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# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
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tags: 645f666f9bcd5a90fca523b33c5a78b7
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@@ -67,135 +36,81 @@
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-<li><a class="reference internal" href="#">jass_preprocessing package</a><ul>
-<li><a class="reference internal" href="#submodules">Submodules</a></li>
-<li><a class="reference internal" href="#module-jass_preprocessing.compute_score">jass_preprocessing.compute_score module</a></li>
-<li><a class="reference internal" href="#module-jass_preprocessing.dna_utils">jass_preprocessing.dna_utils module</a></li>
-<li><a class="reference internal" href="#module-jass_preprocessing.map_gwas">jass_preprocessing.map_gwas module</a></li>
-<li><a class="reference internal" href="#module-jass_preprocessing.map_reference">jass_preprocessing.map_reference module</a></li>
-<li><a class="reference internal" href="#module-jass_preprocessing.save_output">jass_preprocessing.save_output module</a></li>
-<li><a class="reference internal" href="#module-jass_preprocessing">Module contents</a></li>
+ </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
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+<li class="toctree-l1"><a class="reference internal" href="jass_preprocessing.map_reference.html">jass_preprocessing.map_reference</a></li>
+<li class="toctree-l1"><a class="reference internal" href="jass_preprocessing.compute_score.html">jass_preprocessing.compute_score</a></li>
+<li class="toctree-l1"><a class="reference internal" href="jass_preprocessing.save_output.html">jass_preprocessing.save_output</a></li>
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-
- <div class="section" id="jass-preprocessing-package">
-<h1>jass_preprocessing package<a class="headerlink" href="#jass-preprocessing-package" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="submodules">
-<h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this headline">¶</a></h2>
-</div>
-<div class="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 headline">¶</a></h2>
-<dl class="function">
-<dt id="jass_preprocessing.compute_score.compute_sample_size">
-<code class="sig-prename descclassname">jass_preprocessing.compute_score.</code><code class="sig-name descname">compute_sample_size</code><span class="sig-paren">(</span><em class="sig-param">mgwas</em>, <em class="sig-param">diagnostic_folder</em>, <em class="sig-param">trait</em>, <em class="sig-param">perSS=0.7</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/jass_preprocessing/compute_score.html#compute_sample_size"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#jass_preprocessing.compute_score.compute_sample_size" title="Permalink to this definition">¶</a></dt>
+
+ <section id="jass-preprocessing-package">
+<h1>jass_preprocessing package<a class="headerlink" href="#jass-preprocessing-package" title="Permalink to this heading">ïƒ</a></h1>
+<section id="submodules">
+<h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this heading">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>
+<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>
<dd></dd></dl>
-<dl class="function">
-<dt id="jass_preprocessing.compute_score.compute_z_score">
-<code class="sig-prename descclassname">jass_preprocessing.compute_score.</code><code class="sig-name descname">compute_z_score</code><span class="sig-paren">(</span><em class="sig-param">mgwas</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/jass_preprocessing/compute_score.html#compute_z_score"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#jass_preprocessing.compute_score.compute_z_score" title="Permalink to this definition">¶</a></dt>
+<dl class="py function">
+<dt class="sig sig-object py" id="jass_preprocessing.compute_score.compute_z_score">
+<span class="sig-prename descclassname"><span class="pre">jass_preprocessing.compute_score.</span></span><span class="sig-name descname"><span class="pre">compute_z_score</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">mgwas</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/jass_preprocessing/compute_score.html#compute_z_score"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#jass_preprocessing.compute_score.compute_z_score" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Compute zscore value and sign1
add the corresponding column to the mgwas dataframe</p>
</dd></dl>
-</div>
-<div class="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 headline">¶</a></h2>
+</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>
<p>Few fonction to to compute DNA complement</p>
-<dl class="function">
-<dt id="jass_preprocessing.dna_utils.dna_complement">
-<code class="sig-prename descclassname">jass_preprocessing.dna_utils.</code><code class="sig-name descname">dna_complement</code><span class="sig-paren">(</span><em class="sig-param">input</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/jass_preprocessing/dna_utils.html#dna_complement"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#jass_preprocessing.dna_utils.dna_complement" title="Permalink to this definition">¶</a></dt>
+<dl class="py function">
+<dt class="sig sig-object py" id="jass_preprocessing.dna_utils.dna_complement">
+<span class="sig-prename descclassname"><span class="pre">jass_preprocessing.dna_utils.</span></span><span class="sig-name descname"><span class="pre">dna_complement</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">input</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/jass_preprocessing/dna_utils.html#dna_complement"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#jass_preprocessing.dna_utils.dna_complement" title="Permalink to this definition">ïƒ</a></dt>
<dd></dd></dl>
-<dl class="function">
-<dt id="jass_preprocessing.dna_utils.dna_complement_base">
-<code class="sig-prename descclassname">jass_preprocessing.dna_utils.</code><code class="sig-name descname">dna_complement_base</code><span class="sig-paren">(</span><em class="sig-param">inputbase</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/jass_preprocessing/dna_utils.html#dna_complement_base"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#jass_preprocessing.dna_utils.dna_complement_base" title="Permalink to this definition">¶</a></dt>
+<dl class="py function">
+<dt class="sig sig-object py" id="jass_preprocessing.dna_utils.dna_complement_base">
+<span class="sig-prename descclassname"><span class="pre">jass_preprocessing.dna_utils.</span></span><span class="sig-name descname"><span class="pre">dna_complement_base</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">inputbase</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/jass_preprocessing/dna_utils.html#dna_complement_base"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#jass_preprocessing.dna_utils.dna_complement_base" title="Permalink to this definition">ïƒ</a></dt>
<dd></dd></dl>
-</div>
-<div class="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 headline">¶</a></h2>
+</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>
<p>Map GWAS</p>
<p>A set of functions to find GWAS files in subfolder and
to map columns</p>
-<dl class="function">
-<dt id="jass_preprocessing.map_gwas.convert_missing_values">
-<code class="sig-prename descclassname">jass_preprocessing.map_gwas.</code><code class="sig-name descname">convert_missing_values</code><span class="sig-paren">(</span><em class="sig-param">df</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/jass_preprocessing/map_gwas.html#convert_missing_values"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#jass_preprocessing.map_gwas.convert_missing_values" title="Permalink to this definition">¶</a></dt>
+<dl class="py function">
+<dt class="sig sig-object py" id="jass_preprocessing.map_gwas.convert_missing_values">
+<span class="sig-prename descclassname"><span class="pre">jass_preprocessing.map_gwas.</span></span><span class="sig-name descname"><span class="pre">convert_missing_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">df</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/jass_preprocessing/map_gwas.html#convert_missing_values"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#jass_preprocessing.map_gwas.convert_missing_values" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Convert all missing value strings to a standart np.nan value</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
@@ -207,9 +122,9 @@ to map columns</p>
</dl>
</dd></dl>
-<dl class="function">
-<dt id="jass_preprocessing.map_gwas.gwas_internal_link">
-<code class="sig-prename descclassname">jass_preprocessing.map_gwas.</code><code class="sig-name descname">gwas_internal_link</code><span class="sig-paren">(</span><em class="sig-param">GWAS_table</em>, <em class="sig-param">GWAS_path</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/jass_preprocessing/map_gwas.html#gwas_internal_link"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#jass_preprocessing.map_gwas.gwas_internal_link" title="Permalink to this definition">¶</a></dt>
+<dl class="py function">
+<dt class="sig sig-object py" id="jass_preprocessing.map_gwas.gwas_internal_link">
+<span class="sig-prename descclassname"><span class="pre">jass_preprocessing.map_gwas.</span></span><span class="sig-name descname"><span class="pre">gwas_internal_link</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">GWAS_table</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">GWAS_path</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/jass_preprocessing/map_gwas.html#gwas_internal_link"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#jass_preprocessing.map_gwas.gwas_internal_link" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Walk the GWAS path to find the GWAS tables</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
@@ -225,9 +140,9 @@ and one column containing the complete path to the file</p>
</dl>
</dd></dl>
-<dl class="function">
-<dt id="jass_preprocessing.map_gwas.map_columns_position">
-<code class="sig-prename descclassname">jass_preprocessing.map_gwas.</code><code class="sig-name descname">map_columns_position</code><span class="sig-paren">(</span><em class="sig-param">gwas_internal_link</em>, <em class="sig-param">column_dict</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/jass_preprocessing/map_gwas.html#map_columns_position"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#jass_preprocessing.map_gwas.map_columns_position" title="Permalink to this definition">¶</a></dt>
+<dl class="py function">
+<dt class="sig sig-object py" id="jass_preprocessing.map_gwas.map_columns_position">
+<span class="sig-prename descclassname"><span class="pre">jass_preprocessing.map_gwas.</span></span><span class="sig-name descname"><span class="pre">map_columns_position</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">gwas_internal_link</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">column_dict</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/jass_preprocessing/map_gwas.html#map_columns_position"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#jass_preprocessing.map_gwas.map_columns_position" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Find column position for each specific Gwas</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
@@ -242,9 +157,9 @@ and one column containing the complete path to the file</p>
</dl>
</dd></dl>
-<dl class="function">
-<dt id="jass_preprocessing.map_gwas.read_gwas">
-<code class="sig-prename descclassname">jass_preprocessing.map_gwas.</code><code class="sig-name descname">read_gwas</code><span class="sig-paren">(</span><em class="sig-param">gwas_internal_link</em>, <em class="sig-param">column_map</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/jass_preprocessing/map_gwas.html#read_gwas"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#jass_preprocessing.map_gwas.read_gwas" title="Permalink to this definition">¶</a></dt>
+<dl class="py function">
+<dt class="sig sig-object py" id="jass_preprocessing.map_gwas.read_gwas">
+<span class="sig-prename descclassname"><span class="pre">jass_preprocessing.map_gwas.</span></span><span class="sig-name descname"><span class="pre">read_gwas</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">gwas_internal_link</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">column_map</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">imputation_treshold</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/jass_preprocessing/map_gwas.html#read_gwas"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#jass_preprocessing.map_gwas.read_gwas" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Read gwas raw data, fetch columns thanks to position stored in
column_map and rename columns according to column_map.index</p>
<dl class="field-list simple">
@@ -252,7 +167,7 @@ column_map and rename columns according to column_map.index</p>
<dd class="field-odd"><ul class="simple">
<li><p><strong>gwas_internal_link</strong> (<em>str</em>) – GWAS data as a dataframe</p></li>
<li><p><strong>column_map</strong> (<em>pandas Series</em>) – Series containing the position of column in</p></li>
-<li><p><strong>raw data</strong> (<em>the</em>) – </p></li>
+<li><p><strong>data</strong> (<em>the raw</em>) – </p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
@@ -261,9 +176,9 @@ column_map and rename columns according to column_map.index</p>
</dl>
</dd></dl>
-<dl class="function">
-<dt id="jass_preprocessing.map_gwas.walkfs">
-<code class="sig-prename descclassname">jass_preprocessing.map_gwas.</code><code class="sig-name descname">walkfs</code><span class="sig-paren">(</span><em class="sig-param">startdir</em>, <em class="sig-param">findfile</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/jass_preprocessing/map_gwas.html#walkfs"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#jass_preprocessing.map_gwas.walkfs" title="Permalink to this definition">¶</a></dt>
+<dl class="py function">
+<dt class="sig sig-object py" id="jass_preprocessing.map_gwas.walkfs">
+<span class="sig-prename descclassname"><span class="pre">jass_preprocessing.map_gwas.</span></span><span class="sig-name descname"><span class="pre">walkfs</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">startdir</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">findfile</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/jass_preprocessing/map_gwas.html#walkfs"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#jass_preprocessing.map_gwas.walkfs" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Go through the folder and subfolder to find the specified file</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
@@ -275,13 +190,13 @@ column_map and rename columns according to column_map.index</p>
</dl>
</dd></dl>
-</div>
-<div class="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 headline">¶</a></h2>
+</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>
<p>Module of function</p>
-<dl class="function">
-<dt id="jass_preprocessing.map_reference.compute_is_aligned">
-<code class="sig-prename descclassname">jass_preprocessing.map_reference.</code><code class="sig-name descname">compute_is_aligned</code><span class="sig-paren">(</span><em class="sig-param">mgwas</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/jass_preprocessing/map_reference.html#compute_is_aligned"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#jass_preprocessing.map_reference.compute_is_aligned" title="Permalink to this definition">¶</a></dt>
+<dl class="py function">
+<dt class="sig sig-object py" id="jass_preprocessing.map_reference.compute_is_aligned">
+<span class="sig-prename descclassname"><span class="pre">jass_preprocessing.map_reference.</span></span><span class="sig-name descname"><span class="pre">compute_is_aligned</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">mgwas</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/jass_preprocessing/map_reference.html#compute_is_aligned"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#jass_preprocessing.map_reference.compute_is_aligned" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Check if the reference panel and the GWAS data have the same reference
allele. return a boolean vector.
The function should be the complement of “is_flipped†but we still compute
@@ -289,9 +204,9 @@ the two function to eventually detect weird cases (more than two alleles for
instance)</p>
</dd></dl>
-<dl class="function">
-<dt id="jass_preprocessing.map_reference.compute_is_flipped">
-<code class="sig-prename descclassname">jass_preprocessing.map_reference.</code><code class="sig-name descname">compute_is_flipped</code><span class="sig-paren">(</span><em class="sig-param">mgwas</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/jass_preprocessing/map_reference.html#compute_is_flipped"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#jass_preprocessing.map_reference.compute_is_flipped" title="Permalink to this definition">¶</a></dt>
+<dl class="py function">
+<dt class="sig sig-object py" id="jass_preprocessing.map_reference.compute_is_flipped">
+<span class="sig-prename descclassname"><span class="pre">jass_preprocessing.map_reference.</span></span><span class="sig-name descname"><span class="pre">compute_is_flipped</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">mgwas</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/jass_preprocessing/map_reference.html#compute_is_flipped"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#jass_preprocessing.map_reference.compute_is_flipped" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Check if the reference panel and the GWAS data have the same reference
allele. return a boolean vector.</p>
<dl class="field-list simple">
@@ -307,9 +222,9 @@ allele. return a boolean vector.</p>
</dl>
</dd></dl>
-<dl class="function">
-<dt id="jass_preprocessing.map_reference.compute_snp_alignement">
-<code class="sig-prename descclassname">jass_preprocessing.map_reference.</code><code class="sig-name descname">compute_snp_alignement</code><span class="sig-paren">(</span><em class="sig-param">mgwas</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/jass_preprocessing/map_reference.html#compute_snp_alignement"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#jass_preprocessing.map_reference.compute_snp_alignement" title="Permalink to this definition">¶</a></dt>
+<dl class="py function">
+<dt class="sig sig-object py" id="jass_preprocessing.map_reference.compute_snp_alignement">
+<span class="sig-prename descclassname"><span class="pre">jass_preprocessing.map_reference.</span></span><span class="sig-name descname"><span class="pre">compute_snp_alignement</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">mgwas</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/jass_preprocessing/map_reference.html#compute_snp_alignement"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#jass_preprocessing.map_reference.compute_snp_alignement" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Add a column to mgwas indicating if the reference and coded
allele is flipped compared to the reference panel.
