p>Align coded allele of the GWAS with the reference panel</p></li>
-<li><p>Infer Number of sample by SNPs if not present in input data</p></li>
-<li><p>Filter SNPs with a small sample size</p></li>
-<li><p>Normalize the effect size by sample size to have Z-scores</p></li>
+<li><p>Align coded allele of the GWASs data with the reference panel</p></li>
+<li><p>Infer the sample size by SNPs if not present in input data (from MAF, standard deviation and genetic effect)</p></li>
+<li><p>Filter SNPs with an heterogeneous sample size (as JASS and RAISS packages assume sample size to be constant across SNPs)</p></li>
+<li><p>Normalize the effect size to Z-scores</p></li>
<li><p>Save the output by chromosome as the following example:</p></li>
-</ul>
+</ol>
<table class="docutils align-default">
<colgroup>
<col style="width: 28%" />
@@ -162,18 +160,20 @@ heterogeneous GWAS summary statistics and performs standardization and quality c
</tbody>
</table>
<ul class="simple">
-<li><p>(Optional) Save the output to one file with a chromosome column</p></li>
+<li><p>(Optional step) Save the output to one file with a chromosome column</p></li>
</ul>
-<p>(input format needed to perform LD-score)</p>
+<p>(input format needed to perform LD-score). The additional output correspond to: P, the p-value; N_effective (Effective sample size estimated/retrieved from the data).
+Effective sample size refers to the total sample size for continuous trait and to 1 / ( 1/Ncases + 1/Ncontrol ) for binary traits.</p>
<table class="docutils align-default">
<colgroup>
-<col style="width: 16%" />
-<col style="width: 25%" />
-<col style="width: 18%" />
-<col style="width: 9%" />
-<col style="width: 9%" />
-<col style="width: 11%" />
<col style="width: 11%" />
+<col style="width: 18%" />
+<col style="width: 13%" />
+<col style="width: 6%" />
+<col style="width: 6%" />
+<col style="width: 8%" />
+<col style="width: 8%" />
+<col style="width: 29%" />
</colgroup>
<tbody>
<tr class="row-odd"><td><p>chrom</p></td>
@@ -183,6 +183,7 @@ heterogeneous GWAS summary statistics and performs standardization and quality c
<td><p>A1</p></td>
<td><p>Z</p></td>
<td><p>P</p></td>
+<td><p>N_effective</p></td>
</tr>
<tr class="row-even"><td><p>1</p></td>
<td><p>rs4075116</p></td>
@@ -191,24 +192,28 @@ heterogeneous GWAS summary statistics and performs standardization and quality c
<td><p>T</p></td>
<td><p>0.3</p></td>
<td><p>0.76</p></td>
+<td><p>10220.98</p></td>
</tr>
</tbody>
</table>
</section>
<section id="installation">
-<h1>Installation<a class="headerlink" href="#installation" title="Permalink to this heading">ïƒ</a></h1>
+<h1>Installation<a class="headerlink" href="#installation" title="Permalink to this headline">ïƒ</a></h1>
<p>In a terminal, execute the following lines:</p>
<div class="highlight-shell notranslate"><div class="highlight"><pre><span></span>pip3 install git+https://gitlab.pasteur.fr/statistical-genetics/JASS_Pre-processing
</pre></div>
</div>
</section>
<section id="input">
-<h1>Input<a class="headerlink" href="#input" title="Permalink to this heading">ïƒ</a></h1>
+<h1>Input<a class="headerlink" href="#input" title="Permalink to this headline">ïƒ</a></h1>
<ul class="simple">
-<li><p>A reference panel (1000 genome format). The user is expected to provide a reference panel</p></li>
+<li><p><strong>A reference panel</strong> to the format below. The user is expected to provide a reference panel</p></li>
</ul>
<blockquote>
-<div><p>in tsv format with the following columns in the following order, without header:</p>
+<div><dl class="simple">
