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Commit c6751854 authored by Pradat Yoann's avatar Pradat Yoann
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[dev] successfully run tests for each of manual, vcf2maf and vep

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src/htmlcov/coverage_html.js 0 → 100644
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src/htmlcov/index.html 0 → 100644
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<!DOCTYPE html>
<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
<title>Coverage report</title>
<link rel="stylesheet" href="style.css" type="text/css">
<script type="text/javascript" src="jquery.min.js"></script>
<script type="text/javascript" src="jquery.ba-throttle-debounce.min.js"></script>
<script type="text/javascript" src="jquery.tablesorter.min.js"></script>
<script type="text/javascript" src="jquery.hotkeys.js"></script>
<script type="text/javascript" src="coverage_html.js"></script>
<script type="text/javascript">
jQuery(document).ready(coverage.index_ready);
</script>
</head>
<body class="indexfile">
<div id="header">
<div class="content">
<h1>Coverage report:
<span class="pc_cov">10%</span>
</h1>
<img id="keyboard_icon" src="keybd_closed.png" alt="Show keyboard shortcuts" />
<form id="filter_container">
<input id="filter" type="text" value="" placeholder="filter..." />
</form>
</div>
</div>
<div class="help_panel">
<img id="panel_icon" src="keybd_open.png" alt="Hide keyboard shortcuts" />
<p class="legend">Hot-keys on this page</p>
<div>
<p class="keyhelp">
<span class="key">n</span>
<span class="key">s</span>
<span class="key">m</span>
<span class="key">x</span>
<span class="key">c</span> &nbsp; change column sorting
</p>
</div>
</div>
<div id="index">
<table class="index">
<thead>
<tr class="tablehead" title="Click to sort">
<th class="name left headerSortDown shortkey_n">Module</th>
<th class="shortkey_s">statements</th>
<th class="shortkey_m">missing</th>
<th class="shortkey_x">excluded</th>
<th class="right shortkey_c">coverage</th>
</tr>
</thead>
<tfoot>
<tr class="total">
<td class="name left">Total</td>
<td>170</td>
<td>153</td>
<td>0</td>
<td class="right" data-ratio="17 170">10%</td>
</tr>
</tfoot>
<tbody>
<tr class="file">
<td class="name left"><a href="manual_py.html">manual.py</a></td>
<td>134</td>
<td>134</td>
<td>0</td>
<td class="right" data-ratio="0 134">0%</td>
</tr>
<tr class="file">
<td class="name left"><a href="tests_test_util_py.html">tests/test_util.py</a></td>
<td>8</td>
<td>0</td>
<td>0</td>
<td class="right" data-ratio="8 8">100%</td>
</tr>
<tr class="file">
<td class="name left"><a href="util_py.html">util.py</a></td>
<td>28</td>
<td>19</td>
<td>0</td>
<td class="right" data-ratio="9 28">32%</td>
</tr>
</tbody>
</table>
<p id="no_rows">
No items found using the specified filter.
</p>
</div>
<div id="footer">
<div class="content">
<p>
<a class="nav" href="https://coverage.readthedocs.io">coverage.py v5.0</a>,
created at 2020-08-13 15:03
</p>
</div>
</div>
</body>
</html>
src/htmlcov/jquery.ba-throttle-debounce.min.js 0 → 100644
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/*
* jQuery throttle / debounce - v1.1 - 3/7/2010
* http://benalman.com/projects/jquery-throttle-debounce-plugin/
*
* Copyright (c) 2010 "Cowboy" Ben Alman
* Dual licensed under the MIT and GPL licenses.