If it is, the sign of the statistic must be flipped
@@ -319,9 +234,9 @@ If it is, the sign of the statistic must be flipped
</div></blockquote>
</dd></dl>
-<dl class="function">
-<dt id="jass_preprocessing.map_reference.map_on_ref_panel">
-<code class="sig-prename descclassname">jass_preprocessing.map_reference.</code><code class="sig-name descname">map_on_ref_panel</code><span class="sig-paren">(</span><em class="sig-param">gw_df</em>, <em class="sig-param">ref_panel</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/jass_preprocessing/map_reference.html#map_on_ref_panel"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#jass_preprocessing.map_reference.map_on_ref_panel" title="Permalink to this definition">¶</a></dt>
+<dl class="py function">
+<dt class="sig sig-object py" id="jass_preprocessing.map_reference.map_on_ref_panel">
+<span class="sig-prename descclassname"><span class="pre">jass_preprocessing.map_reference.</span></span><span class="sig-name descname"><span class="pre">map_on_ref_panel</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">gw_df</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ref_panel</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">index_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'rs-number'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/jass_preprocessing/map_reference.html#map_on_ref_panel"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#jass_preprocessing.map_reference.map_on_ref_panel" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Merge Gwas dataframe with the reference panel
Make sure that the same SNPs are in the reference panel and the gwas</p>
<dl class="field-list simple">
@@ -340,9 +255,9 @@ Make sure that the same SNPs are in the reference panel and the gwas</p>
</dl>
</dd></dl>
-<dl class="function">
-<dt id="jass_preprocessing.map_reference.read_reference">
-<code class="sig-prename descclassname">jass_preprocessing.map_reference.</code><code class="sig-name descname">read_reference</code><span class="sig-paren">(</span><em class="sig-param">gwas_reference_panel</em>, <em class="sig-param">mask_MHC=False</em>, <em class="sig-param">minimum_MAF=None</em>, <em class="sig-param">region_to_mask=None</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/jass_preprocessing/map_reference.html#read_reference"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#jass_preprocessing.map_reference.read_reference" title="Permalink to this definition">¶</a></dt>
+<dl class="py function">
+<dt class="sig sig-object py" id="jass_preprocessing.map_reference.read_reference">
+<span class="sig-prename descclassname"><span class="pre">jass_preprocessing.map_reference.</span></span><span class="sig-name descname"><span class="pre">read_reference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">gwas_reference_panel</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mask_MHC</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">minimum_MAF</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">region_to_mask</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/jass_preprocessing/map_reference.html#read_reference"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#jass_preprocessing.map_reference.read_reference" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>helper function to name correctly the column
:param gwas_reference_panel: path toward the reference panel file
:type gwas_reference_panel: str
@@ -353,7 +268,9 @@ Make sure that the same SNPs are in the reference panel and the gwas</p>
:param minimum_MAF: minimum allele frequency for a SNPs to be retain in the panel
:type minimum_MAF: float
:param region_to_mask: a list of additional regions to mask
-:type region_to_mask: dict</p>
+:type region_to_mask: dict
+:param type_of_index: ‘rs-number’ or ‘positional’
+:type type_of_index: str</p>
<dl class="field-list simple">
<dt class="field-odd">Returns</dt>
<dd class="field-odd"><p>the reference_panel with the specified filter applied</p>
@@ -364,88 +281,76 @@ Make sure that the same SNPs are in the reference panel and the gwas</p>
</dl>
</dd></dl>
-</div>
-<div class="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 headline">¶</a></h2>
-<dl class="function">
-<dt id="jass_preprocessing.save_output.save_output">
-<code class="sig-prename descclassname">jass_preprocessing.save_output.</code><code class="sig-name descname">save_output</code><span class="sig-paren">(</span><em class="sig-param">mgwas</em>, <em class="sig-param">ImpG_output_Folder</em>, <em class="sig-param">my_study</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/jass_preprocessing/save_output.html#save_output"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#jass_preprocessing.save_output.save_output" title="Permalink to this definition">¶</a></dt>
+</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>
+<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>
<dd><p>Write the preprocessed Gwas for ldscore analysis</p>
</dd></dl>
-<dl class="function">
-<dt id="jass_preprocessing.save_output.save_output_by_chromosome">
-<code class="sig-prename descclassname">jass_preprocessing.save_output.</code><code class="sig-name descname">save_output_by_chromosome</code><span class="sig-paren">(</span><em class="sig-param">mgwas</em>, <em class="sig-param">ImpG_output_Folder</em>, <em class="sig-param">my_study</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/jass_preprocessing/save_output.html#save_output_by_chromosome"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#jass_preprocessing.save_output.save_output_by_chromosome" title="Permalink to this definition">¶</a></dt>
+<dl class="py function">
+<dt class="sig sig-object py" id="jass_preprocessing.save_output.save_output_by_chromosome">
+<span class="sig-prename descclassname"><span class="pre">jass_preprocessing.save_output.</span></span><span class="sig-name descname"><span class="pre">save_output_by_chromosome</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_by_chromosome"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#jass_preprocessing.save_output.save_output_by_chromosome" title="Permalink to this definition">ïƒ</a></dt>
<dd><p>Write the preprocessed Gwas for imputation</p>
</dd></dl>
-</div>
-<div class="section" id="module-jass_preprocessing">
-<span id="module-contents"></span><h2>Module contents<a class="headerlink" href="#module-jass_preprocessing" title="Permalink to this headline">¶</a></h2>
-<table class="longtable docutils align-default">
+</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">
<colgroup>
<col style="width: 10%" />
<col style="width: 90%" />
</colgroup>
<tbody>
-<tr class="row-odd"><td><p><a class="reference internal" href="#module-jass_preprocessing.map_gwas" title="jass_preprocessing.map_gwas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">map_gwas</span></code></a></p></td>
+<tr class="row-odd"><td><p><a class="reference internal" href="jass_preprocessing.map_gwas.html#module-jass_preprocessing.map_gwas" title="jass_preprocessing.map_gwas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">map_gwas</span></code></a></p></td>
<td><p>Map GWAS</p></td>
</tr>
-<tr class="row-even"><td><p><a class="reference internal" href="#module-jass_preprocessing.dna_utils" title="jass_preprocessing.dna_utils"><code class="xref py py-obj docutils literal notranslate"><span class="pre">dna_utils</span></code></a></p></td>
+<tr class="row-even"><td><p><a class="reference internal" href="jass_preprocessing.dna_utils.html#module-jass_preprocessing.dna_utils" title="jass_preprocessing.dna_utils"><code class="xref py py-obj docutils literal notranslate"><span class="pre">dna_utils</span></code></a></p></td>
<td><p>Few fonction to to compute DNA complement</p></td>
</tr>
-<tr class="row-odd"><td><p><a class="reference internal" href="#module-jass_preprocessing.map_reference" title="jass_preprocessing.map_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">map_reference</span></code></a></p></td>
+<tr class="row-odd"><td><p><a class="reference internal" href="jass_preprocessing.map_reference.html#module-jass_preprocessing.map_reference" title="jass_preprocessing.map_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">map_reference</span></code></a></p></td>
<td><p>Module of function</p></td>
</tr>
-<tr class="row-even"><td><p><a class="reference internal" href="#module-jass_preprocessing.compute_score" title="jass_preprocessing.compute_score"><code class="xref py py-obj docutils literal notranslate"><span class="pre">compute_score</span></code></a></p></td>
+<tr class="row-even"><td><p><a class="reference internal" href="jass_preprocessing.compute_score.html#module-jass_preprocessing.compute_score" title="jass_preprocessing.compute_score"><code class="xref py py-obj docutils literal notranslate"><span class="pre">compute_score</span></code></a></p></td>
<td><p></p></td>
</tr>
-<tr class="row-odd"><td><p><a class="reference internal" href="#module-jass_preprocessing.save_output" title="jass_preprocessing.save_output"><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_output</span></code></a></p></td>
+<tr class="row-odd"><td><p><a class="reference internal" href="jass_preprocessing.save_output.html#module-jass_preprocessing.save_output" title="jass_preprocessing.save_output"><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_output</span></code></a></p></td>
<td><p></p></td>
</tr>
</tbody>
</table>
-</div>
-</div>
+</section>
+</section>
</div>
-
</div>
<footer>
-
<hr/>
<div role="contentinfo">
- <p>
- © Copyright 2018, Hanna Julienne
-
- </p>
+ <p>© Copyright 2018, Hanna Julienne.</p>
</div>
- Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/rtfd/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
-</footer>
+ Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
+ <a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
+ provided by <a href="https://readthedocs.org">Read the Docs</a>.
+
+</footer>
</div>
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-
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-
-
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- <script type="text/javascript">
+ <script>
jQuery(function () {
SphinxRtdTheme.Navigation.enable(true);
});
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+ </script>
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</html>
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diff --git a/doc/_build/html/_autosummary/modules.html b/doc/_build/html/_autosummary/modules.html
index 1e41c94b01d52fe1c16250ec423862746f327580..10c9aaae92ad670adefd2f655f25d6031389b718 100644
--- a/doc/_build/html/_autosummary/modules.html
+++ b/doc/_build/html/_autosummary/modules.html
@@ -1,65 +1,34 @@
-
-
<!DOCTYPE html>
-<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
-<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]-->
+<html class="writer-html5" lang="en" >
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-
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- <script type="text/javascript" src="../_static/js/modernizr.min.js"></script>
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- <script type="text/javascript" src="../_static/jquery.js"></script>
- <script type="text/javascript" src="../_static/underscore.js"></script>
- <script type="text/javascript" src="../_static/doctools.js"></script>
- <script type="text/javascript" src="../_static/language_data.js"></script>
-
- <script type="text/javascript" src="../_static/js/theme.js"></script>
-
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+ <meta charset="utf-8" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
+ <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+ <section id="jass-preprocessing">
+<h1>jass_preprocessing<a class="headerlink" href="#jass-preprocessing" title="Permalink to this heading">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></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></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">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>
+<li class="toctree-l3"><a class="reference internal" href="_autosummary/jass_preprocessing.map_reference.html">jass_preprocessing.map_reference</a></li>
+<li class="toctree-l3"><a class="reference internal" href="_autosummary/jass_preprocessing.compute_score.html">jass_preprocessing.compute_score</a></li>
+<li class="toctree-l3"><a class="reference internal" href="_autosummary/jass_preprocessing.save_output.html">jass_preprocessing.save_output</a></li>
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+<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>
+<li class="toctree-l1"><a class="reference internal" href="../_autosummary/jass_preprocessing.compute_score.html">jass_preprocessing.compute_score</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../_autosummary/jass_preprocessing.save_output.html">jass_preprocessing.save_output</a></li>
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<h1>All modules for which code is available</h1>
<ul><li><a href="jass_preprocessing/compute_score.html">jass_preprocessing.compute_score</a></li>
<li><a href="jass_preprocessing/dna_utils.html">jass_preprocessing.dna_utils</a></li>
@@ -147,42 +86,30 @@
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- <p>
- © Copyright 2018, Hanna Julienne
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+ <p>© Copyright 2018, Hanna Julienne.</p>
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diff --git a/doc/_build/html/_modules/jass_preprocessing/compute_score.html b/doc/_build/html/_modules/jass_preprocessing/compute_score.html
index 5f539047195caef3eea3cdaa79c4daf6ef95fd2c..75dd0d9212397f1f75714a27c7075b1612a3e31d 100644
--- a/doc/_build/html/_modules/jass_preprocessing/compute_score.html
+++ b/doc/_build/html/_modules/jass_preprocessing/compute_score.html
@@ -1,65 +1,33 @@
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+<li class="toctree-l1"><a class="reference internal" href="../../_autosummary/jass_preprocessing.map_reference.html">jass_preprocessing.map_reference</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../_autosummary/jass_preprocessing.compute_score.html">jass_preprocessing.compute_score</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../_autosummary/jass_preprocessing.save_output.html">jass_preprocessing.save_output</a></li>
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+ <li><a href="../../index.html" class="icon icon-home"></a></li>
+ <li class="breadcrumb-item"><a href="../index.html">Module code</a></li>
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-
+
<h1>Source code for jass_preprocessing.compute_score</h1><div class="highlight"><pre>
<span></span><span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
@@ -211,42 +139,30 @@
</pre></div>
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-
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<footer>
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- <p>
- © Copyright 2018, Hanna Julienne
-
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+ <p>© Copyright 2018, Hanna Julienne.</p>
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diff --git a/doc/_build/html/_modules/jass_preprocessing/dna_utils.html b/doc/_build/html/_modules/jass_preprocessing/dna_utils.html
index 431e99d46d749bee608385325ce385c62ae18b2e..abde84ce0611206d75fff38e9636a05c1df50c3f 100644
--- a/doc/_build/html/_modules/jass_preprocessing/dna_utils.html
+++ b/doc/_build/html/_modules/jass_preprocessing/dna_utils.html
@@ -1,65 +1,33 @@
-
-
<!DOCTYPE html>
-<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
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<title>jass_preprocessing.dna_utils — jass_preprocessing 1.0 documentation</title>
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@@ -67,79 +35,39 @@
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</form>
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+<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>
+<li class="toctree-l1"><a class="reference internal" href="../../_autosummary/jass_preprocessing.compute_score.html">jass_preprocessing.compute_score</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../_autosummary/jass_preprocessing.save_output.html">jass_preprocessing.save_output</a></li>
+</ul>
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+ <li><a href="../../index.html" class="icon icon-home"></a></li>
+ <li class="breadcrumb-item"><a href="../index.html">Module code</a></li>
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-
+
<h1>Source code for jass_preprocessing.dna_utils</h1><div class="highlight"><pre>
<span></span><span class="sd">"""</span>
<span class="sd"> Few fonction to to compute DNA complement</span>
@@ -159,42 +87,30 @@
</pre></div>
</div>
-
</div>
<footer>
-
<hr/>
<div role="contentinfo">
- <p>
- © Copyright 2018, Hanna Julienne
-
- </p>
+ <p>© Copyright 2018, Hanna Julienne.</p>
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- Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/rtfd/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
-</footer>
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+ <a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
+ provided by <a href="https://readthedocs.org">Read the Docs</a>.
