Commit 6e22150e authored by Pradat Yoann's avatar Pradat Yoann

clean src

parent c28c9d1f
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<h1>Coverage report:
<span class="pc_cov">10%</span>
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<td class="name left"><a href="manual_py.html">manual.py</a></td>
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<td class="name left"><a href="tests_test_util_py.html">tests/test_util.py</a></td>
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<td>0</td>
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<td class="right" data-ratio="8 8">100%</td>
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<td class="name left"><a href="util_py.html">util.py</a></td>
<td>28</td>
<td>19</td>
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<a class="nav" href="https://coverage.readthedocs.io">coverage.py v5.0</a>,
created at 2020-08-13 15:03
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<h1>Coverage for <b>tests/test_util.py</b> :
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8 statements &nbsp;
<span class="run shortkey_r button_toggle_run">8 run</span>
<span class="mis show_mis shortkey_m button_toggle_mis">0 missing</span>
<span class="exc show_exc shortkey_x button_toggle_exc">0 excluded</span>
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<div id="source">
<p id="t1" class="pln"><span class="n"><a href="#t1">1</a></span><span class="t"><span class="com"># -*- coding: utf-8 -*-</span>&nbsp;</span><span class="r"></span></p>
<p id="t2" class="run"><span class="n"><a href="#t2">2</a></span><span class="t"><span class="str">"""</span>&nbsp;</span><span class="r"></span></p>
<p id="t3" class="pln"><span class="n"><a href="#t3">3</a></span><span class="t"><span class="str">Created on Thu Aug 13 2020</span>&nbsp;</span><span class="r"></span></p>
<p id="t4" class="pln"><span class="n"><a href="#t4">4</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
<p id="t5" class="pln"><span class="n"><a href="#t5">5</a></span><span class="t"><span class="str">@author: Yoann Pradat</span>&nbsp;</span><span class="r"></span></p>
<p id="t6" class="pln"><span class="n"><a href="#t6">6</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
<p id="t7" class="pln"><span class="n"><a href="#t7">7</a></span><span class="t"><span class="str"> CentraleSupelec</span>&nbsp;</span><span class="r"></span></p>
<p id="t8" class="pln"><span class="n"><a href="#t8">8</a></span><span class="t"><span class="str"> MICS laboratory</span>&nbsp;</span><span class="r"></span></p>
<p id="t9" class="pln"><span class="n"><a href="#t9">9</a></span><span class="t"><span class="str"> 9 rue Juliot Curie, Gif-Sur-Yvette, 91190 France</span>&nbsp;</span><span class="r"></span></p>
<p id="t10" class="pln"><span class="n"><a href="#t10">10</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
<p id="t11" class="pln"><span class="n"><a href="#t11">11</a></span><span class="t"><span class="str">Test functions in util.py module.</span>&nbsp;</span><span class="r"></span></p>
<p id="t12" class="pln"><span class="n"><a href="#t12">12</a></span><span class="t"><span class="str">"""</span>&nbsp;</span><span class="r"></span></p>
<p id="t13" class="pln"><span class="n"><a href="#t13">13</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
<p id="t14" class="run"><span class="n"><a href="#t14">14</a></span><span class="t"><span class="key">import</span> <span class="nam">os</span>&nbsp;</span><span class="r"></span></p>
<p id="t15" class="run"><span class="n"><a href="#t15">15</a></span><span class="t"><span class="key">from</span> <span class="op">.</span><span class="op">.</span><span class="nam">util</span> <span class="key">import</span> <span class="nam">load_vcf</span>&nbsp;</span><span class="r"></span></p>
<p id="t16" class="pln"><span class="n"><a href="#t16">16</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
<p id="t17" class="run"><span class="n"><a href="#t17">17</a></span><span class="t"><span class="key">def</span> <span class="nam">test_load_vcf</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
<p id="t18" class="run"><span class="n"><a href="#t18">18</a></span><span class="t"> <span class="nam">print</span><span class="op">(</span><span class="nam">os</span><span class="op">.</span><span class="nam">getcwd</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
<p id="t19" class="run"><span class="n"><a href="#t19">19</a></span><span class="t"> <span class="nam">folder</span> <span class="op">=</span> <span class="str">"./examples/data/TCGA_GA/"</span>&nbsp;</span><span class="r"></span></p>
<p id="t20" class="run"><span class="n"><a href="#t20">20</a></span><span class="t"> <span class="nam">file</span> <span class="op">=</span> <span class="str">"TCGA-A1-A0SB_db9d40fb-bfce-4c3b-a6c2-41c5c88982f1_a3254f8e-3bbd-42fc-abea-a5f25b7648b3.indel.capture.tcga.vcf"</span>&nbsp;</span><span class="r"></span></p>
<p id="t21" class="pln"><span class="n"><a href="#t21">21</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
<p id="t22" class="run"><span class="n"><a href="#t22">22</a></span><span class="t"> <span class="nam">df_vcf</span> <span class="op">=</span> <span class="nam">load_vcf</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
<p id="t23" class="pln"><span class="n"><a href="#t23">23</a></span><span class="t"> <span class="nam">filepath</span> <span class="op">=</span> <span class="nam">os</span><span class="op">.</span><span class="nam">path</span><span class="op">.</span><span class="nam">join</span><span class="op">(</span><span class="nam">folder</span><span class="op">,</span> <span class="nam">file</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
<p id="t24" class="pln"><span class="n"><a href="#t24">24</a></span><span class="t"> <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
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