+<dt>in tsv format with the following columns in the following order (chromosome, rsID, Minor Allele</dt><dd><p>Frequency, Position, reference, Alternative allele), <strong>without header</strong>.</p>
+</dd>
+</dl>
</div></blockquote>
<table class="docutils align-default">
<colgroup>
@@ -220,37 +225,30 @@ heterogeneous GWAS summary statistics and performs standardization and quality c
<col style="width: 12%" />
</colgroup>
<thead>
-<tr class="row-odd"><th class="head"><p>chr</p></th>
-<th class="head"><p>snp_id</p></th>
-<th class="head"><p>MAF</p></th>
-<th class="head"><p>pos</p></th>
-<th class="head"><p>ref</p></th>
-<th class="head"><p>alt</p></th>
+<tr class="row-odd"><th class="head"><p>1</p></th>
+<th class="head"><p>rs62635286</p></th>
+<th class="head"><p>0.0970447</p></th>
+<th class="head"><p>13116</p></th>
+<th class="head"><p>T</p></th>
+<th class="head"><p>G</p></th>
</tr>
</thead>
<tbody>
<tr class="row-even"><td><p>1</p></td>
-<td><p>rs62635286</p></td>
-<td><p>0.0970447</p></td>
-<td><p>13116</p></td>
-<td><p>T</p></td>
-<td><p>G</p></td>
-</tr>
-<tr class="row-odd"><td><p>1</p></td>
<td><p>rs63125786</p></td>
<td><p>0.0970447</p></td>
<td><p>15116</p></td>
<td><p>T</p></td>
<td><p>A</p></td>
</tr>
-<tr class="row-even"><td><p>1</p></td>
+<tr class="row-odd"><td><p>1</p></td>
<td><p>rs5686</p></td>
<td><p>0.1970447</p></td>
<td><p>17116</p></td>
<td><p>A</p></td>
<td><p>G</p></td>
</tr>
-<tr class="row-odd"><td><p>1</p></td>
+<tr class="row-even"><td><p>1</p></td>
<td><p>rs892586</p></td>
<td><p>0.7670447</p></td>
<td><p>23116</p></td>
@@ -260,15 +258,11 @@ heterogeneous GWAS summary statistics and performs standardization and quality c
</tbody>
</table>
<ul class="simple">
-<li><p>Folder containing all raw gwas data : (all chromosomes in one file) (minimal conditions?? tab separated?)</p></li>
-<li><p>a list containing the name of GWAS file to the string format.</p></li>
-<li><p>A descriptor csv files that will described each GWAS summary statistic files:</p>
-<ul>
-<li><p>a header</p></li>
-<li><p>1 line per study</p></li>
-<li><p>the fields are:</p></li>
-</ul>
-</li>
+<li><p>The <strong>GWAS Folder</strong> containing all raw gwas data (correspond to the –gwas-info command line parameter): all chromosomes in one file, compressed or uncompressed</p></li>
+<li><p>A descriptor csv files (see example below and <a class="reference external" href="https://gitlab.pasteur.fr/statistical-genetics/jass_suite_pipeline/-/blob/master/input_files/Data_test_EAS.csv">here</a>)that will described each GWAS summary statistic files (correspond to the –input-folder command line parameter):
+* a header
+* 1 line per study
+* the fields categories are:</p></li>
</ul>
<table class="docutils align-default">
<colgroup>
@@ -285,18 +279,46 @@ heterogeneous GWAS summary statistics and performs standardization and quality c
<td><p>filename</p></td>
</tr>
<tr class="row-odd"><td><p>study info fields</p></td>
-<td><p>Consortium,Outcome,fullName,type,Nsample,Ncase,Ncontrol,Nsnp</p></td>
+<td><p>Consortium,Outcome,fullName,Nsample,Ncase,Ncontrol,Nsnp</p></td>
</tr>
<tr class="row-even"><td><p>names of the header in the GWAS file</p></td>
<td><p>snpid,a1,a2,freq,pval,n,z,OR,se,code,imp,ncas,ncont</p></td>
</tr>
</tbody>
</table>
-<p>Note that the combination of Consortium and outcome must be unique because it will be used as an index in the cleaning process.</p>
-<p>Here is an example of descriptor field, the field irrelevant (for example odd ratio for continuous trait) for the study must be filled with na.