+
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\ No newline at end of file
diff --git a/doc/_build/html/_modules/jass_preprocessing/map_gwas.html b/doc/_build/html/_modules/jass_preprocessing/map_gwas.html
index 0cbd1a37a6dc7374ba5b02b22212c807640724d0..79620a57f06c2e054af970d900e1b5826f0c6281 100644
--- a/doc/_build/html/_modules/jass_preprocessing/map_gwas.html
+++ b/doc/_build/html/_modules/jass_preprocessing/map_gwas.html
@@ -1,65 +1,33 @@
-
-
<!DOCTYPE html>
-<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
-<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]-->
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+ <meta charset="utf-8" />
+ <meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>jass_preprocessing.map_gwas — jass_preprocessing 1.0 documentation</title>
+ <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
+ <link rel="stylesheet" href="../../_static/css/theme.css" type="text/css" />
+ <!--[if lt IE 9]>
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@@ -67,79 +35,39 @@
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</form>
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+ <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>
+<li class="toctree-l1"><a class="reference internal" href="../../_autosummary/jass_preprocessing.compute_score.html">jass_preprocessing.compute_score</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../_autosummary/jass_preprocessing.save_output.html">jass_preprocessing.save_output</a></li>
+</ul>
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-
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+ <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>
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<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
-
+
<h1>Source code for jass_preprocessing.map_gwas</h1><div class="highlight"><pre>
<span></span><span class="sd">"""</span>
<span class="sd">Map GWAS</span>
@@ -156,10 +84,8 @@
<span class="kn">import</span> <span class="nn">gzip</span>
<span class="kn">import</span> <span class="nn">re</span>
-
<div class="viewcode-block" id="walkfs"><a class="viewcode-back" href="../../_autosummary/jass_preprocessing.html#jass_preprocessing.map_gwas.walkfs">[docs]</a><span class="k">def</span> <span class="nf">walkfs</span><span class="p">(</span><span class="n">startdir</span><span class="p">,</span> <span class="n">findfile</span><span class="p">):</span>
<span class="sd">"""</span>
-
<span class="sd"> Go through the folder and subfolder to find the specified file</span>
<span class="sd"> Args:</span>
@@ -264,7 +190,7 @@
<span class="n">f</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
<span class="k">return</span> <span class="n">mapgw</span></div>
-<div class="viewcode-block" id="read_gwas"><a class="viewcode-back" href="../../_autosummary/jass_preprocessing.html#jass_preprocessing.map_gwas.read_gwas">[docs]</a><span class="k">def</span> <span class="nf">read_gwas</span><span class="p">(</span> <span class="n">gwas_internal_link</span><span class="p">,</span> <span class="n">column_map</span><span class="p">):</span>
+<div class="viewcode-block" id="read_gwas"><a class="viewcode-back" href="../../_autosummary/jass_preprocessing.html#jass_preprocessing.map_gwas.read_gwas">[docs]</a><span class="k">def</span> <span class="nf">read_gwas</span><span class="p">(</span> <span class="n">gwas_internal_link</span><span class="p">,</span> <span class="n">column_map</span><span class="p">,</span> <span class="n">imputation_treshold</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Read gwas raw data, fetch columns thanks to position stored in</span>
<span class="sd"> column_map and rename columns according to column_map.index</span>
@@ -276,9 +202,11 @@
<span class="sd"> Return:</span>
<span class="sd"> a pandas dataframe with missing value all equal to np.nan</span>
<span class="sd"> """</span>
+
<span class="nb">print</span><span class="p">(</span><span class="s2">"Reading file:"</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="n">gwas_internal_link</span><span class="p">)</span>
- <span class="n">is_gzipped</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="sa">r</span><span class="s2">".gz$"</span><span class="p">,</span> <span class="n">gwas_internal_link</span><span class="p">)</span>
+ <span class="n">is_gzipped</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="sa">r</span><span class="s2">".gz|.bgz$"</span><span class="p">,</span> <span class="n">gwas_internal_link</span><span class="p">)</span>
+
<span class="k">if</span> <span class="n">is_gzipped</span><span class="p">:</span>
<span class="n">compression</span> <span class="o">=</span> <span class="s1">'gzip'</span>
<span class="k">else</span><span class="p">:</span>
@@ -296,8 +224,29 @@
<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="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>
+
+ <span class="n">fullGWAS</span><span class="o">.</span><span class="n">a1</span> <span class="o">=</span> <span class="n">fullGWAS</span><span class="o">.</span><span class="n">a1</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">upper</span><span class="p">()</span>
+ <span class="n">fullGWAS</span><span class="o">.</span><span class="n">a2</span> <span class="o">=</span> <span class="n">fullGWAS</span><span class="o">.</span><span class="n">a2</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">upper</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"># either rs ID or full position must be available:</span>
+
+ <span class="k">if</span> <span class="ow">not</span><span class="p">((</span><span class="s2">"CHR"</span> <span class="ow">in</span> <span class="n">fullGWAS</span><span class="o">.</span><span class="n">columns</span><span class="p">)</span> <span class="ow">and</span> <span class="p">(</span><span class="s2">"POS"</span> <span class="ow">in</span> <span class="n">fullGWAS</span><span class="o">.</span><span class="n">columns</span><span class="p">))</span> <span class="ow">and</span> <span class="p">(</span><span class="s2">"snpid"</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">fullGWAS</span><span class="o">.</span><span class="n">columns</span><span class="p">):</span>
+ <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">"Summary statistic file </span><span class="si">{0}</span><span class="s2"> doesn't contain rsID or full SNP position"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">gwas_internal_link</span><span class="p">))</span>
+
+ <span class="k">if</span> <span class="p">(</span><span class="s2">"CHR"</span> <span class="ow">in</span> <span class="n">fullGWAS</span><span class="o">.</span><span class="n">columns</span><span class="p">)</span> <span class="ow">and</span> <span class="p">(</span><span class="s2">"POS"</span> <span class="ow">in</span> <span class="n">fullGWAS</span><span class="o">.</span><span class="n">columns</span><span class="p">):</span>
+ <span class="n">fullGWAS</span><span class="p">[</span><span class="s2">"positional_index"</span><span class="p">]</span> <span class="o">=</span> <span class="n">fullGWAS</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">fullGWAS</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">fullGWAS</span><span class="o">.</span><span class="n">a1</span><span class="o">+</span><span class="n">fullGWAS</span><span class="o">.</span><span class="n">a2</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="p">(</span><span class="s2">"snpid"</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">fullGWAS</span><span class="o">.</span><span class="n">columns</span><span class="p">):</span>
+ <span class="n">fullGWAS</span><span class="p">[</span><span class="s2">"snpid"</span><span class="p">]</span> <span class="o">=</span> <span class="n">fullGWAS</span><span class="p">[</span><span class="s2">"positional_index"</span><span class="p">]</span>
<span class="n">fullGWAS</span><span class="o">.</span><span class="n">set_index</span><span class="p">(</span><span class="s2">"snpid"</span><span class="p">,</span> <span class="n">inplace</span><span class="o">=</span><span class="kc">True</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="k">if</span> <span class="n">imputation_treshold</span><span class="p">:</span>
+ <span class="n">fullGWAS</span> <span class="o">=</span> <span class="n">fullGWAS</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="n">fullGWAS</span><span class="o">.</span><span class="n">imputation_quality</span> <span class="o">></span> <span class="n">imputation_treshold</span><span class="p">]</span>
<span class="n">fullGWAS</span> <span class="o">=</span> <span class="n">fullGWAS</span><span class="p">[</span><span class="o">~</span><span class="n">fullGWAS</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">duplicated</span><span class="p">(</span><span class="n">keep</span><span class="o">=</span><span class="s1">'first'</span><span class="p">)]</span>
<span class="c1">#fullGWAS = convert_missing_values(fullGWAS)</span>
@@ -305,42 +254,30 @@
</pre></div>
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diff --git a/doc/_build/html/_modules/jass_preprocessing/map_reference.html b/doc/_build/html/_modules/jass_preprocessing/map_reference.html
index 3279e2ded5c2e64158a10b9eec98bd84647232fe..7abe24dfa0ded9729542a99b437e68786af034f3 100644
--- a/doc/_build/html/_modules/jass_preprocessing/map_reference.html
+++ b/doc/_build/html/_modules/jass_preprocessing/map_reference.html
@@ -1,65 +1,33 @@
-
-
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+ <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
+ <link rel="stylesheet" href="../../_static/css/theme.css" type="text/css" />
+ <!--[if lt IE 9]>
+ <script src="../../_static/js/html5shiv.min.js"></script>
+ <![endif]-->
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<input type="text" name="q" placeholder="Search docs" />
@@ -67,84 +35,42 @@
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+<li class="toctree-l1"><a class="reference internal" href="../../_autosummary/jass_preprocessing.map_reference.html">jass_preprocessing.map_reference</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../_autosummary/jass_preprocessing.compute_score.html">jass_preprocessing.compute_score</a></li>
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<h1>Source code for jass_preprocessing.map_reference</h1><div class="highlight"><pre>
<span></span><span class="sd">"""</span>
<span class="sd"> Module of function</span>
-
-
<span class="sd">"""</span>
<span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
@@ -160,15 +86,22 @@
<span class="sd"> Filter the reference panel by minimum allele frequency (hg19 coordinate)</span>
<span class="sd"> minimum_MAF (float): minimum allele frequency for a SNPs to be retain in the panel</span>
<span class="sd"> region_to_mask (dict): a list of additional regions to mask</span>
+<span class="sd"> type_of_index(str): 'rs-number' or 'positional'</span>
<span class="sd"> Return:</span>
<span class="sd"> ref (pandas dataframe): the reference_panel with the specified filter applied</span>
<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">"pos"</span><span class="p">,</span> <span class="s2">"snp_id"</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="s2">"MAF"</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">index_col</span><span class="o">=</span><span class="s2">"snp_id"</span><span class="p">)</span>
- <span class="c1">#Filter Strand ambiguous</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="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>
<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="n">ref</span><span class="o">.</span><span class="n">chr</span> <span class="o">!=</span><span class="mi">6</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">pos</span> <span class="o"><</span> <span class="mi">28477797</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">pos</span> <span class="o">></span> <span class="mi">33448354</span><span class="p">)]</span>
@@ -182,7 +115,7 @@
-<div class="viewcode-block" id="map_on_ref_panel"><a class="viewcode-back" href="../../_autosummary/jass_preprocessing.html#jass_preprocessing.map_reference.map_on_ref_panel">[docs]</a><span class="k">def</span> <span class="nf">map_on_ref_panel</span><span class="p">(</span><span class="n">gw_df</span> <span class="p">,</span> <span class="n">ref_panel</span><span class="p">):</span>
+<div class="viewcode-block" id="map_on_ref_panel"><a class="viewcode-back" href="../../_autosummary/jass_preprocessing.html#jass_preprocessing.map_reference.map_on_ref_panel">[docs]</a><span class="k">def</span> <span class="nf">map_on_ref_panel</span><span class="p">(</span><span class="n">gw_df</span> <span class="p">,</span> <span class="n">ref_panel</span><span class="p">,</span> <span class="n">index_type</span><span class="o">=</span><span class="s2">"rs-number"</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Merge Gwas dataframe with the reference panel</span>
<span class="sd"> Make sure that the same SNPs are in the reference panel and the gwas</span>
@@ -194,23 +127,46 @@
<span class="sd"> Return:</span>
<span class="sd"> merge_GWAS (pandas dataframe): merge studies,</span>
<span class="sd"> """</span>
- <span class="n">inter_index</span> <span class="o">=</span> <span class="n">ref_panel</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">intersection</span><span class="p">(</span><span class="n">gw_df</span><span class="o">.</span><span class="n">index</span><span class="p">)</span>
-
- <span class="n">merge_GWAS</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">merge</span><span class="p">(</span><span class="n">ref_panel</span><span class="p">,</span> <span class="n">gw_df</span><span class="p">,</span>
- <span class="n">how</span><span class="o">=</span><span class="s1">'inner'</span><span class="p">,</span> <span class="n">indicator</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">left_index</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">right_index</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
- <span class="nb">print</span><span class="p">(</span><span class="s2">"SNPs </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">merge_GWAS</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</span><span class="p">]))</span>
- <span class="c1"># If the GWAS file contains indexes of the kind chr*:position, perform a</span>
- <span class="c1"># second join</span>
- <span class="k">if</span> <span class="n">gw_df</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">map</span><span class="p">(</span><span class="nb">str</span><span class="p">)</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">contains</span><span class="p">(</span><span class="s2">"^chr*"</span><span class="p">,</span> <span class="n">case</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span><span class="o">.</span><span class="n">any</span><span class="p">():</span>
- <span class="n">ref_panel</span><span class="p">[</span><span class="s1">'key2'</span><span class="p">]</span> <span class="o">=</span> <span class="s2">"chr"</span><span class="o">+</span><span class="n">ref_panel</span><span class="o">.</span><span class="n">chr</span><span class="o">.</span><span class="n">map</span><span class="p">(</span><span class="nb">str</span><span class="p">)</span> <span class="o">+</span> <span class="s2">":"</span> <span class="o">+</span><span class="n">ref_panel</span><span class="o">.</span><span class="n">pos</span><span class="o">.</span><span class="n">map</span><span class="p">(</span><span class="nb">str</span><span class="p">)</span>
- <span class="n">other_snp</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">merge</span><span class="p">(</span><span class="n">ref_panel</span><span class="p">,</span> <span class="n">gw_df</span><span class="p">,</span> <span class="n">how</span><span class="o">=</span><span class="s1">'inner'</span><span class="p">,</span> <span class="n">indicator</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
- <span class="n">left_on</span> <span class="o">=</span><span class="s1">'key2'</span><span class="p">,</span> <span class="n">right_index</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
- <span class="n">merge_GWAS</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">concat</span><span class="p">([</span><span class="n">other_snp</span><span class="p">,</span> <span class="n">merge_GWAS</span><span class="p">])</span>
+ <span class="k">if</span> <span class="n">index_type</span><span class="o">==</span><span class="s2">"rs-number"</span><span class="p">:</span>
+ <span class="n">merge_GWAS</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">merge</span><span class="p">(</span><span class="n">ref_panel</span><span class="p">,</span> <span class="n">gw_df</span><span class="p">,</span>
+ <span class="n">how</span><span class="o">=</span><span class="s1">'inner'</span><span class="p">,</span> <span class="n">indicator</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">left_index</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">right_index</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+ <span class="nb">print</span><span class="p">(</span><span class="s2">"SNPs </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">merge_GWAS</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</span><span class="p">]))</span>
+
+ <span class="c1"># If the GWAS file contains indexes of the kind chr*:position, perform a</span>
+ <span class="c1"># second join</span>
+ <span class="k">if</span> <span class="n">gw_df</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">map</span><span class="p">(</span><span class="nb">str</span><span class="p">)</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">contains</span><span class="p">(</span><span class="s2">"^chr*"</span><span class="p">,</span> <span class="n">case</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span><span class="o">.</span><span class="n">any</span><span class="p">():</span>
+ <span class="n">ref_panel</span><span class="p">[</span><span class="s1">'key2'</span><span class="p">]</span> <span class="o">=</span> <span class="s2">"chr"</span><span class="o">+</span><span class="n">ref_panel</span><span class="o">.</span><span class="n">chr</span><span class="o">.</span><span class="n">map</span><span class="p">(</span><span class="nb">str</span><span class="p">)</span> <span class="o">+</span> <span class="s2">":"</span> <span class="o">+</span><span class="n">ref_panel</span><span class="o">.</span><span class="n">pos</span><span class="o">.</span><span class="n">map</span><span class="p">(</span><span class="nb">str</span><span class="p">)</span>
+ <span class="n">other_snp</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">merge</span><span class="p">(</span><span class="n">ref_panel</span><span class="p">,</span> <span class="n">gw_df</span><span class="p">,</span> <span class="n">how</span><span class="o">=</span><span class="s1">'inner'</span><span class="p">,</span> <span class="n">indicator</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
+ <span class="n">left_on</span> <span class="o">=</span><span class="s1">'key2'</span><span class="p">,</span> <span class="n">right_index</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+ <span class="n">merge_GWAS</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">concat</span><span class="p">([</span><span class="n">other_snp</span><span class="p">,</span> <span class="n">merge_GWAS</span><span class="p">])</span>
+
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">index_type</span><span class="o">==</span><span class="s2">"positional"</span><span class="p">:</span>
+ <span class="nb">print</span><span class="p">(</span><span class="s2">"length of intersection"</span><span class="p">)</span>
+ <span class="nb">print</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">pd</span><span class="o">.</span><span class="n">Index</span><span class="p">(</span><span class="n">ref_panel</span><span class="o">.</span><span class="n">positional_index</span><span class="p">)</span><span class="o">.</span><span class="n">intersection</span><span class="p">(</span><span class="n">pd</span><span class="o">.</span><span class="n">Index</span><span class="p">(</span><span class="n">gw_df</span><span class="o">.</span><span class="n">positional_index</span><span class="p">))))</span>
+ <span class="n">merge_GWAS</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">merge</span><span class="p">(</span><span class="n">ref_panel</span><span class="o">.</span><span class="n">reset_index</span><span class="p">(),</span> <span class="n">gw_df</span><span class="p">,</span>
+ <span class="n">how</span><span class="o">=</span><span class="s1">'inner'</span><span class="p">,</span> <span class="n">indicator</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">on</span><span class="o">=</span><span class="s2">"positional_index"</span><span class="p">)</span>
+ <span class="nb">print</span><span class="p">(</span><span class="n">merge_GWAS</span><span class="p">)</span>
+ <span class="n">merge_GWAS</span><span class="o">.</span><span class="n">set_index</span><span class="p">(</span><span class="s2">"snp_id"</span><span class="p">,</span> <span class="n">inplace</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">"index_type can take only two values: 'rs-number' or 'positional'"</span><span class="p">)</span>
+
+ <span class="k">if</span> <span class="p">((</span><span class="s2">"pos"</span> <span class="ow">in</span> <span class="n">merge_GWAS</span><span class="o">.</span><span class="n">columns</span><span class="p">)</span> <span class="ow">and</span> <span class="p">(</span><span class="s2">"POS"</span> <span class="ow">in</span> <span class="n">merge_GWAS</span><span class="o">.</span><span class="n">columns</span><span class="p">)):</span>
+ <span class="k">if</span> <span class="p">((</span><span class="n">merge_GWAS</span><span class="o">.</span><span class="n">pos</span> <span class="o">==</span> <span class="n">merge_GWAS</span><span class="o">.</span><span class="n">POS</span><span class="p">)</span><span class="o">.</span><span class="n">mean</span><span class="p">()</span><span class="o">></span> <span class="mf">0.95</span><span class="p">):</span>
+ <span class="n">merge_GWAS</span> <span class="o">=</span> <span class="n">merge_GWAS</span><span class="o">.</span><span class="n">loc</span><span class="p">[(</span><span class="n">merge_GWAS</span><span class="o">.</span><span class="n">pos</span> <span class="o">==</span> <span class="n">merge_GWAS</span><span class="o">.</span><span class="n">POS</span><span class="p">)]</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">"SNP positions in reference panel and in Summary statistic are different! Different assembly?"</span><span class="p">)</span>
+
+ <span class="nb">print</span><span class="p">(</span><span class="s2">"before filter"</span><span class="p">)</span>
+ <span class="nb">print</span><span class="p">(</span><span class="n">merge_GWAS</span><span class="o">.</span><span class="n">shape</span><span class="p">)</span>
<span class="n">merge_GWAS</span> <span class="o">=</span> <span class="n">merge_GWAS</span><span class="p">[</span><span class="o">~</span><span class="n">merge_GWAS</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">duplicated</span><span class="p">(</span><span class="n">keep</span><span class="o">=</span><span class="s1">'first'</span><span class="p">)]</span>
+ <span class="nb">print</span><span class="p">(</span><span class="s2">"after filter"</span><span class="p">)</span>
+ <span class="nb">print</span><span class="p">(</span><span class="n">merge_GWAS</span><span class="o">.</span><span class="n">shape</span><span class="p">)</span>
+
<span class="n">merge_GWAS</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">rename</span><span class="p">(</span><span class="s2">"snp_id"</span><span class="p">,</span> <span class="n">inplace</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="k">return</span><span class="p">(</span><span class="n">merge_GWAS</span><span class="p">)</span></div>
@@ -290,42 +246,30 @@
</pre></div>
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diff --git a/doc/_build/html/_modules/jass_preprocessing/save_output.html b/doc/_build/html/_modules/jass_preprocessing/save_output.html
index 4b47c439e7b90fb787f760230fdf54828bd6241b..93894fbb3c27d2277c958b7123cb7672d84e8807 100644
--- a/doc/_build/html/_modules/jass_preprocessing/save_output.html
+++ b/doc/_build/html/_modules/jass_preprocessing/save_output.html
@@ -1,65 +1,33 @@
-
-
<!DOCTYPE html>
-<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
-<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]-->
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+ <meta charset="utf-8" />
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<title>jass_preprocessing.save_output — jass_preprocessing 1.0 documentation</title>
+ <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
+ <link rel="stylesheet" href="../../_static/css/theme.css" type="text/css" />
+ <!--[if lt IE 9]>
+ <script src="../../_static/js/html5shiv.min.js"></script>
+ <![endif]-->
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<input type="text" name="q" placeholder="Search docs" />
@@ -67,79 +35,39 @@
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+<li class="toctree-l1"><a class="reference internal" href="../../_autosummary/jass_preprocessing.compute_score.html">jass_preprocessing.compute_score</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../_autosummary/jass_preprocessing.save_output.html">jass_preprocessing.save_output</a></li>
+</ul>
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<h1>Source code for jass_preprocessing.save_output</h1><div class="highlight"><pre>
<span></span><span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
@@ -153,20 +81,23 @@
<span class="n">mgwas_copy</span><span class="o">.</span><span class="n">set_index</span><span class="p">(</span><span class="s2">"chr"</span><span class="p">,</span> <span class="n">inplace</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="n">mgwas_copy</span><span class="o">.</span><span class="n">dropna</span><span class="p">(</span><span class="n">subset</span><span class="o">=</span><span class="p">[</span><span class="s2">"computed_z"</span><span class="p">],</span> <span class="n">how</span><span class="o">=</span><span class="s2">"any"</span><span class="p">,</span> <span class="n">inplace</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+ <span class="nb">print</span><span class="p">(</span><span class="n">mgwas_copy</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">unique</span><span class="p">())</span>
<span class="k">for</span> <span class="n">chrom</span> <span class="ow">in</span> <span class="n">mgwas_copy</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">unique</span><span class="p">():</span>
-
- <span class="n">mgwas_chr</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">({</span>
- <span class="s1">'rsID'</span><span class="p">:</span> <span class="n">mgwas_copy</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="n">chrom</span><span class="p">]</span><span class="o">.</span><span class="n">snp_id</span><span class="p">,</span>
- <span class="s1">'pos'</span><span class="p">:</span> <span class="n">mgwas_copy</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="n">chrom</span><span class="p">]</span><span class="o">.</span><span class="n">pos</span><span class="p">,</span>
- <span class="s1">'A0'</span><span class="p">:</span> <span class="n">mgwas_copy</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="n">chrom</span><span class="p">]</span><span class="o">.</span><span class="n">ref</span><span class="p">,</span>
- <span class="s1">'A1'</span><span class="p">:</span><span class="n">mgwas_copy</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="n">chrom</span><span class="p">]</span><span class="o">.</span><span class="n">alt</span><span class="p">,</span>
- <span class="s1">'Z'</span><span class="p">:</span> <span class="n">mgwas_copy</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="n">chrom</span><span class="p">]</span><span class="o">.</span><span class="n">computed_z</span><span class="p">,</span>
- <span class="s1">'P'</span><span class="p">:</span> <span class="n">mgwas_copy</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="n">chrom</span><span class="p">]</span><span class="o">.</span><span class="n">pval</span>
- <span class="p">},</span> <span class="n">columns</span><span class="o">=</span> <span class="p">[</span><span class="s1">'rsID'</span><span class="p">,</span> <span class="s1">'pos'</span><span class="p">,</span> <span class="s1">'A0'</span><span class="p">,</span> <span class="s2">"A1"</span><span class="p">,</span> <span class="s2">"Z"</span><span class="p">,</span> <span class="s2">"P"</span> <span class="p">])</span>
-
- <span class="n">impg_output_file</span> <span class="o">=</span> <span class="n">ImpG_output_Folder</span> <span class="o">+</span> <span class="s1">'z_'</span><span class="o">+</span> <span class="n">my_study</span> <span class="o">+</span><span class="s1">'_chr'</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">chrom</span><span class="p">)</span><span class="o">+</span><span class="s2">".txt"</span>
- <span class="nb">print</span><span class="p">(</span><span class="s2">"WRITING CHR </span><span class="si">{}</span><span class="s2"> results for </span><span class="si">{}</span><span class="s2"> to: </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">chrom</span><span class="p">,</span> <span class="n">my_study</span><span class="p">,</span> <span class="n">ImpG_output_Folder</span><span class="p">))</span>
- <span class="n">mgwas_chr</span><span class="o">.</span><span class="n">sort_values</span><span class="p">(</span><span class="n">by</span><span class="o">=</span><span class="s2">"pos"</span><span class="p">)</span><span class="o">.</span><span class="n">to_csv</span><span class="p">(</span><span class="n">impg_output_file</span><span class="p">,</span> <span class="n">sep</span><span class="o">=</span><span class="s2">"</span><span class="se">\t</span><span class="s2">"</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span></div>
+ <span class="k">if</span> <span class="nb">type</span><span class="p">(</span><span class="n">mgwas_copy</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="n">chrom</span><span class="p">])</span> <span class="ow">is</span> <span class="n">pd</span><span class="o">.</span><span class="n">core</span><span class="o">.</span><span class="n">frame</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">:</span>
+ <span class="n">mgwas_chr</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">({</span>
+ <span class="s1">'rsID'</span><span class="p">:</span> <span class="n">mgwas_copy</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="n">chrom</span><span class="p">]</span><span class="o">.</span><span class="n">snp_id</span><span class="p">,</span>
+ <span class="s1">'pos'</span><span class="p">:</span> <span class="n">mgwas_copy</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="n">chrom</span><span class="p">]</span><span class="o">.</span><span class="n">pos</span><span class="p">,</span>
+ <span class="s1">'A0'</span><span class="p">:</span> <span class="n">mgwas_copy</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="n">chrom</span><span class="p">]</span><span class="o">.</span><span class="n">ref</span><span class="p">,</span>
+ <span class="s1">'A1'</span><span class="p">:</span><span class="n">mgwas_copy</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="n">chrom</span><span class="p">]</span><span class="o">.</span><span class="n">alt</span><span class="p">,</span>
+ <span class="s1">'Z'</span><span class="p">:</span> <span class="n">mgwas_copy</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="n">chrom</span><span class="p">]</span><span class="o">.</span><span class="n">computed_z</span><span class="p">,</span>
+ <span class="s1">'P'</span><span class="p">:</span> <span class="n">mgwas_copy</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="n">chrom</span><span class="p">]</span><span class="o">.</span><span class="n">pval</span>
+ <span class="p">},</span> <span class="n">columns</span><span class="o">=</span> <span class="p">[</span><span class="s1">'rsID'</span><span class="p">,</span> <span class="s1">'pos'</span><span class="p">,</span> <span class="s1">'A0'</span><span class="p">,</span> <span class="s2">"A1"</span><span class="p">,</span> <span class="s2">"Z"</span><span class="p">,</span> <span class="s2">"P"</span> <span class="p">])</span>
+
+ <span class="n">impg_output_file</span> <span class="o">=</span> <span class="n">ImpG_output_Folder</span> <span class="o">+</span> <span class="s1">'z_'</span><span class="o">+</span> <span class="n">my_study</span> <span class="o">+</span><span class="s1">'_chr'</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">chrom</span><span class="p">)</span><span class="o">+</span><span class="s2">".txt"</span>
+ <span class="nb">print</span><span class="p">(</span><span class="s2">"WRITING CHR </span><span class="si">{}</span><span class="s2"> results for </span><span class="si">{}</span><span class="s2"> to: </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">chrom</span><span class="p">,</span> <span class="n">my_study</span><span class="p">,</span> <span class="n">ImpG_output_Folder</span><span class="p">))</span>
+ <span class="n">mgwas_chr</span><span class="o">.</span><span class="n">sort_values</span><span class="p">(</span><span class="n">by</span><span class="o">=</span><span class="s2">"pos"</span><span class="p">)</span><span class="o">.</span><span class="n">to_csv</span><span class="p">(</span><span class="n">impg_output_file</span><span class="p">,</span> <span class="n">sep</span><span class="o">=</span><span class="s2">"</span><span class="se">\t</span><span class="s2">"</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="nb">print</span><span class="p">(</span><span class="s2">"NO or 1 value for CHR </span><span class="si">{}</span><span class="s2"> results for </span><span class="si">{}</span><span class="s2"> to: </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">chrom</span><span class="p">,</span> <span class="n">my_study</span><span class="p">,</span> <span class="n">ImpG_output_Folder</span><span class="p">))</span></div>
<div class="viewcode-block" id="save_output"><a class="viewcode-back" href="../../_autosummary/jass_preprocessing.html#jass_preprocessing.save_output.save_output">[docs]</a><span class="k">def</span> <span class="nf">save_output</span><span class="p">(</span><span class="n">mgwas</span><span class="p">,</span> <span class="n">ImpG_output_Folder</span><span class="p">,</span> <span class="n">my_study</span><span class="p">):</span>
@@ -193,42 +124,30 @@
</pre></div>
</div>
-
</div>
<footer>
-
<hr/>
<div role="contentinfo">
- <p>
- © Copyright 2018, Hanna Julienne
-
- </p>
+ <p>© Copyright 2018, Hanna Julienne.</p>
</div>
- Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/rtfd/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
-</footer>
+ Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
+ <a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
+ provided by <a href="https://readthedocs.org">Read the Docs</a>.
+
+</footer>
</div>
</div>
-
</section>
-
</div>
-
-
-
- <script type="text/javascript">
+ <script>
jQuery(function () {
SphinxRtdTheme.Navigation.enable(true);
});
- </script>
-
-
-
-
-
+ </script>
</body>
</html>
\ No newline at end of file
diff --git a/doc/_build/html/_sources/index.rst.txt b/doc/_build/html/_sources/index.rst.txt
index 83387d811424fce8607e4741070f08c1c1c48550..1998c87266db096afb055e1ca8b7f5200aa3aabb 100644
--- a/doc/_build/html/_sources/index.rst.txt
+++ b/doc/_build/html/_sources/index.rst.txt
@@ -10,6 +10,8 @@ Welcome to jass_preprocessing's documentation!
:maxdepth: 2
:caption: Contents:
+ index
+
What is jass preprocessing ?
============================
Jass preprocessing is a tool that takes in input
@@ -38,9 +40,9 @@ The QC and preprocessing step goes as follow:
(input format needed to perform LD-score)
+-------+-----------+--------+----+----+-----+-----+
-| chrom | rsID | pos | A0 | A1 | Z | P |
+| chrom | rsID | pos | A0 | A1 | Z | P |
+-------+-----------+--------+----+----+-----+-----+
-| 1 | rs4075116 |1003629 | C | T |0.30 | 0.76|
+| 1 | rs4075116 |1003629 | C | T | 0.3 | 0.76|
+-------+-----------+--------+----+----+-----+-----+
@@ -56,19 +58,21 @@ 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 that order, without header:
+* 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:
+
++-----+------------+---------+-------+-----+-----+
+| 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 |
++-----+------------+---------+-------+-----+-----+
+| 1 | rs892586 |0.7670447| 23116 | C | G |
++-----+------------+---------+-------+-----+-----+
-+-----+-----+------------+-----+-----+---------+
-| chr | pos | snp_id | ref | alt | MAF |
-+=====+=====+============+=====+=====+=========+
-| 1 |13116| rs62635286 | T | G |0.0970447|
-+-----+-----+------------+-----+-----+---------+
-| 1 |13118| rs200579949| A | G |0.0970447|
-+-----+-----+------------+-----+-----+---------+
-| 1 |14604| rs541940975| A | G | 0.147564|
-+-----+-----+------------+-----+-----+---------+
-| 1 |14930| rs75454623 | A | G | 0.482228|
-+-----+-----+------------+-----+-----+---------+
* 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.
@@ -79,27 +83,31 @@ Input
* the fields are:
-+-------------------------------------------+------------------------------------------------------------+
-| category | field name |
-+===========================================+============================================================+
-| path to the data | filename |
-+-------------------------------------------+------------------------------------------------------------+
-| study info fields | Consortium,Outcome,fullName,type,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 |
-+-------------------------------------------+------------------------------------------------------------+
++-------------------------------------------+---------------------------------------------------------------+
+| category | field name |
++===========================================+===============================================================+
+| path to the data | filename |
++-------------------------------------------+---------------------------------------------------------------+
+| study info fields | Consortium,Outcome,fullName,type,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.
+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.
+
+.. 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"
-.. csv-table:: GWAS information table!
- :header: "filename","consortia","outcome","fullName","type","Nsample","Ncase","Ncontrol","Nsnp","snpid","a1","a2","freq","pval","n","z","OR","se","code","imp","ncas","ncont"
- "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
Command line usage example:
@@ -117,6 +125,6 @@ Indices and tables
* :ref:`genindex`
* :ref:`modindex`
-.. automodule:: impute_jass
+.. automodule:: jass_preprocessing
:members:
* :ref:`search`
diff --git a/doc/_build/html/_static/basic.css b/doc/_build/html/_static/basic.css
index ea6972d55273ba89dd060c362ed5662aa53049dd..eeb0519a69bacca5e0d1dc516e93d845743dabf0 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 2007-2019 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2022 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
@@ -15,6 +15,12 @@ div.clearer {
clear: both;
}
+div.section::after {
+ display: block;
+ content: '';
+ clear: left;
+}
+
/* -- relbar ---------------------------------------------------------------- */
div.related {
@@ -124,7 +130,7 @@ ul.search li a {
font-weight: bold;
}
-ul.search li div.context {
+ul.search li p.context {
color: #888;
margin: 2px 0 0 30px;
text-align: left;
@@ -216,7 +222,7 @@ table.modindextable td {
/* -- general body styles --------------------------------------------------- */
div.body {
- min-width: 450px;
+ min-width: 360px;
max-width: 800px;
}
@@ -230,7 +236,6 @@ div.body p, div.body dd, div.body li, div.body blockquote {
a.headerlink {
visibility: hidden;
}
-
a.brackets:before,
span.brackets > a:before{
content: "[";
@@ -241,6 +246,7 @@ span.brackets > a:after {
content: "]";
}
+
h1:hover > a.headerlink,
h2:hover > a.headerlink,
h3:hover > a.headerlink,
@@ -271,25 +277,25 @@ p.rubric {
font-weight: bold;
}
-img.align-left, .figure.align-left, object.align-left {
+img.align-left, figure.align-left, .figure.align-left, object.align-left {
clear: left;
float: left;
margin-right: 1em;
}
-img.align-right, .figure.align-right, object.align-right {
+img.align-right, figure.align-right, .figure.align-right, object.align-right {
clear: right;
float: right;
margin-left: 1em;
}
-img.align-center, .figure.align-center, object.align-center {
+img.align-center, figure.align-center, .figure.align-center, object.align-center {
display: block;
margin-left: auto;
margin-right: auto;
}
-img.align-default, .figure.align-default {
+img.align-default, figure.align-default, .figure.align-default {
display: block;
margin-left: auto;
margin-right: auto;
@@ -313,24 +319,29 @@ img.align-default, .figure.align-default {
/* -- sidebars -------------------------------------------------------------- */
-div.sidebar {
+div.sidebar,
+aside.sidebar {
margin: 0 0 0.5em 1em;
border: 1px solid #ddb;
- padding: 7px 7px 0 7px;
+ padding: 7px;
background-color: #ffe;
width: 40%;
float: right;
+ clear: right;
+ overflow-x: auto;
}
p.sidebar-title {
font-weight: bold;
}
+div.admonition, div.topic, blockquote {
+ clear: left;
+}
/* -- topics ---------------------------------------------------------------- */
-
div.topic {
border: 1px solid #ccc;
- padding: 7px 7px 0 7px;
+ padding: 7px;
margin: 10px 0 10px 0;
}
@@ -352,10 +363,6 @@ div.admonition dt {
font-weight: bold;
}
-div.admonition dl {
- margin-bottom: 0;
-}
-
p.admonition-title {
margin: 0px 10px 5px 0px;
font-weight: bold;
@@ -366,9 +373,30 @@ div.body p.centered {
margin-top: 25px;
}
+/* -- content of sidebars/topics/admonitions -------------------------------- */
+
+div.sidebar > :last-child,
+aside.sidebar > :last-child,
+div.topic > :last-child,
+div.admonition > :last-child {
+ margin-bottom: 0;
+}
+
+div.sidebar::after,
+aside.sidebar::after,
+div.topic::after,
+div.admonition::after,
+blockquote::after {
+ display: block;
+ content: '';
+ clear: both;
+}
+
/* -- tables ---------------------------------------------------------------- */
table.docutils {
+ margin-top: 10px;
+ margin-bottom: 10px;
border: 0;
border-collapse: collapse;
}
@@ -398,10 +426,6 @@ 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;
@@ -416,32 +440,34 @@ table.citation td {
border-bottom: none;
}
-th > p:first-child,
-td > p:first-child {
+th > :first-child,
+td > :first-child {
margin-top: 0px;
}
-th > p:last-child,
-td > p:last-child {
+th > :last-child,
+td > :last-child {
margin-bottom: 0px;
}
/* -- figures --------------------------------------------------------------- */
-div.figure {
+div.figure, figure {
margin: 0.5em;
padding: 0.5em;
}
-div.figure p.caption {
+div.figure p.caption, figcaption {
padding: 0.3em;
}
-div.figure p.caption span.caption-number {
+div.figure p.caption span.caption-number,
+figcaption span.caption-number {
font-style: italic;
}
-div.figure p.caption span.caption-text {
+div.figure p.caption span.caption-text,
+figcaption span.caption-text {
}
/* -- field list styles ----------------------------------------------------- */
@@ -468,10 +494,71 @@ table.field-list td, table.field-list th {
/* -- hlist styles ---------------------------------------------------------- */
+table.hlist {
+ margin: 1em 0;
+}
+
table.hlist td {
vertical-align: top;
}
+/* -- object description styles --------------------------------------------- */
+
+.sig {
+ font-family: 'Consolas', 'Menlo', 'DejaVu Sans Mono', 'Bitstream Vera Sans Mono', monospace;
+}
+
+.sig-name, code.descname {
+ background-color: transparent;
+ font-weight: bold;
+}
+
+.sig-name {
+ font-size: 1.1em;
+}
+
+code.descname {
+ font-size: 1.2em;
+}
+
+.sig-prename, code.descclassname {
+ background-color: transparent;
+}
+
+.optional {
+ font-size: 1.3em;
+}
+
+.sig-paren {
+ font-size: larger;
+}
+
+.sig-param.n {
+ font-style: italic;
+}
+
+/* C++ specific styling */
+
+.sig-inline.c-texpr,
+.sig-inline.cpp-texpr {
+ font-family: unset;
+}
+
+.sig.c .k, .sig.c .kt,
+.sig.cpp .k, .sig.cpp .kt {
+ color: #0033B3;
+}
+
+.sig.c .m,
+.sig.cpp .m {
+ color: #1750EB;
+}
+
+.sig.c .s, .sig.c .sc,
+.sig.cpp .s, .sig.cpp .sc {
+ color: #067D17;
+}
+
/* -- other body styles ----------------------------------------------------- */
@@ -495,17 +582,36 @@ ol.upperroman {
list-style: upper-roman;
}
-li > p:first-child {
+:not(li) > ol > li:first-child > :first-child,
+:not(li) > ul > li:first-child > :first-child {
margin-top: 0px;
}
-li > p:last-child {
+:not(li) > ol > li:last-child > :last-child,
+:not(li) > ul > li:last-child > :last-child {
margin-bottom: 0px;
}
+ol.simple ol p,
+ol.simple ul p,
+ul.simple ol p,
+ul.simple ul p {
+ margin-top: 0;
+}
+
+ol.simple > li:not(:first-child) > p,
+ul.simple > li:not(:first-child) > p {
+ margin-top: 0;
+}
+
+ol.simple p,
+ul.simple p {
+ margin-bottom: 0;
+}
dl.footnote > dt,
dl.citation > dt {
float: left;
+ margin-right: 0.5em;
}
dl.footnote > dd,
@@ -530,11 +636,11 @@ 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;
@@ -546,7 +652,7 @@ dl {
margin-bottom: 15px;
}
-dd > p:first-child {
+dd > :first-child {
margin-top: 0px;
}
@@ -560,6 +666,11 @@ dd {
margin-left: 30px;
}
+dl > dd:last-child,
+dl > dd:last-child > :last-child {
+ margin-bottom: 0;
+}
+
dt:target, span.highlighted {
background-color: #fbe54e;
}
@@ -573,14 +684,6 @@ dl.glossary dt {
font-size: 1.1em;
}
-.optional {
- font-size: 1.3em;
-}
-
-.sig-paren {
- font-size: larger;
-}
-
.versionmodified {
font-style: italic;
}
@@ -621,8 +724,9 @@ dl.glossary dt {
.classifier:before {
font-style: normal;
- margin: 0.5em;
+ margin: 0 0.5em;
content: ":";
+ display: inline-block;
}
abbr, acronym {
@@ -637,29 +741,69 @@ pre {
overflow-y: hidden; /* fixes display issues on Chrome browsers */
}
+pre, div[class*="highlight-"] {
+ clear: both;
+}
+
span.pre {
-moz-hyphens: none;
-ms-hyphens: none;
-webkit-hyphens: none;
hyphens: none;
+ white-space: nowrap;
+}
+
+div[class*="highlight-"] {
+ margin: 1em 0;
}
td.linenos pre {
- padding: 5px 0px;
border: 0;
background-color: transparent;
color: #aaa;
}
table.highlighttable {
- margin-left: 0.5em;
+ display: block;
+}
+
+table.highlighttable tbody {
+ display: block;
+}
+
+table.highlighttable tr {
+ display: flex;
}
table.highlighttable td {
- padding: 0 0.5em 0 0.5em;
+ margin: 0;
+ padding: 0;
+}
+
+table.highlighttable td.linenos {
+ padding-right: 0.5em;
+}
+
+table.highlighttable td.code {
+ flex: 1;
+ overflow: hidden;
+}
+
+.highlight .hll {
+ display: block;
+}
+
+div.highlight pre,
+table.highlighttable pre {
+ margin: 0;
+}
+
+div.code-block-caption + div {
+ margin-top: 0;
}
div.code-block-caption {
+ margin-top: 1em;
padding: 2px 5px;
font-size: small;
}
@@ -668,8 +812,14 @@ div.code-block-caption code {
background-color: transparent;
}
-div.code-block-caption + div > div.highlight > pre {
- margin-top: 0;
+table.highlighttable td.linenos,
+span.linenos,
+div.highlight span.gp { /* gp: Generic.Prompt */
+ user-select: none;
+ -webkit-user-select: text; /* Safari fallback only */
+ -webkit-user-select: none; /* Chrome/Safari */
+ -moz-user-select: none; /* Firefox */
+ -ms-user-select: none; /* IE10+ */
}
div.code-block-caption span.caption-number {
@@ -681,21 +831,7 @@ div.code-block-caption span.caption-text {
}
div.literal-block-wrapper {
- padding: 1em 1em 0;
-}
-
-div.literal-block-wrapper div.highlight {
- margin: 0;
-}
-
-code.descname {
- background-color: transparent;
- font-weight: bold;
- font-size: 1.2em;
-}
-
-code.descclassname {
- background-color: transparent;
+ margin: 1em 0;
}
code.xref, a code {
@@ -736,8 +872,7 @@ span.eqno {
}
span.eqno a.headerlink {
- position: relative;
- left: 0px;
+ position: absolute;
z-index: 1;
}
diff --git a/doc/_build/html/_static/doctools.js b/doc/_build/html/_static/doctools.js
index b33f87fcb249ea9b0e0a07fa9c5f2595ea925709..527b876ca636d9a23d0cb3cc73ff6355b94fd7da 100644
--- a/doc/_build/html/_static/doctools.js
+++ b/doc/_build/html/_static/doctools.js
@@ -2,313 +2,155 @@
* doctools.js
* ~~~~~~~~~~~
*
- * Sphinx JavaScript utilities for all documentation.
+ * Base JavaScript utilities for all Sphinx HTML documentation.
*
- * :copyright: Copyright 2007-2019 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2022 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
-
-/**
- * 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
- */
-jQuery.urldecode = function(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];
+"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);
}
- 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.
*/
-var Documentation = {
-
- init : function() {
- this.fixFirefoxAnchorBug();
- this.highlightSearchWords();
- this.initIndexTable();
- if (DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) {
- this.initOnKeyListeners();
- }
+const Documentation = {
+ init: () => {
+ Documentation.initDomainIndexTable();
+ Documentation.initOnKeyListeners();
},
/**
* i18n support
*/
- TRANSLATIONS : {},
- PLURAL_EXPR : function(n) { return n === 1 ? 0 : 1; },
- LOCALE : 'unknown',
+ TRANSLATIONS: {},
+ PLURAL_EXPR: (n) => (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 : function(string) {
- var translated = Documentation.TRANSLATIONS[string];
- if (typeof translated === 'undefined')
- return string;
- return (typeof translated === 'string') ? translated : translated[0];
- },
-
- ngettext : function(singular, plural, n) {
- var translated = Documentation.TRANSLATIONS[singular];
- if (typeof translated === 'undefined')
- return (n == 1) ? singular : plural;
- return translated[Documentation.PLURALEXPR(n)];
+ 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
+ }
},
- 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;
+ ngettext: (singular, plural, n) => {
+ const translated = Documentation.TRANSLATIONS[singular];
+ if (typeof translated !== "undefined")
+ return translated[Documentation.PLURAL_EXPR(n)];
+ return n === 1 ? singular : plural;
},
- /**
- * add context elements like header anchor links
- */
- 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() {
- $('<a class="headerlink">\u00B6</a>').
- attr('href', '#' + this.id).
- attr('title', _('Permalink to this definition')).
- appendTo(this);
- });
+ addTranslations: (catalog) => {
+ Object.assign(Documentation.TRANSLATIONS, catalog.messages);
+ Documentation.PLURAL_EXPR = new Function(
+ "n",
+ `return (${catalog.plural_expr})`
+ );
+ Documentation.LOCALE = catalog.locale;
},
/**
- * workaround a firefox stupidity
- * see: https://bugzilla.mozilla.org/show_bug.cgi?id=645075
+ * helper function to focus on search bar
*/
- fixFirefoxAnchorBug : function() {
- if (document.location.hash && $.browser.mozilla)
- window.setTimeout(function() {
- document.location.href += '';
- }, 10);
+ focusSearchBar: () => {
+ document.querySelectorAll("input[name=q]")[0]?.focus();
},
/**
- * highlight the search words provided in the url in the text
+ * Initialise the domain index toggle buttons
*/
- 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 = $('body');
+ initDomainIndexTable: () => {
+ const toggler = (el) => {
+ const idNumber = el.id.substr(7);
+ const toggledRows = document.querySelectorAll(`tr.cg-${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 = ""));
}
- 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();
- }
- },
-
- /**
- * helper function to hide the search marks again
- */
- hideSearchWords : function() {
- $('#searchbox .highlight-link').fadeOut(300);
- $('span.highlighted').removeClass('highlighted');
- },
-
- /**
- * 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);
+ 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);
},
- initOnKeyListeners: function() {
- $(document).keyup(function(event) {
- var activeElementType = document.activeElement.tagName;
- // don't navigate when in search box or textarea
- if (activeElementType !== 'TEXTAREA' && activeElementType !== 'INPUT' && activeElementType !== 'SELECT') {
- switch (event.keyCode) {
- case 37: // left
- var prevHref = $('link[rel="prev"]').prop('href');
- if (prevHref) {
- window.location.href = prevHref;
- return false;
+ 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();
}
- case 39: // right
- var nextHref = $('link[rel="next"]').prop('href');
- if (nextHref) {
- window.location.href = nextHref;
- return false;
+ break;
+ case "ArrowRight":
+ if (!DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) break;
+
+ const nextLink = document.querySelector('link[rel="next"]');
+ if (nextLink && nextLink.href) {
+ window.location.href = nextLink.href;
+ event.preventDefault();
}
+ break;
}
}
+
+ // some keyboard layouts may need Shift to get /
+ switch (event.key) {
+ case "/":
+ if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) break;
+ Documentation.focusSearchBar();
+ event.preventDefault();
+ }
});
- }
+ },
};
// quick alias for translations
-_ = Documentation.gettext;
+const _ = Documentation.gettext;
-$(document).ready(function() {
- Documentation.init();
-});
+_ready(Documentation.init);
diff --git a/doc/_build/html/_static/documentation_options.js b/doc/_build/html/_static/documentation_options.js
index ad3a3d9951050f3fd099b523db3c945db6691c36..a7f754b66f245c8342c8dfc42de1b439f620054f 100644
--- a/doc/_build/html/_static/documentation_options.js
+++ b/doc/_build/html/_static/documentation_options.js
@@ -1,10 +1,14 @@
var DOCUMENTATION_OPTIONS = {
URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
VERSION: '1.0',
- LANGUAGE: 'None',
+ LANGUAGE: 'en',
COLLAPSE_INDEX: false,
+ BUILDER: 'html',
FILE_SUFFIX: '.html',
+ LINK_SUFFIX: '.html',
HAS_SOURCE: true,
SOURCELINK_SUFFIX: '.txt',
- NAVIGATION_WITH_KEYS: false
+ NAVIGATION_WITH_KEYS: false,
+ SHOW_SEARCH_SUMMARY: true,
+ ENABLE_SEARCH_SHORTCUTS: true,
};
\ No newline at end of file
diff --git a/doc/_build/html/_static/jquery.js b/doc/_build/html/_static/jquery.js
index a1c07fd803b5fc9c54f44e31123ae4fa11e134b0..c4c6022f2982e8dae64cebd6b9a2b59f2547faad 100644
--- a/doc/_build/html/_static/jquery.js
+++ b/doc/_build/html/_static/jquery.js
@@ -1,2 +1,2 @@
-/*! jQuery v3.4.1 | (c) JS Foundation and other contributors | jquery.org/license */
-!function(e,t){"use strict";"object"==typeof module&&"object"==typeof module.exports?module.exports=e.document?t(e,!0):function(e){if(!e.document)throw new Error("jQuery requires a window with a document");return t(e)}:t(e)}("undefined"!=typeof window?window:this,function(C,e){"use strict";var t=[],E=C.document,r=Object.getPrototypeOf,s=t.slice,g=t.concat,u=t.push,i=t.indexOf,n={},o=n.toString,v=n.hasOwnProperty,a=v.toString,l=a.call(Object),y={},m=function(e){return"function"==typeof e&&"number"!=typeof e.nodeType},x=function(e){return null!=e&&e===e.window},c={type:!0,src:!0,nonce:!0,noModule:!0};function b(e,t,n){var r,i,o=(n=n||E).createElement("script");if(o.text=e,t)for(r in c)(i=t[r]||t.getAttribute&&t.getAttribute(r))&&o.setAttribute(r,i);n.head.appendChild(o).parentNode.removeChild(o)}function w(e){return null==e?e+"":"object"==typeof e||"function"==typeof e?n[o.call(e)]||"object":typeof e}var f="3.4.1",k=function(e,t){return new k.fn.init(e,t)},p=/^[\s\uFEFF\xA0]+|[\s\uFEFF\xA0]+$/g;function d(e){var t=!!e&&"length"in e&&e.length,n=w(e);return!m(e)&&!x(e)&&("array"===n||0===t||"number"==typeof t&&0<t&&t-1 in e)}k.fn=k.prototype={jquery:f,constructor:k,length:0,toArray:function(){return s.call(this)},get:function(e){return null==e?s.call(this):e<0?this[e+this.length]:this[e]},pushStack:function(e){var t=k.merge(this.constructor(),e);return t.prevObject=this,t},each:function(e){return k.each(this,e)},map:function(n){return this.pushStack(k.map(this,function(e,t){return n.call(e,t,e)}))},slice:function(){return this.pushStack(s.apply(this,arguments))},first:function(){return this.eq(0)},last:function(){return this.eq(-1)},eq:function(e){var t=this.length,n=+e+(e<0?t:0);return this.pushStack(0<=n&&n<t?[this[n]]:[])},end:function(){return this.prevObject||this.constructor()},push:u,sort:t.sort,splice:t.splice},k.extend=k.fn.extend=function(){var 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diff --git a/doc/_build/html/_static/pygments.css b/doc/_build/html/_static/pygments.css
index 20c4814dcf0d3f437ee9a46f5957e3165aa5fb17..691aeb82d0057a353637453f168872571a8e5328 100644
--- a/doc/_build/html/_static/pygments.css
+++ b/doc/_build/html/_static/pygments.css
@@ -1,5 +1,10 @@
+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; }
.highlight .hll { background-color: #ffffcc }
-.highlight { background: #eeffcc; }
+.highlight { background: #eeffcc; }
.highlight .c { color: #408090; font-style: italic } /* Comment */
.highlight .err { border: 1px solid #FF0000 } /* Error */
.highlight .k { color: #007020; font-weight: bold } /* Keyword */
diff --git a/doc/_build/html/_static/searchtools.js b/doc/_build/html/_static/searchtools.js
index 6031f991319e4a258c6aba6ad0512fd7b91fe5cb..e89e34d4e7729c9cf60e90e97ecc0507ebc398ec 100644
--- a/doc/_build/html/_static/searchtools.js
+++ b/doc/_build/html/_static/searchtools.js
@@ -4,22 +4,24 @@
*
* Sphinx JavaScript utilities for the full-text search.
*
- * :copyright: Copyright 2007-2019 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2022 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
+"use strict";
-if (!Scorer) {
- /**
- * Simple result scoring code.
- */
+/**
+ * Simple result scoring code.
+ */
+if (typeof Scorer === "undefined") {
var Scorer = {
// Implement the following function to further tweak the score for each result
- // The function takes a result array [filename, title, anchor, descr, score]
+ // The function takes a result array [docname, title, anchor, descr, score, filename]
// and returns the new score.
/*
- score: function(result) {
- return result[4];
+ score: result => {
+ const [docname, title, anchor, descr, score, filename] = result
+ return score
},
*/
@@ -28,9 +30,11 @@ if (!Scorer) {
// 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,
@@ -39,436 +43,495 @@ if (!Scorer) {
partialTitle: 7,
// query found in terms
term: 5,
- partialTerm: 2
+ partialTerm: 2,
};
}
-if (!splitQuery) {
- function splitQuery(query) {
- return query.split(/\s+/);
+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;
+ }
+ 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
*/
-var Search = {
-
- _index : null,
- _queued_query : null,
- _pulse_status : -1,
-
- htmlToText : function(htmlString) {
- var htmlElement = document.createElement('span');
- htmlElement.innerHTML = htmlString;
- $(htmlElement).find('.headerlink').remove();
- docContent = $(htmlElement).find('[role=main]')[0];
- return docContent.textContent || docContent.innerText;
+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 "";
},
- init : function() {
- var params = $.getQueryParameters();
- if (params.q) {
- var query = params.q[0];
- $('input[name="q"]')[0].value = query;
- this.performSearch(query);
- }
+ 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);
},
- 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;
- }
- }});
- },
+ loadIndex: (url) =>
+ (document.body.appendChild(document.createElement("script")).src = url),
- setIndex : function(index) {
- var q;
- this._index = index;
- if ((q = this._queued_query) !== null) {
- this._queued_query = null;
- Search.query(q);
+ setIndex: (index) => {
+ Search._index = index;
+ if (Search._queued_query !== null) {
+ const query = Search._queued_query;
+ Search._queued_query = null;
+ Search.query(query);
}
},
- hasIndex : function() {
- return this._index !== null;
- },
+ hasIndex: () => Search._index !== null,
- deferQuery : function(query) {
- this._queued_query = query;
- },
+ deferQuery: (query) => (Search._queued_query = query),
- stopPulse : function() {
- this._pulse_status = 0;
- },
+ stopPulse: () => (Search._pulse_status = -1),
- startPulse : function() {
- if (this._pulse_status >= 0)
- return;
- function pulse() {
- var i;
+ startPulse: () => {
+ if (Search._pulse_status >= 0) return;
+
+ const pulse = () => {
Search._pulse_status = (Search._pulse_status + 1) % 4;
- var dotString = '';
- for (i = 0; i < Search._pulse_status; i++)
- dotString += '.';
- Search.dots.text(dotString);
- if (Search._pulse_status > -1)
- window.setTimeout(pulse, 500);
- }
+ Search.dots.innerText = ".".repeat(Search._pulse_status);
+ if (Search._pulse_status >= 0) window.setTimeout(pulse, 500);
+ };
pulse();
},
/**
* perform a search for something (or wait until index is loaded)
*/
- performSearch : function(query) {
+ performSearch: (query) => {
// create the required interface elements
- 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();
+ 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();
// index already loaded, the browser was quick!
- if (this.hasIndex())
- this.query(query);
- else
- this.deferQuery(query);
+ if (Search.hasIndex()) Search.query(query);
+ else Search.deferQuery(query);
},
/**
* execute search (requires search index to be loaded)
*/
- 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());
- }
+ 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;
- if ($u.indexOf(stopwords, tmp[i].toLowerCase()) != -1 || tmp[i].match(/^\d+$/) ||
- tmp[i] === "") {
- // skip this "word"
- continue;
- }
// stem the word
- 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;
+ let word = stemmer.stemWord(queryTermLower);
// select the correct list
- if (word[0] == '-') {
- toAppend = excluded;
- word = word.substr(1);
- }
+ if (word[0] === "-") excludedTerms.add(word.substr(1));
else {
- toAppend = searchterms;
- hlterms.push(tmp[i].toLowerCase());
+ searchTerms.add(word);
+ highlightTerms.add(queryTermLower);
}
- // only add if not already in the list
- if (!$u.contains(toAppend, word))
- toAppend.push(word);
- }
- var highlightstring = '?highlight=' + $.urlencode(hlterms.join(" "));
+ });
- // console.debug('SEARCH: searching for:');
- // console.info('required: ', searchterms);
- // console.info('excluded: ', excluded);
+ if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js
+ localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" "))
+ }
- // prepare search
- var terms = this._index.terms;
- var titleterms = this._index.titleterms;
+ // console.debug("SEARCH: searching for:");
+ // console.info("required: ", [...searchTerms]);
+ // console.info("excluded: ", [...excludedTerms]);
+
+ // array of [docname, title, anchor, descr, score, filename]
+ let results = [];
+ _removeChildren(document.getElementById("search-progress"));
+
+ const queryLower = query.toLowerCase();
+ for (const [title, foundTitles] of Object.entries(allTitles)) {
+ if (title.toLowerCase().includes(queryLower) && (queryLower.length >= title.length/2)) {
+ for (const [file, id] of foundTitles) {
+ let score = Math.round(100 * queryLower.length / title.length)
+ results.push([
+ docNames[file],
+ titles[file] !== title ? `${titles[file]} > ${title}` : title,
+ id !== null ? "#" + id : "",
+ null,
+ score,
+ filenames[file],
+ ]);
+ }
+ }
+ }
- // array of [filename, title, anchor, descr, score]
- var results = [];
- $('#search-progress').empty();
+ // 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],
+ ]);
+ }
+ }
+ }
// lookup as object
- 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));
- }
+ objectTerms.forEach((term) =>
+ results.push(...Search.performObjectSearch(term, objectTerms))
+ );
// lookup as search terms in fulltext
- results = results.concat(this.performTermsSearch(searchterms, excluded, terms, titleterms));
+ results.push(...Search.performTermsSearch(searchTerms, excludedTerms));
// let the scorer override scores with a custom scoring function
- if (Scorer.score) {
- for (i = 0; i < results.length; i++)
- results[i][4] = Scorer.score(results[i]);
- }
+ if (Scorer.score) results.forEach((item) => (item[4] = Scorer.score(item)));
// 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(function(a, b) {
- var left = a[4];
- var right = b[4];
- if (left > right) {
- return 1;
- } else if (left < right) {
- return -1;
- } else {
+ results.sort((a, b) => {
+ const leftScore = a[4];
+ const rightScore = b[4];
+ if (leftScore === rightScore) {
// same score: sort alphabetically
- left = a[1].toLowerCase();
- right = b[1].toLowerCase();
- return (left > right) ? -1 : ((left < right) ? 1 : 0);
+ const leftTitle = a[1].toLowerCase();
+ const rightTitle = b[1].toLowerCase();
+ if (leftTitle === rightTitle) return 0;
+ return leftTitle > rightTitle ? -1 : 1; // inverted is intentional
}
+ 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
- var resultCount = results.length;
- function displayNextItem() {
- // results left, load the summary and display it
- if (results.length) {
- var item = results.pop();
- var listItem = $('<li style="display:none"></li>');
- if (DOCUMENTATION_OPTIONS.FILE_SUFFIX === '') {
- // dirhtml builder
- var dirname = item[0] + '/';
- if (dirname.match(/\/index\/$/)) {
- dirname = dirname.substring(0, dirname.length-6);
- } else if (dirname == 'index/') {
- dirname = '';
- }
- listItem.append($('<a/>').attr('href',
- DOCUMENTATION_OPTIONS.URL_ROOT + dirname +
- highlightstring + item[2]).html(item[1]));
- } else {
- // normal html builders
- listItem.append($('<a/>').attr('href',
- item[0] + DOCUMENTATION_OPTIONS.FILE_SUFFIX +
- highlightstring + item[2]).html(item[1]));
- }
- if (item[3]) {
- listItem.append($('<span> (' + item[3] + ')</span>'));
- Search.output.append(listItem);
- listItem.slideDown(5, function() {
- displayNextItem();
- });
- } else if (DOCUMENTATION_OPTIONS.HAS_SOURCE) {
- $.ajax({url: DOCUMENTATION_OPTIONS.URL_ROOT + item[0] + DOCUMENTATION_OPTIONS.FILE_SUFFIX,
- dataType: "text",
- complete: function(jqxhr, textstatus) {
- var data = jqxhr.responseText;
- if (data !== '' && data !== undefined) {
- listItem.append(Search.makeSearchSummary(data, searchterms, hlterms));
- }
- Search.output.append(listItem);
- listItem.slideDown(5, function() {
- displayNextItem();
- });
- }});
- } else {
- // no source available, just display title
- Search.output.append(listItem);
- listItem.slideDown(5, function() {
- displayNextItem();
- });
- }
- }
- // 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();
+ _displayNextItem(results, results.length, searchTerms);
},
/**
* search for object names
*/
- 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]]]);
- }
+ 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;
}
- }
+ 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;
},
/**
* search for full-text terms in the index
*/
- performTermsSearch : function(searchterms, excluded, terms, titleterms) {
- var docnames = this._index.docnames;
- var filenames = this._index.filenames;
- var titles = this._index.titles;
+ 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;
- var i, j, file;
- var fileMap = {};
- var scoreMap = {};
- var results = [];
+ const scoreMap = new Map();
+ const fileMap = new Map();
// perform the search on the required terms
- 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}
+ searchTerms.forEach((word) => {
+ const files = [];
+ const arr = [
+ { files: terms[word], score: Scorer.term },
+ { files: titleTerms[word], score: Scorer.title },
];
// add support for partial matches
if (word.length > 2) {
- for (var w in terms) {
- if (w.match(word) && !terms[word]) {
- _o.push({files: terms[w], score: Scorer.partialTerm})
- }
- }
- for (var w in titleterms) {
- if (w.match(word) && !titleterms[word]) {
- _o.push({files: titleterms[w], score: Scorer.partialTitle})
- }
- }
+ 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 });
+ });
}
// no match but word was a required one
- if ($u.every(_o, function(o){return o.files === undefined;})) {
- break;
- }
+ if (arr.every((record) => record.files === undefined)) return;
+
// found search word in contents
- $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;
- }
+ 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;
+ });
});
// create the mapping
- for (j = 0; j < files.length; j++) {
- file = files[j];
- if (file in fileMap)
- fileMap[file].push(word);
- else
- fileMap[file] = [word];
- }
- }
+ files.forEach((file) => {
+ if (fileMap.has(file) && fileMap.get(file).indexOf(word) === -1)
+ fileMap.get(file).push(word);
+ else fileMap.set(file, [word]);
+ });
+ });
// now check if the files don't contain excluded terms
- for (file in fileMap) {
- var valid = true;
-
+ const results = [];
+ for (const [file, wordList] of fileMap) {
// 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
+
+ // as search terms with length < 3 are discarded
+ const filteredTermCount = [...searchTerms].filter(
+ (term) => term.length > 2
+ ).length;
if (
- fileMap[file].length != searchterms.length &&
- fileMap[file].length != filteredTermCount
- ) continue;
+ wordList.length !== searchTerms.size &&
+ wordList.length !== filteredTermCount
+ )
+ continue;
// ensure that none of the excluded terms is in the search result
- 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;
- }
- }
+ if (
+ [...excludedTerms].some(
+ (term) =>
+ terms[term] === file ||
+ titleTerms[term] === file ||
+ (terms[term] || []).includes(file) ||
+ (titleTerms[term] || []).includes(file)
+ )
+ )
+ break;
- // 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]]);
- }
+ // 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],
+ ]);
}
return results;
},
@@ -476,31 +539,28 @@ var Search = {
/**
* helper function to return a node containing the
* search summary for a given text. keywords is a list
- * 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.
+ * of stemmed words.
*/
- makeSearchSummary : function(htmlText, keywords, hlwords) {
- var text = Search.htmlToText(htmlText);
- 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 = $('<div class="context"></div>').text(excerpt);
- $.each(hlwords, function() {
- rv = rv.highlightText(this, 'highlighted');
- });
- return rv;
- }
+ makeSearchSummary: (htmlText, keywords) => {
+ const text = Search.htmlToText(htmlText);
+ if (text === "") return null;
+
+ const textLower = text.toLowerCase();
+ const actualStartPosition = [...keywords]
+ .map((k) => textLower.indexOf(k.toLowerCase()))
+ .filter((i) => i > -1)
+ .slice(-1)[0];
+ const startWithContext = Math.max(actualStartPosition - 120, 0);
+
+ const top = startWithContext === 0 ? "" : "...";
+ const tail = startWithContext + 240 < text.length ? "..." : "";
+
+ let summary = document.createElement("p");
+ summary.classList.add("context");
+ summary.textContent = top + text.substr(startWithContext, 240).trim() + tail;
+
+ return summary;
+ },
};
-$(document).ready(function() {
- Search.init();
-});
+_ready(Search.init);
diff --git a/doc/_build/html/_static/underscore.js b/doc/_build/html/_static/underscore.js
index 5b55f32beaca186f84cca115514f02cddbd1bbd5..cf177d4285ab55fbc16406a5ec827b80e7eecd53 100644
--- a/doc/_build/html/_static/underscore.js
+++ b/doc/_build/html/_static/underscore.js
@@ -1,31 +1,6 @@
-// Underscore.js 1.3.1
-// (c) 2009-2012 Jeremy Ashkenas, DocumentCloud Inc.
-// Underscore is freely distributable under the MIT license.
-// Portions of Underscore are inspired or borrowed from Prototype,
-// Oliver Steele's Functional, and John Resig's Micro-Templating.
-// For all details and documentation:
-// http://documentcloud.github.com/underscore
-(function(){function q(a,c,d){if(a===c)return a!==0||1/a==1/c;if(a==null||c==null)return a===c;if(a._chain)a=a._wrapped;if(c._chain)c=c._wrapped;if(a.isEqual&&b.isFunction(a.isEqual))return a.isEqual(c);if(c.isEqual&&b.isFunction(c.isEqual))return c.isEqual(a);var e=l.call(a);if(e!=l.call(c))return false;switch(e){case "[object String]":return a==String(c);case "[object Number]":return a!=+a?c!=+c:a==0?1/a==1/c:a==+c;case "[object Date]":case "[object Boolean]":return+a==+c;case "[object RegExp]":return a.source==
-c.source&&a.global==c.global&&a.multiline==c.multiline&&a.ignoreCase==c.ignoreCase}if(typeof a!="object"||typeof c!="object")return false;for(var f=d.length;f--;)if(d[f]==a)return true;d.push(a);var f=0,g=true;if(e=="[object Array]"){if(f=a.length,g=f==c.length)for(;f--;)if(!(g=f in a==f in c&&q(a[f],c[f],d)))break}else{if("constructor"in a!="constructor"in c||a.constructor!=c.constructor)return false;for(var h in a)if(b.has(a,h)&&(f++,!(g=b.has(c,h)&&q(a[h],c[h],d))))break;if(g){for(h in c)if(b.has(c,
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@@ -68,79 +35,48 @@
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+ </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
+ <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>
+<li class="toctree-l1"><a class="reference internal" href="_autosummary/jass_preprocessing.compute_score.html">jass_preprocessing.compute_score</a></li>
+<li class="toctree-l1"><a class="reference internal" href="_autosummary/jass_preprocessing.save_output.html">jass_preprocessing.save_output</a></li>
+</ul>
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<div itemprop="articleBody">
-
+
<h1 id="index">Index</h1>
@@ -198,20 +134,50 @@
<h2 id="J">J</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
- <li><a href="_autosummary/jass_preprocessing.html#module-jass_preprocessing">jass_preprocessing (module)</a>
+ <li>
+ jass_preprocessing
+
+ <ul>
+ <li><a href="_autosummary/jass_preprocessing.html#module-jass_preprocessing">module</a>, <a href="index.html#module-jass_preprocessing">[1]</a>
</li>
- <li><a href="_autosummary/jass_preprocessing.html#module-jass_preprocessing.compute_score">jass_preprocessing.compute_score (module)</a>
+ </ul></li>
+ <li>
+ jass_preprocessing.compute_score
+
+ <ul>
+ <li><a href="_autosummary/_autosummary/jass_preprocessing.compute_score.html#module-jass_preprocessing.compute_score">module</a>, <a href="_autosummary/jass_preprocessing.compute_score.html#module-jass_preprocessing.compute_score">[1]</a>, <a href="_autosummary/jass_preprocessing.html#module-jass_preprocessing.compute_score">[2]</a>
</li>
- <li><a href="_autosummary/jass_preprocessing.html#module-jass_preprocessing.dna_utils">jass_preprocessing.dna_utils (module)</a>
+ </ul></li>
+ <li>
+ jass_preprocessing.dna_utils
+
+ <ul>
+ <li><a href="_autosummary/_autosummary/jass_preprocessing.dna_utils.html#module-jass_preprocessing.dna_utils">module</a>, <a href="_autosummary/jass_preprocessing.dna_utils.html#module-jass_preprocessing.dna_utils">[1]</a>, <a href="_autosummary/jass_preprocessing.html#module-jass_preprocessing.dna_utils">[2]</a>
</li>
+ </ul></li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
- <li><a href="_autosummary/jass_preprocessing.html#module-jass_preprocessing.map_gwas">jass_preprocessing.map_gwas (module)</a>
+ <li>
+ jass_preprocessing.map_gwas
+
+ <ul>
+ <li><a href="_autosummary/_autosummary/jass_preprocessing.map_gwas.html#module-jass_preprocessing.map_gwas">module</a>, <a href="_autosummary/jass_preprocessing.html#module-jass_preprocessing.map_gwas">[1]</a>, <a href="_autosummary/jass_preprocessing.map_gwas.html#module-jass_preprocessing.map_gwas">[2]</a>
</li>
- <li><a href="_autosummary/jass_preprocessing.html#module-jass_preprocessing.map_reference">jass_preprocessing.map_reference (module)</a>
+ </ul></li>
+ <li>
+ jass_preprocessing.map_reference
+
+ <ul>
+ <li><a href="_autosummary/_autosummary/jass_preprocessing.map_reference.html#module-jass_preprocessing.map_reference">module</a>, <a href="_autosummary/jass_preprocessing.html#module-jass_preprocessing.map_reference">[1]</a>, <a href="_autosummary/jass_preprocessing.map_reference.html#module-jass_preprocessing.map_reference">[2]</a>
</li>
- <li><a href="_autosummary/jass_preprocessing.html#module-jass_preprocessing.save_output">jass_preprocessing.save_output (module)</a>
+ </ul></li>
+ <li>
+ jass_preprocessing.save_output
+
+ <ul>
+ <li><a href="_autosummary/_autosummary/jass_preprocessing.save_output.html#module-jass_preprocessing.save_output">module</a>, <a href="_autosummary/jass_preprocessing.html#module-jass_preprocessing.save_output">[1]</a>, <a href="_autosummary/jass_preprocessing.save_output.html#module-jass_preprocessing.save_output">[2]</a>
</li>
+ </ul></li>
</ul></td>
</tr></table>
@@ -220,10 +186,25 @@
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="_autosummary/jass_preprocessing.html#jass_preprocessing.map_gwas.map_columns_position">map_columns_position() (in module jass_preprocessing.map_gwas)</a>
</li>
- </ul></td>
- <td style="width: 33%; vertical-align: top;"><ul>
<li><a href="_autosummary/jass_preprocessing.html#jass_preprocessing.map_reference.map_on_ref_panel">map_on_ref_panel() (in module jass_preprocessing.map_reference)</a>
</li>
+ <li>
+ module
+
+ <ul>
+ <li><a href="_autosummary/jass_preprocessing.html#module-jass_preprocessing">jass_preprocessing</a>, <a href="index.html#module-jass_preprocessing">[1]</a>
+</li>
+ <li><a href="_autosummary/_autosummary/jass_preprocessing.compute_score.html#module-jass_preprocessing.compute_score">jass_preprocessing.compute_score</a>, <a href="_autosummary/jass_preprocessing.compute_score.html#module-jass_preprocessing.compute_score">[1]</a>, <a href="_autosummary/jass_preprocessing.html#module-jass_preprocessing.compute_score">[2]</a>
+</li>
+ <li><a href="_autosummary/_autosummary/jass_preprocessing.dna_utils.html#module-jass_preprocessing.dna_utils">jass_preprocessing.dna_utils</a>, <a href="_autosummary/jass_preprocessing.dna_utils.html#module-jass_preprocessing.dna_utils">[1]</a>, <a href="_autosummary/jass_preprocessing.html#module-jass_preprocessing.dna_utils">[2]</a>
+</li>
+ <li><a href="_autosummary/_autosummary/jass_preprocessing.map_gwas.html#module-jass_preprocessing.map_gwas">jass_preprocessing.map_gwas</a>, <a href="_autosummary/jass_preprocessing.html#module-jass_preprocessing.map_gwas">[1]</a>, <a href="_autosummary/jass_preprocessing.map_gwas.html#module-jass_preprocessing.map_gwas">[2]</a>
+</li>
+ <li><a href="_autosummary/_autosummary/jass_preprocessing.map_reference.html#module-jass_preprocessing.map_reference">jass_preprocessing.map_reference</a>, <a href="_autosummary/jass_preprocessing.html#module-jass_preprocessing.map_reference">[1]</a>, <a href="_autosummary/jass_preprocessing.map_reference.html#module-jass_preprocessing.map_reference">[2]</a>
+</li>
+ <li><a href="_autosummary/_autosummary/jass_preprocessing.save_output.html#module-jass_preprocessing.save_output">jass_preprocessing.save_output</a>, <a href="_autosummary/jass_preprocessing.html#module-jass_preprocessing.save_output">[1]</a>, <a href="_autosummary/jass_preprocessing.save_output.html#module-jass_preprocessing.save_output">[2]</a>
+</li>
+ </ul></li>
</ul></td>
</tr></table>
@@ -262,42 +243,30 @@
</div>
-
</div>
<footer>
-
<hr/>
<div role="contentinfo">
- <p>
- © Copyright 2018, Hanna Julienne
-
- </p>
+ <p>© Copyright 2018, Hanna Julienne.</p>
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- Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/rtfd/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
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diff --git a/doc/_build/html/index.html b/doc/_build/html/index.html
index 0e893cadb0a3f55a886fe8095b8deac35646e149..59f8bac8780ced67ee1f4e9c68650c790b869523 100644
--- a/doc/_build/html/index.html
+++ b/doc/_build/html/index.html
@@ -1,65 +1,35 @@
-
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<!DOCTYPE html>
-<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
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+ <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+ <title>Welcome to jass_preprocessing’s documentation! — jass_preprocessing 1.0 documentation</title>
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+ <link rel="next" title="jass_preprocessing.map_gwas" href="_autosummary/jass_preprocessing.map_gwas.html" />
</head>
-<body class="wy-body-for-nav">
-
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+<body class="wy-body-for-nav">
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-<li><a class="reference internal" href="#">Welcome to jass_preprocessing’s documentation!</a></li>
-<li><a class="reference internal" href="#what-is-jass-preprocessing">What is jass preprocessing ?</a></li>
-<li><a class="reference internal" href="#overview">Overview</a></li>
-<li><a class="reference internal" href="#installation">Installation</a></li>
-<li><a class="reference internal" href="#input">Input</a></li>
-<li><a class="reference internal" href="#command-line-usage-example">Command line usage example:</a><ul>
-<li><a class="reference internal" href="#Named Arguments">Named Arguments</a></li>
+ </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
+ <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
+<ul class="current">
+<li class="toctree-l1 current"><a class="current reference internal" href="#">Welcome to jass_preprocessing’s documentation!</a><ul class="simple">
</ul>
</li>
-<li><a class="reference internal" href="#indices-and-tables">Indices and tables</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#what-is-jass-preprocessing">What is jass preprocessing ?</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#overview">Overview</a></li>
+<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>
</ul>
-</div>
-
-
+</li>
+<li class="toctree-l1"><a class="reference internal" href="#indices-and-tables">Indices and tables</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="_autosummary/jass_preprocessing.map_gwas.html">jass_preprocessing.map_gwas</a></li>
+<li class="toctree-l2"><a class="reference internal" href="_autosummary/jass_preprocessing.dna_utils.html">jass_preprocessing.dna_utils</a></li>
+<li class="toctree-l2"><a class="reference internal" href="_autosummary/jass_preprocessing.map_reference.html">jass_preprocessing.map_reference</a></li>
+<li class="toctree-l2"><a class="reference internal" href="_autosummary/jass_preprocessing.compute_score.html">jass_preprocessing.compute_score</a></li>
+<li class="toctree-l2"><a class="reference internal" href="_autosummary/jass_preprocessing.save_output.html">jass_preprocessing.save_output</a></li>
+</ul>
+</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>
+<li class="toctree-l1"><a class="reference internal" href="_autosummary/jass_preprocessing.compute_score.html">jass_preprocessing.compute_score</a></li>
+<li class="toctree-l1"><a class="reference internal" href="_autosummary/jass_preprocessing.save_output.html">jass_preprocessing.save_output</a></li>
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-
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-<h1>Welcome to jass_preprocessing’s documentation!<a class="headerlink" href="#welcome-to-jass-preprocessing-s-documentation" title="Permalink to this headline">¶</a></h1>
+
+ <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>
<div class="toctree-wrapper compound">
+<p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
+<ul class="current">
+<li class="toctree-l1 current"><a class="current reference internal" href="#">Welcome to jass_preprocessing’s documentation!</a><ul class="simple">
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="#what-is-jass-preprocessing">What is jass preprocessing ?</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#overview">Overview</a></li>
+<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>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="#indices-and-tables">Indices and tables</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="_autosummary/jass_preprocessing.map_gwas.html">jass_preprocessing.map_gwas</a></li>
+<li class="toctree-l2"><a class="reference internal" href="_autosummary/jass_preprocessing.dna_utils.html">jass_preprocessing.dna_utils</a></li>
+<li class="toctree-l2"><a class="reference internal" href="_autosummary/jass_preprocessing.map_reference.html">jass_preprocessing.map_reference</a></li>
+<li class="toctree-l2"><a class="reference internal" href="_autosummary/jass_preprocessing.compute_score.html">jass_preprocessing.compute_score</a></li>
+<li class="toctree-l2"><a class="reference internal" href="_autosummary/jass_preprocessing.save_output.html">jass_preprocessing.save_output</a></li>
+</ul>
+</li>
+</ul>
</div>
-</div>
-<div class="section" id="what-is-jass-preprocessing">
-<h1>What is jass preprocessing ?<a class="headerlink" href="#what-is-jass-preprocessing" title="Permalink to this headline">¶</a></h1>
+</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
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>
-</div>
-<div class="section" id="overview">
-<h1>Overview<a class="headerlink" href="#overview" title="Permalink to this headline">¶</a></h1>
+</section>
+<section id="overview">
+<h1>Overview<a class="headerlink" href="#overview" title="Permalink to this heading">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>
@@ -205,65 +165,97 @@ heterogeneous GWAS summary statistics and performs standardization and quality c
<li><p>(Optional) Save the output to one file with a chromosome column</p></li>
</ul>
<p>(input format needed to perform LD-score)</p>
-</div>
-<div class="section" id="installation">
-<h1>Installation<a class="headerlink" href="#installation" title="Permalink to this headline">¶</a></h1>
+<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%" />
+</colgroup>
+<tbody>
+<tr class="row-odd"><td><p>chrom</p></td>
+<td><p>rsID</p></td>
+<td><p>pos</p></td>
+<td><p>A0</p></td>
+<td><p>A1</p></td>
+<td><p>Z</p></td>
+<td><p>P</p></td>
+</tr>
+<tr class="row-even"><td><p>1</p></td>
+<td><p>rs4075116</p></td>
+<td><p>1003629</p></td>
+<td><p>C</p></td>
+<td><p>T</p></td>
+<td><p>0.3</p></td>
+<td><p>0.76</p></td>
+</tr>
+</tbody>
+</table>
+</section>
+<section id="installation">
+<h1>Installation<a class="headerlink" href="#installation" title="Permalink to this heading">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>
-</div>
-<div class="section" id="input">
-<h1>Input<a class="headerlink" href="#input" title="Permalink to this headline">¶</a></h1>
+</section>
+<section id="input">
+<h1>Input<a class="headerlink" href="#input" title="Permalink to this heading">ïƒ</a></h1>
<ul class="simple">
-<li><p>A reference panel (1000 genome format). The user is expected to provide a reference panel in tsv format with the following columns in that order, without header:</p></li>
+<li><p>A reference panel (1000 genome format). 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></blockquote>
<table class="docutils align-default">
<colgroup>
<col style="width: 12%" />
-<col style="width: 12%" />
-<col style="width: 29%" />
+<col style="width: 28%" />
+<col style="width: 21%" />
+<col style="width: 16%" />
<col style="width: 12%" />
<col style="width: 12%" />
-<col style="width: 22%" />
</colgroup>
<thead>
<tr class="row-odd"><th class="head"><p>chr</p></th>
-<th class="head"><p>pos</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>
-<th class="head"><p>MAF</p></th>
</tr>
</thead>
<tbody>
<tr class="row-even"><td><p>1</p></td>
-<td><p>13116</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>
-<td><p>0.0970447</p></td>
</tr>
<tr class="row-odd"><td><p>1</p></td>
-<td><p>13118</p></td>
-<td><p>rs200579949</p></td>
-<td><p>A</p></td>
-<td><p>G</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>
-<td><p>14604</p></td>
-<td><p>rs541940975</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>
-<td><p>0.147564</p></td>
</tr>
<tr class="row-odd"><td><p>1</p></td>
-<td><p>14930</p></td>
-<td><p>rs75454623</p></td>
-<td><p>A</p></td>
+<td><p>rs892586</p></td>
+<td><p>0.7670447</p></td>
+<td><p>23116</p></td>
+<td><p>C</p></td>
<td><p>G</p></td>
-<td><p>0.482228</p></td>
</tr>
</tbody>
</table>
@@ -278,63 +270,87 @@ heterogeneous GWAS summary statistics and performs standardization and quality c
</ul>
</li>
</ul>
+<table class="docutils align-default">
+<colgroup>
+<col style="width: 41%" />
+<col style="width: 59%" />
+</colgroup>
+<thead>
+<tr class="row-odd"><th class="head"><p>category</p></th>
+<th class="head"><p>field name</p></th>
+</tr>
+</thead>
+<tbody>
+<tr class="row-even"><td><p>path to the data</p></td>
+<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>
+</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>
+<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.
+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">¶</a></caption>
+<caption><span class="caption-text">GWAS information table</span><a class="headerlink" href="#id1" title="Permalink to this table">ïƒ</a></caption>
<colgroup>
-<col style="width: 5%" />
-<col style="width: 5%" />
-<col style="width: 5%" />
-<col style="width: 5%" />
-<col style="width: 5%" />
-<col style="width: 5%" />
-<col style="width: 5%" />
-<col style="width: 5%" />
-<col style="width: 5%" />
-<col style="width: 5%" />
-<col style="width: 5%" />
-<col style="width: 5%" />
-<col style="width: 5%" />
-<col style="width: 5%" />
-<col style="width: 5%" />
-<col style="width: 5%" />
-<col style="width: 5%" />
-<col style="width: 5%" />
-<col style="width: 5%" />
-<col style="width: 5%" />
-<col style="width: 5%" />
-<col style="width: 5%" />
+<col style="width: 4%" />
+<col style="width: 4%" />
+<col style="width: 4%" />
+<col style="width: 4%" />
+<col style="width: 4%" />
+<col style="width: 4%" />
+<col style="width: 4%" />
+<col style="width: 4%" />
+<col style="width: 4%" />
+<col style="width: 4%" />
+<col style="width: 4%" />
+<col style="width: 4%" />
+<col style="width: 4%" />
+<col style="width: 4%" />
+<col style="width: 4%" />
+<col style="width: 4%" />
+<col style="width: 4%" />
+<col style="width: 4%" />
+<col style="width: 4%" />
+<col style="width: 4%" />
+<col style="width: 4%" />
+<col style="width: 4%" />
+<col style="width: 4%" />
+<col style="width: 4%" />
</colgroup>
-<tbody>
-<tr class="row-odd"><td><dl class="field-list simple">
-<dt class="field-odd">header</dt>
-<dd class="field-odd"><p>“filenameâ€</p>
-</dd>
-</dl>
-</td>
-<td><p>consortia</p></td>
-<td><p>outcome</p></td>
-<td><p>fullName</p></td>
-<td><p>type</p></td>
-<td><p>Nsample</p></td>
-<td><p>Ncase</p></td>
-<td><p>Ncontrol</p></td>
-<td><p>Nsnp</p></td>
-<td><p>snpid</p></td>
-<td><p>a1</p></td>
-<td><p>a2</p></td>
-<td><p>freq</p></td>
-<td><p>pval</p></td>
-<td><p>n</p></td>
-<td><p>z</p></td>
-<td><p>OR</p></td>
-<td><p>se</p></td>
-<td><p>code</p></td>
-<td><p>imp</p></td>
-<td><p>ncas</p></td>
-<td><p>ncont</p></td>
+<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>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>a1</p></th>
+<th class="head"><p>a2</p></th>
+<th class="head"><p>freq</p></th>
+<th class="head"><p>pval</p></th>
+<th class="head"><p>n</p></th>
+<th class="head"><p>z</p></th>
+<th class="head"><p>OR</p></th>
+<th class="head"><p>se</p></th>
+<th class="head"><p>code</p></th>
+<th class="head"><p>imp</p></th>
+<th class="head"><p>ncas</p></th>
+<th class="head"><p>ncont</p></th>
+<th class="head"><p>imputation_quality</p></th>
+<th class="head"><p>index_type</p></th>
</tr>
+</thead>
+<tbody>
<tr class="row-even"><td><p>GIANT_HEIGHT_Wood_et_al.txt</p></td>
<td><p>GIANT</p></td>
<td><p>HEIGHT</p></td>
@@ -357,24 +373,23 @@ heterogeneous GWAS summary statistics and performs standardization and quality c
<td><p>na</p></td>
<td><p>na</p></td>
<td><p>na</p></td>
+<td><p>imputationInfo</p></td>
+<td><p>rsID</p></td>
</tr>
</tbody>
</table>
-</div>
-<div class="section" id="command-line-usage-example">
-<h1>Command line usage example:<a class="headerlink" href="#command-line-usage-example" title="Permalink to this headline">¶</a></h1>
+</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>
<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>
+<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>
-<div class="section" id="Named Arguments">
-<h2>Named Arguments<a class="headerlink" href="#Named Arguments" title="Permalink to this headline">¶</a></h2>
+<section id="named-arguments">
+<h2>Named Arguments<a class="headerlink" href="#named-arguments" title="Permalink to this heading">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>
@@ -400,67 +415,85 @@ heterogeneous GWAS summary statistics and performs standardization and quality c
</dd>
<dt><kbd>--minimum-MAF</kbd></dt>
<dd><p>Filter the reference panel by minimum allele frequency</p>
-<p>Default: 0.01</p>
+<p>Default: “0.01â€</p>
</dd>
<dt><kbd>--mask-MHC</kbd></dt>
<dd><p>Whether the MHC region should be masked or not. default is False</p>
-<p>Default: False</p>
+<p>Default: “Falseâ€</p>
</dd>
<dt><kbd>--additional-masked-region</kbd></dt>
<dd><p>List of dictionary containing coordinate of region to mask. For example :[{‘chr’:6, ‘start’:50000000, ‘end’: 70000000}, {‘chr’:6, ‘start’:100000000, ‘end’: 120000000}]</p>
+<p>Default: “Noneâ€</p>
+</dd>
+<dt><kbd>--imputation-quality-treshold</kbd></dt>
+<dd><p>minimum imputation quality in summary statistics</p>
+<p>Default: “Noneâ€</p>
</dd>
</dl>
-</div>
-</div>
-<div class="section" id="indices-and-tables">
-<h1>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Permalink to this headline">¶</a></h1>
+</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>
<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">
+<colgroup>
+<col style="width: 10%" />
+<col style="width: 90%" />
+</colgroup>
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="_autosummary/jass_preprocessing.map_gwas.html#module-jass_preprocessing.map_gwas" title="jass_preprocessing.map_gwas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">map_gwas</span></code></a></p></td>
+<td><p>Map GWAS</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="_autosummary/jass_preprocessing.dna_utils.html#module-jass_preprocessing.dna_utils" title="jass_preprocessing.dna_utils"><code class="xref py py-obj docutils literal notranslate"><span class="pre">dna_utils</span></code></a></p></td>
+<td><p>Few fonction to to compute DNA complement</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="_autosummary/jass_preprocessing.map_reference.html#module-jass_preprocessing.map_reference" title="jass_preprocessing.map_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">map_reference</span></code></a></p></td>
+<td><p>Module of function</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="_autosummary/jass_preprocessing.compute_score.html#module-jass_preprocessing.compute_score" title="jass_preprocessing.compute_score"><code class="xref py py-obj docutils literal notranslate"><span class="pre">compute_score</span></code></a></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="_autosummary/jass_preprocessing.save_output.html#module-jass_preprocessing.save_output" title="jass_preprocessing.save_output"><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_output</span></code></a></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
<ul class="simple">
<li><p><a class="reference internal" href="search.html"><span class="std std-ref">Search Page</span></a></p></li>
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diff --git a/doc/_build/html/objects.inv b/doc/_build/html/objects.inv
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+ <meta charset="utf-8" />
+ <meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Python Module Index — jass_preprocessing 1.0 documentation</title>
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+<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>
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<td>   
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<td>   
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<em></em></td></tr>
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-
</div>
<footer>
-
<hr/>
<div role="contentinfo">
- <p>
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- </p>
+ <p>© Copyright 2018, Hanna Julienne.</p>
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- <meta name="viewport" content="width=device-width, initial-scale=1.0">
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+ <meta charset="utf-8" />
+ <meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Search — jass_preprocessing 1.0 documentation</title>
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- <script type="text/javascript" src="_static/js/modernizr.min.js"></script>
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- <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
- <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+ <!--[if lt IE 9]>
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+<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>
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+<li class="toctree-l1"><a class="reference internal" href="index.html#indices-and-tables">Indices and tables</a></li>
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<ul class="wy-breadcrumbs">
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-
- <li>Search</li>
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+ <li><a href="index.html" class="icon icon-home"></a></li>
+ <li class="breadcrumb-item active">Search</li>
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- Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/rtfd/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
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+ <a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
+ provided by <a href="https://readthedocs.org">Read the Docs</a>.
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diff --git a/jass_preprocessing/__main__.py b/jass_preprocessing/__main__.py
index b089d3cbd56aaf02b8e4d7cca8c3d01e0e9e3256..30d6985e955c69f27618fe80b589f39679bd1e4b 100644
--- a/jass_preprocessing/__main__.py
+++ b/jass_preprocessing/__main__.py
@@ -47,30 +47,26 @@ def launch_preprocessing(args):
start = time.time()
print(args.input_folder)
GWAS_link = jp.map_gwas.walkfs(args.input_folder, gwas_filename)[2]
- print(GWAS_link)
+ print('GWAS file found at: {}'.format(GWAS_link))
mapgw = jp.map_gwas.map_columns_position(GWAS_link, gwas_map.loc[tag])
- print(mapgw)
- print(args.imputation_quality_treshold)
if args.imputation_quality_treshold is not 'None':
gw_df = jp.map_gwas.read_gwas(GWAS_link, mapgw, imputation_treshold=eval(args.imputation_quality_treshold))
else:
gw_df = jp.map_gwas.read_gwas(GWAS_link, mapgw)
+ print("#SNPs in GWAS summary statistic file: {}".format(gw_df.shape[0]))
ref = jp.map_reference.read_reference(args.ref_path, bool(args.mask_MHC), float(args.minimum_MAF), region_to_mask=eval(args.additional_masked_region))
- print(ref.shape)
- print(ref.head())
- print(gw_df.shape)
- print(gw_df.head())
mgwas = jp.map_reference.map_on_ref_panel(gw_df, ref, gwas_map.loc[tag, "index_type"])
- print(mgwas.shape)
+
+ print("#SNPs mapped to reference panel: {}".format(mgwas.shape[0]))
mgwas = jp.map_reference.compute_snp_alignement(mgwas)
mgwas = jp.compute_score.compute_z_score(mgwas)
mgwas = jp.compute_score.compute_sample_size(mgwas, args.diagnostic_folder, tag, args.percent_sample_size)
end = time.time()
-
+
+ print("#SNPs remaining after sample size filter: {}".format(mgwas.shape[0]))
print("Preprocessing of {0} in {1}s".format(tag, end-start))
- print(mgwas.head())
jp.save_output.save_output_by_chromosome(mgwas, args.output_folder, tag)
if(args.output_folder_1_file):