* http://benalman.com/about/license/
*/
(function(b,c){var $=b.jQuery||b.Cowboy||(b.Cowboy={}),a;$.throttle=a=function(e,f,j,i){var h,d=0;if(typeof f!=="boolean"){i=j;j=f;f=c}function g(){var o=this,m=+new Date()-d,n=arguments;function l(){d=+new Date();j.apply(o,n)}function k(){h=c}if(i&&!h){l()}h&&clearTimeout(h);if(i===c&&m>e){l()}else{if(f!==true){h=setTimeout(i?k:l,i===c?e-m:e)}}}if($.guid){g.guid=j.guid=j.guid||$.guid++}return g};$.debounce=function(d,e,f){return f===c?a(d,e,false):a(d,f,e!==false)}})(this);
src/htmlcov/jquery.hotkeys.js 0 → 100644
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/*
* jQuery Hotkeys Plugin
* Copyright 2010, John Resig
* Dual licensed under the MIT or GPL Version 2 licenses.
*
* Based upon the plugin by Tzury Bar Yochay:
* http://github.com/tzuryby/hotkeys
*
* Original idea by:
* Binny V A, http://www.openjs.com/scripts/events/keyboard_shortcuts/
*/
(function(jQuery){
jQuery.hotkeys = {
version: "0.8",
specialKeys: {
8: "backspace", 9: "tab", 13: "return", 16: "shift", 17: "ctrl", 18: "alt", 19: "pause",
20: "capslock", 27: "esc", 32: "space", 33: "pageup", 34: "pagedown", 35: "end", 36: "home",
37: "left", 38: "up", 39: "right", 40: "down", 45: "insert", 46: "del",
96: "0", 97: "1", 98: "2", 99: "3", 100: "4", 101: "5", 102: "6", 103: "7",
104: "8", 105: "9", 106: "*", 107: "+", 109: "-", 110: ".", 111 : "/",
112: "f1", 113: "f2", 114: "f3", 115: "f4", 116: "f5", 117: "f6", 118: "f7", 119: "f8",
120: "f9", 121: "f10", 122: "f11", 123: "f12", 144: "numlock", 145: "scroll", 191: "/", 224: "meta"
},
shiftNums: {
"`": "~", "1": "!", "2": "@", "3": "#", "4": "$", "5": "%", "6": "^", "7": "&",
"8": "*", "9": "(", "0": ")", "-": "_", "=": "+", ";": ": ", "'": "\"", ",": "<",
".": ">", "/": "?", "\\": "|"
}
};
function keyHandler( handleObj ) {
// Only care when a possible input has been specified
if ( typeof handleObj.data !== "string" ) {
return;
}
var origHandler = handleObj.handler,
keys = handleObj.data.toLowerCase().split(" ");
handleObj.handler = function( event ) {
// Don't fire in text-accepting inputs that we didn't directly bind to
if ( this !== event.target && (/textarea|select/i.test( event.target.nodeName ) ||
event.target.type === "text") ) {
return;
}
// Keypress represents characters, not special keys
var special = event.type !== "keypress" && jQuery.hotkeys.specialKeys[ event.which ],
character = String.fromCharCode( event.which ).toLowerCase(),
key, modif = "", possible = {};
// check combinations (alt|ctrl|shift+anything)
if ( event.altKey && special !== "alt" ) {
modif += "alt+";
}
if ( event.ctrlKey && special !== "ctrl" ) {
modif += "ctrl+";
}
// TODO: Need to make sure this works consistently across platforms
if ( event.metaKey && !event.ctrlKey && special !== "meta" ) {
modif += "meta+";
}
if ( event.shiftKey && special !== "shift" ) {
modif += "shift+";
}
if ( special ) {
possible[ modif + special ] = true;
} else {
possible[ modif + character ] = true;
possible[ modif + jQuery.hotkeys.shiftNums[ character ] ] = true;
// "$" can be triggered as "Shift+4" or "Shift+$" or just "$"
if ( modif === "shift+" ) {
possible[ jQuery.hotkeys.shiftNums[ character ] ] = true;
}
}
for ( var i = 0, l = keys.length; i < l; i++ ) {
if ( possible[ keys[i] ] ) {
return origHandler.apply( this, arguments );
}
}
};
}
jQuery.each([ "keydown", "keyup", "keypress" ], function() {
jQuery.event.special[ this ] = { add: keyHandler };
});
})( jQuery );
src/htmlcov/jquery.isonscreen.js 0 → 100644
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/* Copyright (c) 2010
* @author Laurence Wheway
* Dual licensed under the MIT (http://www.opensource.org/licenses/mit-license.php)
* and GPL (http://www.opensource.org/licenses/gpl-license.php) licenses.