+<p><strong>Study field definition</strong>:</p>
+<ul class="simple">
+<li><p>filename: gwas summary statistic name as it appear in the <strong>GWAS folder</strong></p></li>
+<li><p>Consortium : the Consortium of the study (can also be the category of the trait) in <strong>upper case and without _ characters</strong></p></li>
+<li><p>Outcome: a short tag for the Outcome of the study in <strong>upper case and without _ characters</strong></p></li>
+<li><p>FullName: full description of the trait (for your own information not used in the cleaning process)</p></li>
+<li><p>Nsample: Number of sample in the study</p></li>
+<li><p>Ncase: Number of cases in the study (left empty if trait is continuous)</p></li>
+<li><p>Ncontrol: Number of control in the study (left empty if trait is continuous)</p></li>
+</ul>
+<p><strong>Field corresping to column names in the summary statistic</strong></p>
+<ul class="simple">
+<li><p>snpid: name of the column storing rsid in the gwas file</p></li>
+<li><p>POS: name of the column storing the position in the gwas file</p></li>
+<li><p>CHR: name of the column storing the chromosome in the gwas file</p></li>
+<li><p>a1: effect allele</p></li>
+<li><p>a2: Other allele</p></li>
+<li><p>freq: name of the column storing the minor allele frequence in the gwas file</p></li>
+<li><p>pval: name of the column storing the pvalue in the gwas file</p></li>
+<li><p>n: name of the column storing the sample size by variants (optional, will be inferred from the MAF, genetic effect and standard deviation if absent)</p></li>
+<li><p>z: name of the column storing the genetic effect (beta) in the gwas file</p></li>
+<li><p>index-type: precise the type of index</p></li>
+<li><p>imputation_quality: (Optional) column containing individual-based imputation quality. Will be used to filter low quality imputation data from GWASs if the option –imputation-quality-treshold is used</p></li>
+</ul>
+<div class="admonition warning">
+<p class="admonition-title">Warning</p>
+<p>Note that the concatenation of Consortium and Outcome must be <strong>unique</strong> because as it will be used as an index in the cleaning process.
+Both Outcome and Consortium must be in <strong>uppercase and with no _ characters</strong></p>
+</div>
+<p>Here is an example of descriptor field (downloadable example <a class="reference external" href="https://gitlab.pasteur.fr/statistical-genetics/jass_suite_pipeline/-/blob/master/input_files/Data_test_EAS.csv">here</a>), the field irrelevant (for example odd ratio for continuous trait) for the study must be filled with na or left empty.
Some fields are optional like the imputation_quality. If not used they can be filled with na.</p>
-<table class="docutils align-default" id="id1">
-<caption><span class="caption-text">GWAS information table</span><a class="headerlink" href="#id1" title="Permalink to this table">ïƒ</a></caption>
+<table class="docutils align-default" id="id2">
+<caption><span class="caption-text">GWAS information table</span><a class="headerlink" href="#id2" title="Permalink to this table">ïƒ</a></caption>
<colgroup>
<col style="width: 4%" />
<col style="width: 4%" />
@@ -322,18 +344,20 @@ Some fields are optional like the imputation_quality. If not used they can be fi
<col style="width: 4%" />
<col style="width: 4%" />
<col style="width: 4%" />
+<col style="width: 4%" />
</colgroup>
<thead>
<tr class="row-odd"><th class="head"><p>filename</p></th>
-<th class="head"><p>consortia</p></th>
-<th class="head"><p>outcome</p></th>
-<th class="head"><p>fullName</p></th>
-<th class="head"><p>type</p></th>
+<th class="head"><p>Consortium</p></th>
+<th class="head"><p>Outcome</p></th>
+<th class="head"><p>FullName</p></th>
+<th class="head"><p>Type</p></th>
<th class="head"><p>Nsample</p></th>
<th class="head"><p>Ncase</p></th>
<th class="head"><p>Ncontrol</p></th>
<th class="head"><p>Nsnp</p></th>
<th class="head"><p>snpid</p></th>
+<th class="head"><p>POS</p></th>
<th class="head"><p>a1</p></th>
<th class="head"><p>a2</p></th>
<th class="head"><p>freq</p></th>
@@ -361,6 +385,7 @@ Some fields are optional like the imputation_quality. If not used they can be fi
<td><p>na</p></td>
<td><p>2550858</p></td>
<td><p>MarkerName</p></td>
+<td><p>position</p></td>
<td><p>Allele1</p></td>
<td><p>Allele2</p></td>
<td><p>Freq.Allele1.HapMapCEU</p></td>
@@ -374,22 +399,21 @@ Some fields are optional like the imputation_quality. If not used they can be fi
<td><p>na</p></td>
<td><p>na</p></td>
<td><p>imputationInfo</p></td>
-<td><p>rsID</p></td>
+<td><p>rs-number</p></td>
</tr>
</tbody>
</table>
</section>