*
* @version 1.2.0
*/
(function($) {
jQuery.extend({
isOnScreen: function(box, container) {
//ensure numbers come in as intgers (not strings) and remove 'px' is it's there
for(var i in box){box[i] = parseFloat(box[i])};
for(var i in container){container[i] = parseFloat(container[i])};
if(!container){
container = {
left: $(window).scrollLeft(),
top: $(window).scrollTop(),
width: $(window).width(),
height: $(window).height()
}
}
if( box.left+box.width-container.left > 0 &&
box.left < container.width+container.left &&
box.top+box.height-container.top > 0 &&
box.top < container.height+container.top
) return true;
return false;
}
})
jQuery.fn.isOnScreen = function (container) {
for(var i in container){container[i] = parseFloat(container[i])};
if(!container){
container = {
left: $(window).scrollLeft(),
top: $(window).scrollTop(),
width: $(window).width(),
height: $(window).height()
}
}
if( $(this).offset().left+$(this).width()-container.left > 0 &&
$(this).offset().left < container.width+container.left &&
$(this).offset().top+$(this).height()-container.top > 0 &&
$(this).offset().top < container.height+container.top
) return true;
return false;
}
})(jQuery);
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src/htmlcov/jquery.tablesorter.min.js 0 → 100644
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src/htmlcov/manual_py.html 0 → 100644
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src/htmlcov/status.json 0 → 100644
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{"format":2,"version":"5.0","globals":"ac56ab2160baf83d705414c037b31831","files":{"manual_py":{"hash":"0b106239d0697e24e720a51d4e05a0a6","index":{"nums":[1,134,0,134,0,0,0],"html_filename":"manual_py.html","relative_filename":"manual.py"}},"tests_test_util_py":{"hash":"525247b1b4f127bde0033bb1727a8fcd","index":{"nums":[1,8,0,0,0,0,0],"html_filename":"tests_test_util_py.html","relative_filename":"tests/test_util.py"}},"util_py":{"hash":"46102e1ce44618bfc98877f01460541c","index":{"nums":[1,28,0,19,0,0,0],"html_filename":"util_py.html","relative_filename":"util.py"}}}}
\ No newline at end of file
src/htmlcov/style.css 0 → 100644
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@charset "UTF-8";
/* Licensed under the Apache License: http://www.apache.org/licenses/LICENSE-2.0 */
/* For details: https://github.com/nedbat/coveragepy/blob/master/NOTICE.txt */
/* Don't edit this .css file. Edit the .scss file instead! */
html, body, h1, h2, h3, p, table, td, th { margin: 0; padding: 0; border: 0; font-weight: inherit; font-style: inherit; font-size: 100%; font-family: inherit; vertical-align: baseline; }
body { font-family: georgia, serif; font-size: 1em; }
html > body { font-size: 16px; }
p { font-size: .75em; line-height: 1.33333333em; }
table { border-collapse: collapse; }
td { vertical-align: top; }
table tr.hidden { display: none !important; }
p#no_rows { display: none; font-size: 1.2em; }
a.nav { text-decoration: none; color: inherit; }
a.nav:hover { text-decoration: underline; color: inherit; }
#header { background: #f8f8f8; width: 100%; border-bottom: 1px solid #eee; }
.indexfile #footer { margin: 1em 3em; }
.pyfile #footer { margin: 1em 1em; }
#footer .content { padding: 0; font-size: 85%; font-family: verdana, sans-serif; color: #666666; font-style: italic; }
#index { margin: 1em 0 0 3em; }
#header .content { padding: 1em 3rem; }
h1 { font-size: 1.25em; display: inline-block; }
#filter_container { display: inline-block; float: right; margin: 0 2em 0 0; }
#filter_container input { width: 10em; }
h2.stats { margin-top: .5em; font-size: 1em; }
.stats span { border: 1px solid; border-radius: .1em; padding: .1em .5em; margin: 0 .1em; cursor: pointer; border-color: #ccc #999 #999 #ccc; }