<section id="command-line-usage-example">
-<h1>Command line usage example:<a class="headerlink" href="#command-line-usage-example" title="Permalink to this heading">ïƒ</a></h1>
+<h1>Command line usage example:<a class="headerlink" href="#command-line-usage-example" title="Permalink to this headline">ïƒ</a></h1>
<p>It is possible to launch the complete preprocessing (all steps described in section Overview section) 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">jass_preprocessing</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">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">path</span> <span class="n">REF_PATH</span> <span class="o">--</span><span class="nb">input</span><span class="o">-</span><span class="n">folder</span> <span class="n">INPUT_FOLDER</span> <span class="o">--</span><span class="n">diagnostic</span><span class="o">-</span><span class="n">folder</span> <span class="n">DIAGNOSTIC_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> <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="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">minimum</span><span class="o">-</span><span class="n">MAF</span> <span class="n">MINIMUM_MAF</span><span class="p">]</span>
- <span class="p">[</span><span class="o">--</span><span class="n">mask</span><span class="o">-</span><span class="n">MHC</span> <span class="n">MASK_MHC</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">additional</span><span class="o">-</span><span class="n">masked</span><span class="o">-</span><span class="n">region</span> <span class="n">ADDITIONAL_MASKED_REGION</span><span class="p">]</span>
- <span class="p">[</span><span class="o">--</span><span class="n">imputation</span><span class="o">-</span><span class="n">quality</span><span class="o">-</span><span class="n">treshold</span> <span class="n">IMPUTATION_QUALITY_TRESHOLD</span><span class="p">]</span>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">usage</span><span class="p">:</span> <span class="n">jass_preprocessing</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">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">path</span> <span class="n">REF_PATH</span> <span class="o">--</span><span class="nb">input</span><span class="o">-</span><span class="n">folder</span> <span class="n">INPUT_FOLDER</span> <span class="o">--</span><span class="n">diagnostic</span><span class="o">-</span><span class="n">folder</span> <span class="n">DIAGNOSTIC_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> <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="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">minimum</span><span class="o">-</span><span class="n">MAF</span> <span class="n">MINIMUM_MAF</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">mask</span><span class="o">-</span><span class="n">MHC</span> <span class="n">MASK_MHC</span><span class="p">]</span>
+ <span class="p">[</span><span class="o">--</span><span class="n">additional</span><span class="o">-</span><span class="n">masked</span><span class="o">-</span><span class="n">region</span> <span class="n">ADDITIONAL_MASKED_REGION</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">imputation</span><span class="o">-</span><span class="n">quality</span><span class="o">-</span><span class="n">treshold</span> <span class="n">IMPUTATION_QUALITY_TRESHOLD</span><span class="p">]</span>
</pre></div>
</div>
-<section id="named-arguments">
-<h2>Named Arguments<a class="headerlink" href="#named-arguments" title="Permalink to this heading">ïƒ</a></h2>
+<section id="Named Arguments">
+<h2>Named Arguments<a class="headerlink" href="#Named Arguments" title="Permalink to this headline">ïƒ</a></h2>
<dl class="option-list">
<dt><kbd>--gwas-info</kbd></dt>
<dd><p>Path to the file describing the format of the individual GWASs files with correct header</p>
@@ -433,12 +457,12 @@ Some fields are optional like the imputation_quality. If not used they can be fi
</section>
</section>
<section id="indices-and-tables">
-<h1>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Permalink to this heading">ïƒ</a></h1>
+<h1>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Permalink to this headline">ïƒ</a></h1>
<ul class="simple">
<li><p><a class="reference internal" href="genindex.html"><span class="std std-ref">Index</span></a></p></li>
<li><p><a class="reference internal" href="py-modindex.html"><span class="std std-ref">Module Index</span></a></p></li>
</ul>
-<span class="target" id="module-jass_preprocessing"></span><table class="autosummary longtable docutils align-default">
+<span class="target" id="module-jass_preprocessing"></span><table class="longtable docutils align-default">
<colgroup>
<col style="width: 10%" />
<col style="width: 90%" />
diff --git a/doc/_build/html/py-modindex.html b/doc/_build/html/py-modindex.html
index 418283928ddb552d7109f15d750a6a1076e0598e..8ff279940ecf83106b22f141bb775117a8f6fc85 100644
--- a/doc/_build/html/py-modindex.html
+++ b/doc/_build/html/py-modindex.html
@@ -13,9 +13,7 @@
<script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
<script src="_static/jquery.js"></script>
<script src="_static/underscore.js"></script>
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<script src="_static/doctools.js"></script>
- <script src="_static/sphinx_highlight.js"></script>
<script src="_static/js/theme.js"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
@@ -70,8 +68,8 @@
<div class="rst-content">
<div role="navigation" aria-label="Page navigation">
<ul class="wy-breadcrumbs">
- <li><a href="index.html" class="icon icon-home"></a></li>
- <li class="breadcrumb-item active">Python Module Index</li>
+ <li><a href="index.html" class="icon icon-home"></a> »</li>
+ <li>Python Module Index</li>
<li class="wy-breadcrumbs-aside">
</li>
</ul>
diff --git a/doc/_build/html/search.html b/doc/_build/html/search.html
index 626b0ed47ba1e008156e8f814872017d83e52206..502fda6a51ef2530b5de4cdfd42a15666fabe13a 100644
--- a/doc/_build/html/search.html
+++ b/doc/_build/html/search.html
@@ -14,9 +14,7 @@
<script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
<script src="_static/jquery.js"></script>
<script src="_static/underscore.js"></script>
- <script src="_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="_static/doctools.js"></script>
- <script src="_static/sphinx_highlight.js"></script>
<script src="_static/js/theme.js"></script>
<script src="_static/searchtools.js"></script>
<script src="_static/language_data.js"></script>
@@ -70,8 +68,8 @@
<div class="rst-content">
<div role="navigation" aria-label="Page navigation">
<ul class="wy-breadcrumbs">
- <li><a href="index.html" class="icon icon-home"></a></li>
- <li class="breadcrumb-item active">Search</li>
+ <li><a href="index.html" class="icon icon-home"></a> »</li>
+ <li>Search</li>
<li class="wy-breadcrumbs-aside">
</li>
</ul>
diff --git a/doc/_build/html/searchindex.js b/doc/_build/html/searchindex.js
index 3770a44097f148b559bf5d49d656ddef185f55bc..017421a063fd292e3fb7a80cd1b56bf338fbcd50 100644
--- a/doc/_build/html/searchindex.js
+++ b/doc/_build/html/searchindex.js
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diff --git a/doc/source/index.rst b/doc/source/index.rst
index c21c5b3b87f078b80aeaaeaed8286b25fe1a3306..297fd70bed6913d9af16cbaacb6d6067651f7a6b 100644
--- a/doc/source/index.rst
+++ b/doc/source/index.rst
@@ -14,7 +14,7 @@ Welcome to jass_preprocessing's documentation!
What is jass preprocessing ?
============================
-Jass preprocessing is a tool that takes in input
+Jass preprocessing is a command line tool that takes in input
heterogeneous GWAS summary statistics and performs standardization and quality checks to output standardized summary statistic files that can be used as input in the JASS python package and the RAISS imputation package.
@@ -22,13 +22,13 @@ Overview
========
The QC and preprocessing step goes as follow:
-* Map column from of a specific GWAS to standardize names
-* 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:
+#. Map column from of a heterogeneous GWAS entry file to standardize names
+#. Select GWAS SNPs that are in the input reference panel
+#. Align coded allele of the GWASs data with the reference panel
+#. Infer the sample size by SNPs if not present in input data (from MAF, standard deviation and genetic effect)
+#. Filter SNPs with an heterogeneous sample size (as JASS and RAISS packages assume sample size to be constant across SNPs)
+#. Normalize the effect size to Z-scores
+#. Save the output by chromosome as the following example:
+----------+-------+------+-----+--------+
| rsID | pos | A0 | A1 | Z |
@@ -36,14 +36,15 @@ The QC and preprocessing step goes as follow:
| rs6548219| 30762 | A | G | -1.133 |
+----------+-------+------+-----+--------+
-* (Optional) Save the output to one file with a chromosome column
-(input format needed to perform LD-score)
+* (Optional step) Save the output to one file with a chromosome column
+(input format needed to perform LD-score). The additional output correspond to: P, the p-value; N_effective (Effective sample size estimated/retrieved from the data).
+Effective sample size refers to the total sample size for continuous trait and to 1 / ( 1/Ncases + 1/Ncontrol ) for binary traits.