.stats span.run { background: #eeffee; }
.stats span.run.show_run { border-color: #999 #ccc #ccc #999; background: #ddffdd; }
.stats span.mis { background: #ffeeee; }
.stats span.mis.show_mis { border-color: #999 #ccc #ccc #999; background: #ffdddd; }
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#source p .annotate.long { white-space: normal; float: right; top: 1.75em; right: 1em; height: auto; }
#keyboard_icon { float: right; margin: 5px; cursor: pointer; }
.help_panel { padding: .5em; border: 1px solid #883; }
.help_panel .legend { font-style: italic; margin-bottom: 1em; }
.indexfile .help_panel { width: 20em; height: 4em; }
.pyfile .help_panel { width: 16em; height: 8em; }
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#source p .t { display: inline-block; width: 100%; box-sizing: border-box; margin-left: -.5em; padding-left: 0.3em; border-left: 0.2em solid white; }
#source p .t:hover { background: #f2f2f2; }
#source p .t:hover ~ .r .annotate.long { display: block; }
#source p .t .com { color: green; font-style: italic; line-height: 1px; }
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#source p.exc.show_exc .t { background: #eeeeee; }
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#source p.par.show_par .t { background: #ffffaa; }
#source p.par.show_par .t:hover { background: #f2f2a2; }
#source p .r { position: absolute; top: 0; right: 2.5em; font-family: verdana, sans-serif; }
#source p .annotate { font-family: georgia; color: #666; padding-right: .5em; }
#source p .annotate.short:hover ~ .long { display: block; }
#source p .annotate.long { width: 30em; right: 2.5em; }
#source p input { display: none; }
#source p input ~ .r label.ctx { cursor: pointer; border-radius: .25em; }
#source p input ~ .r label.ctx::before { content: "▶ "; }
#source p input ~ .r label.ctx:hover { background: #d5f7ff; color: #666; }
#source p input:checked ~ .r label.ctx { background: #aaeeff; color: #666; border-radius: .75em .75em 0 0; padding: 0 .5em; margin: -.25em 0; }
#source p input:checked ~ .r label.ctx::before { content: "▼ "; }
#source p input:checked ~ .ctxs { padding: .25em .5em; overflow-y: scroll; max-height: 10.5em; }
#source p label.ctx { color: #999; display: inline-block; padding: 0 .5em; font-size: .8333em; }
#source p .ctxs { display: block; max-height: 0; overflow-y: hidden; transition: all .2s; padding: 0 .5em; font-family: verdana, sans-serif; white-space: nowrap; background: #aaeeff; border-radius: .25em; margin-right: 1.75em; }
#source p .ctxs span { display: block; text-align: right; }
#index td, #index th { text-align: right; width: 5em; padding: .25em .5em; border-bottom: 1px solid #eee; }
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#index td.name a { text-decoration: none; color: #000; }
#index tr.total td, #index tr.total_dynamic td { font-weight: bold; border-top: 1px solid #ccc; border-bottom: none; }
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#scroll_marker .marker { background: #ddd; position: absolute; min-height: 3px; width: 100%; }
src/htmlcov/tests_test_util_py.html 0 → 100644
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<!DOCTYPE html>
<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=emulateIE7" />
<title>Coverage for tests/test_util.py: 100%</title>
<link rel="stylesheet" href="style.css" type="text/css">
<script type="text/javascript" src="jquery.min.js"></script>
<script type="text/javascript" src="jquery.hotkeys.js"></script>
<script type="text/javascript" src="jquery.isonscreen.js"></script>
<script type="text/javascript" src="coverage_html.js"></script>
<script type="text/javascript">
jQuery(document).ready(coverage.pyfile_ready);
</script>
</head>
<body class="pyfile">
<div id="header">
<div class="content">
<h1>Coverage for <b>tests/test_util.py</b> :
<span class="pc_cov">100%</span>
</h1>
<img id="keyboard_icon" src="keybd_closed.png" alt="Show keyboard shortcuts" />
<h2 class="stats">
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>
</h2>
</div>
</div>
<div class="help_panel">
<img id="panel_icon" src="keybd_open.png" alt="Hide keyboard shortcuts" />
<p class="legend">Hot-keys on this page</p>
<div>
<p class="keyhelp">
<span class="key">r</span>
<span class="key">m</span>
<span class="key">x</span>
<span class="key">p</span> &nbsp; toggle line displays
</p>
<p class="keyhelp">
<span class="key">j</span>
<span class="key">k</span> &nbsp; next/prev highlighted chunk
</p>
<p class="keyhelp">
<span class="key">0</span> &nbsp; (zero) top of page
</p>
<p class="keyhelp">
<span class="key">1</span> &nbsp; (one) first highlighted chunk
</p>
</div>
</div>
<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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src/main.py 0 → 100644
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# -*- coding: utf-8 -*-
"""
Created on Thu Aug 13 2020
@author: Yoann Pradat
CentraleSupelec
MICS laboratory
9 rue Juliot Curie, Gif-Sur-Yvette, 91190 France
Main functions for running each step and the assembling step.
"""
def run_annotator(i_split: int, n_split: int, vcf2maf: str, vep_folder: str, vep_data: str, fasta: str):
"""
Run the manual, vcf2maf and vep annotations and assemble.
Paramters
--------
i_split: int
the split processed.
n_split: int
the number of splits for processing a set of vcf files
vcf2maf: str
path to the vcf2maf perl script
vep_folder: str
path to the folder where the vep command is
vep_data: str
path to the .vep data where the reference genome is located
fasta: str
relative path to fasta file from vep_folder
"""
#### # SCRIPT PARAMETERS
#### #####################################################################################################
parser = argparse.ArgumentParser()
parser.add_argument('--i_split' , type=int , default=1 , help='the split processed')
parser.add_argument('--n_split' , type=int , default=1 , help='total number of splits')
parser.add_argument('--vcf2maf' , type=str , default="" , help='path to the vcf2maf perl script')
parser.add_argument('--vep_folder' , type=str , default="" , help='path to the folder of the vep command')
parser.add_argument('--vep_data' , type=str , default="" , help='path to the .vep data folder')
parser.add_argument('--fasta' , type=str , default="" , help='path to reference genome FASTA file')
args = parser.parse_args()
print("Parameters", flush=True)
for arg in vars(args):
print("%s: %s" % (arg, getattr(args, arg)), flush=True)
if __name__ == "__main__":
#### change working dir
current_wd = setwd_to_data()
#### Parameters
dt_paths = {
'vcf_meta' : './raw/vcf/mbc/info/mbc_vcf_identifiers.txt',
'vcf_dir' : './raw/vcf/mbc/files_filtered/',
'vcf_list' : './raw/vcf/mbc/info/list_vcf_mbc.txt',
'vep_manual_dir' : './raw/vep/vep_manual/mbc',
'vep_alone_dir' : './raw/vep/vep_alone/mbc',
'vep_vcf2maf_dir' : './raw/vep/vep_vcf2maf/mbc/vep',
'maf_vcf2maf_dir' : './raw/vep/vep_vcf2maf/mbc/maf',
'maf_one_dir' : './raw/maf/mbc',
}
#### make dir if does not exist already
for k, v in dt_paths.items():
if "dir" in k:
os.makedirs(v, exist_ok=True)
#### load meta data
df_meta = pd.read_csv(
filepath_or_buffer = dt_paths["vcf_meta"],
sep = "\t"
)
if os.path.exists(dt_paths["vcf_list"]):
with open(dt_paths["vcf_list"]) as file:
vcf_names_orig = file.read().splitlines()
else:
vcf_names_orig = df_meta.loc[df_meta.keep == True, "vcf"].tolist()