-+-------+-----------+--------+----+----+-----+-----+
-| chrom | rsID | pos | A0 | A1 | Z | P |
-+-------+-----------+--------+----+----+-----+-----+
-| 1 | rs4075116 |1003629 | C | T | 0.3 | 0.76|
-+-------+-----------+--------+----+----+-----+-----+
++-------+-----------+--------+----+----+-----+-----+------------------+
+| chrom | rsID | pos | A0 | A1 | Z | P | N_effective |
++-------+-----------+--------+----+----+-----+-----+------------------+
+| 1 | rs4075116 |1003629 | C | T | 0.3 | 0.76| 10220.98 |
++-------+-----------+--------+----+----+-----+-----+------------------+
Installation
@@ -84,20 +85,23 @@ Input
+===========================================+===============================================================+
| path to the data | filename |
+-------------------------------------------+---------------------------------------------------------------+
-| study info fields | Consortium,Outcome,fullName,Nsample,Ncase,Ncontrol,Nsnp |
+| study info fields | Consortium,Outcome,fullName,Nsample,Ncase,Ncontrol,Nsnp |
+-------------------------------------------+---------------------------------------------------------------+
| names of the header in the GWAS file | snpid,a1,a2,freq,pval,n,z,OR,se,code,imp,ncas,ncont |
+-------------------------------------------+---------------------------------------------------------------+
**Study field definition**:
+
* filename: gwas summary statistic name as it appear in the **GWAS folder**
-* Consortium : the Consortium of the study (can also be the category of the trait) in upper case and without _ characters
-* Outcome: a short tag for the Outcome of the study in upper case and without _ characters
+* Consortium : the Consortium of the study (can also be the category of the trait) in **upper case and without _ characters**
+* Outcome: a short tag for the Outcome of the study in **upper case and without _ characters**
* FullName: full description of the trait (for your own information not used in the cleaning process)
* Nsample: Number of sample in the study
* Ncase: Number of cases in the study (left empty if trait is continuous)
* Ncontrol: Number of control in the study (left empty if trait is continuous)
+
**Field corresping to column names in the summary statistic**
+
* snpid: name of the column storing rsid in the gwas file
* POS: name of the column storing the position in the gwas file
* CHR: name of the column storing the chromosome in the gwas file
@@ -108,19 +112,20 @@ Input
* n: name of the column storing the sample size by variants (optional, will be inferred from the MAF, genetic effect and standard deviation if absent)
* z: name of the column storing the genetic effect (beta) in the gwas file
* index-type: precise the type of index
-
+* imputation_quality: (Optional) column containing individual-based imputation quality. Will be used to filter low quality imputation data from GWASs if the option --imputation-quality-treshold is used
.. warning::
- Note that the combination of Consortium and outcome must be unique because as it will be used as an index in the cleaning process.
+ Note that the concatenation of Consortium and Outcome must be **unique** because as it will be used as an index in the cleaning process.
+ Both Outcome and Consortium must be in **uppercase and with no _ characters**
-Here is an example of descriptor field, the field irrelevant (for example odd ratio for continuous trait) for the study must be filled with na or left empty.
-Some fields are optional like the imputation_quality. If not used they can be filled with na.
+Here is an example of descriptor field (downloadable example `here <https://gitlab.pasteur.fr/statistical-genetics/jass_suite_pipeline/-/blob/master/input_files/Data_test_EAS.csv>`_), the field irrelevant (for example odd ratio for continuous trait) for the study must be filled with na or left empty.
+Some fields are optional like the imputation_quality. If not used they can be filled with na.
.. csv-table:: GWAS information table
:header-rows: 1
- "filename","consortia","outcome","fullName","type","Nsample","Ncase","Ncontrol","Nsnp","snpid","a1","a2","freq","pval","n","z","OR","se","code","imp","ncas","ncont","imputation_quality","index_type"
- "GIANT_HEIGHT_Wood_et_al.txt","GIANT","HEIGHT","Height","Anthropometry",253288, na, na, 2550858, "MarkerName", "Allele1", "Allele2", "Freq.Allele1.HapMapCEU","p","N","b",na,"SE",na,na,na,na, "imputationInfo","rs-number"
+ "filename","Consortium","Outcome","FullName","Type","Nsample","Ncase","Ncontrol","Nsnp","snpid", "POS", "a1","a2","freq","pval","n","z","OR","se","code","imp","ncas","ncont","imputation_quality","index_type"
+ "GIANT_HEIGHT_Wood_et_al.txt","GIANT","HEIGHT","Height","Anthropometry",253288, na, na, 2550858, "MarkerName", "position","Allele1", "Allele2", "Freq.Allele1.HapMapCEU","p","N","b",na,"SE",na,na,na,na, "imputationInfo","rs-number"
Command line usage example: