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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/discosnp">Debian Med / discosnp</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/discosnp/commit/24a8436fbcbf9c7d15e4654f044ddf5354539ad8">24a8436f</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-01-27T14:08:48+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix python interpreter in several scripts
</pre>
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<h4>1 changed file:</h4>
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<li class="file-stats">
<a href="#555c85016bd79aa8bbb523506af81b69d9c69534">
debian/patches/2to3.patch
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<h4>Changes:</h4>
<li id="555c85016bd79aa8bbb523506af81b69d9c69534">
<a href="https://salsa.debian.org/med-team/discosnp/commit/24a8436fbcbf9c7d15e4654f044ddf5354539ad8#555c85016bd79aa8bbb523506af81b69d9c69534"><strong>debian/patches/2to3.patch</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,10 +2,8 @@ Author: Andreas Tille <tille@debian.org></td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Mon, 21 Jan 2019 09:01:19 +0100</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="p">Description: Result of 2to3</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff">Index: discosnp/scripts/filter_out_using_MAF.py</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- discosnp.orig/scripts/filter_out_using_MAF.py</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ discosnp/scripts/filter_out_using_MAF.py</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">--- a/scripts/filter_out_using_MAF.py</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/filter_out_using_MAF.py</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="p">@@ -2,8 +2,8 @@</span> import sys</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"> import gzip</span>
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<td class="diff-line-num old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13,7 +11,7 @@ Index: discosnp/scripts/filter_out_using_MAF.py</td>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "This tool filters out discoSnp prediction having a minor allele frequency lower than a provided threshold for ALL datasets."</span></span>
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<td class="diff-line-num old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "python filter_out_using_MAF.py \".fa from discoSnp\" \"MAF threshold\""</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("This tool filters out discoSnp prediction having a minor allele frequency lower than a provided threshold for ALL datasets.")</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("python filter_out_using_MAF.py \".fa from discoSnp\" \"MAF threshold\"")</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("python<span class="idiff left right">3</span> filter_out_using_MAF.py \".fa from discoSnp\" \"MAF threshold\"")</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"> sys.exit()</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="diff"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -26,10 +24,14 @@ Index: discosnp/scripts/filter_out_using_MAF.py</td>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"><span class="gh" style="color: #999;">Index: discosnp/scripts/ClassVCF_creator.py</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- discosnp.orig/scripts/ClassVCF_creator.py</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ discosnp/scripts/ClassVCF_creator.py</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/ClassVCF_creator.py</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/ClassVCF_creator.py</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/bin/python</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> # -*- coding: utf-8 -*-</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> ###############################################</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> #Dresscode : class : uppercase</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="diff"><span class="p">@@ -218,7 +218,7 @@</span> class VARIANT():</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="diff"> #--------------------------------------------------------------------------------------------------------------------------- </span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="diff"> def RetrievePolymorphismFromHeader(self):</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -59,10 +61,18 @@ Index: discosnp/scripts/ClassVCF_creator.py</td>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="diff"> else : return (error) </span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="diff"><span class="gh" style="color: #999;">Index: discosnp/scripts/discoSnp++_to_csv.py</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- discosnp.orig/scripts/discoSnp++_to_csv.py</span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ discosnp/scripts/discoSnp++_to_csv.py</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/discoSnp++_to_csv.py</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/discoSnp++_to_csv.py</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="p">@@ -1,7 +1,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"> import sys</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> if len(sys.argv) !=2:</span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- sys.stdout.write("Mandatory: python discoSnp_to_csv.py prefix_coherent_k_kval_c_cval.fa\n")</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ sys.stdout.write("Mandatory: python3 discoSnp_to_csv.py prefix_coherent_k_kval_c_cval.fa\n")</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"> sys.stdout.write("This program formats the .fa to .csv format by puting each couple of .fa sequence (4 lines = 2 comments + 2 nucleotide sequences) into one line, replacing the '|' character by spaces and removing the CX_ formating")</span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> sys.exit(1)</span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="diff"><span class="p">@@ -64,7 +64,7 @@</span> while 1:</span>
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77
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="diff"> i+=1</span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="diff"> sys.stdout.write( com2_tab[i][:-1]+",")</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -72,10 +82,18 @@ Index: discosnp/scripts/discoSnp++_to_csv.py</td>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="diff"><span class="gh" style="color: #999;">Index: discosnp/scripts/filterOnBestDP_multiple_variant_at_same_pos.py</span></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- discosnp.orig/scripts/filterOnBestDP_multiple_variant_at_same_pos.py</span></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ discosnp/scripts/filterOnBestDP_multiple_variant_at_same_pos.py</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/filterOnBestDP_multiple_variant_at_same_pos.py</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/filterOnBestDP_multiple_variant_at_same_pos.py</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"><span class="p">@@ -1,7 +1,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"> # -*- coding: utf-8 -*-</span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"> #To apply on sorted vcf by position</span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#Usage : python filterOnBestDP_multiple_variant_at_same_pos.py <vcf_for_igv> > output.vcf</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#Usage : python3 filterOnBestDP_multiple_variant_at_same_pos.py <vcf_for_igv> > output.vcf</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"> import sys</span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"> import gzip</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"> import re</span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="diff"><span class="p">@@ -25,7 +25,7 @@</span> while True:</span>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="diff"> line = vcf_for_igv.readline()</span>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="diff"> if not line: break</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -97,10 +115,17 @@ Index: discosnp/scripts/filterOnBestDP_multiple_variant_at_same_pos.py</td>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="diff"> if out:break </span>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="diff"> vcf_for_igv.close() </span>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="diff"><span class="gh" style="color: #999;">Index: discosnp/scripts/filter_out_using_ratio_of_covered_files.py</span></span>
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101
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- discosnp.orig/scripts/filter_out_using_ratio_of_covered_files.py</span></span>
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103
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ discosnp/scripts/filter_out_using_ratio_of_covered_files.py</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/filter_out_using_ratio_of_covered_files.py</span></span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/filter_out_using_ratio_of_covered_files.py</span></span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"><span class="p">@@ -3,7 +3,7 @@</span> import gzip</span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"> </span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"> if len(sys.argv)<4:</span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"> print ("This tool filters out discoSnp prediction whose number of read sets covering it is lower than a user defined threshold. A set covers a prediction if its coverage in at least one of the two alleles is higher than a user defined threshold")</span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print ("python filter_out_using_ratio_of_covered_files.py \".fa from discoSnp\" \"number of sets threshold\" \"minimal coverage\"")</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print ("python3 filter_out_using_ratio_of_covered_files.py \".fa from discoSnp\" \"number of sets threshold\" \"minimal coverage\"")</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"> sys.exit()</span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"> </span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"> </span>
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104
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129
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="diff"><span class="p">@@ -53,7 +53,7 @@</span> while True:</span>
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105
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130
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="diff"> if coverage_high[i]>=minimal_coverage or coverage_low[i]>=minimal_coverage: number_of_covered_sets+=1</span>
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106
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131
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="diff"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -110,10 +135,14 @@ Index: discosnp/scripts/filter_out_using_ratio_of_covered_files.py</td>
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110
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135
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="diff"> </span>
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111
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136
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="diff"> </span>
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112
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137
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="diff"> </span>
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113
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="diff"><span class="gh" style="color: #999;">Index: discosnp/scripts/functionObjectVCF_creator.py</span></span>
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114
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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115
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- discosnp.orig/scripts/functionObjectVCF_creator.py</span></span>
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116
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ discosnp/scripts/functionObjectVCF_creator.py</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/functionObjectVCF_creator.py</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/functionObjectVCF_creator.py</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/bin/python</span></span>
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<td class="diff-line-num new new_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<td class="diff-line-num new new_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"> # -*- coding: utf-8 -*-</span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"> ###############################################</span>
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"> import os</span>
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="diff"><span class="p">@@ -191,25 +191,25 @@</span> def CheckAtDistanceXBestHits(upper_path,</span>
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="diff"> best_up=1024</span>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="diff"> if int(upper_path.mappingPosition)==0 and int(lower_path.mappingPosition)==0:#Checks if paths are unmappped</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -144,10 +173,14 @@ Index: discosnp/scripts/functionObjectVCF_creator.py</td>
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="diff"> if nbMismatch == best_low:</span>
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="diff"> position_set.add(position)</span>
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="diff"> if len(position_set) > 1: </span>
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="diff"><span class="gh" style="color: #999;">Index: discosnp/scripts/VCF_creator.py</span></span>
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148
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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149
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- discosnp.orig/scripts/VCF_creator.py</span></span>
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ discosnp/scripts/VCF_creator.py</span></span>
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/VCF_creator.py</span></span>
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/VCF_creator.py</span></span>
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/bin/python</span></span>
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="diff"> # -*- coding: utf-8 -*-</span>
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="diff"> #*****************************************************************************</span>
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="diff"> # VCF_Creator: mapping and VCF creation feature in DiscoSnp++</span>
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="diff"><span class="p">@@ -78,7 +78,7 @@</span> def main():</span>
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="diff"> listName[1]=listName[1].replace("_", " ")</span>
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="diff"> stream_file=open(fileName,'r')</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -166,3 +199,422 @@ Index: discosnp/scripts/VCF_creator.py</td>
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166
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="diff"> usage()</span>
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="diff"> sys.exit(2)</span>
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168
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201
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/format_phased_variants_for_haplotyping.py</span></span>
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/format_phased_variants_for_haplotyping.py</span></span>
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="diff"><span class="p">@@ -3,11 +3,11 @@</span> import sys</span>
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="diff"> ### first create connected components from disco (-A option)</span>
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="diff"> #sh from_phased_alleles_to_clusters.sh phased_alleles_read_set_id_1.txt # creates file connected_components_phased_alleles_read_set_id_1.txt</span>
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="diff"> ### them from the .fa file, the id of the set your interested in (e.g. 1 for phased_alleles_read_set_id_1.txt, this will correspond to C1 coverage in the fa file), the file containing the connected components, and the phased_alleles_read_set_id_X.txt file, generate the fact file</span>
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#python format_phased_variants_for_haplotyping.py mapping_k_31_c_auto_D_100_P_10_b_0_coherent.fa 1 connected_components_phased_alleles_read_set_id_1.txt phased_alleles_read_set_id_1.txt > phased_alles_read_set_1_facts.txt</span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#python3 format_phased_variants_for_haplotyping.py mapping_k_31_c_auto_D_100_P_10_b_0_coherent.fa 1 connected_components_phased_alleles_read_set_id_1.txt phased_alleles_read_set_id_1.txt > phased_alles_read_set_1_facts.txt</span></span>
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="diff"> if not len(sys.argv)==5:</span>
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print ("usage: python format_phased_variants_for_haplotyping.py <file coherent.fa> <id number><connected_component_file><phased_allele_file>")</span></span>
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print ("usage: python3 format_phased_variants_for_haplotyping.py <file coherent.fa> <id number><connected_component_file><phased_allele_file>")</span></span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="diff"> print (" * coherent.fa file: the file generated by discoSnp")</span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="diff"> print (" * id number is the id of the read set, for which variants are phased. With i, this corresponds to Ci in the .fa file headers.")</span>
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="diff"> print (" * connected_component_file: file obtained from \"from_phased_alleles_to_clusters.sh phased_alleles_read_set_id_1.txt\" continaing connected component of phased alleles")</span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/remove_non_covered_genotypes.py</span></span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/remove_non_covered_genotypes.py</span></span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="diff"><span class="p">@@ -3,7 +3,7 @@</span> import gzip</span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="diff"> if len(sys.argv)<3:</span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="diff"> print ("This tool replaces discoSnp VCF genotypes with DP lower or equal to a threshold to \"./.\"")</span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print ("python remove_non_covered_genotypes.py \".vcf from discoSnp\" \"DP threshold\"")</span></span>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print ("python3 remove_non_covered_genotypes.py \".vcf from discoSnp\" \"DP threshold\"")</span></span>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="diff"> sys.exit()</span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="diff"> </span>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="diff"> </span>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="diff"><span class="p">@@ -37,4 +37,4 @@</span> while True:</span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="diff"> toprint+= splitted_geno[j]</span>
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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="diff"> if j<len(splitted_geno)-1: toprint+= ":"</span>
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232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="diff"> if i<len(splitted_line): toprint+='\t'</span>
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233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print (toprint)</span></span>
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234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="diff"><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span> No newline at end of file</span>
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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print (toprint)</span></span>
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236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/simulations/multiple_samples_simulator.sh</span></span>
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237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/simulations/multiple_samples_simulator.sh</span></span>
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238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="diff"><span class="p">@@ -68,7 +68,7 @@</span> fi</span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="diff"> for p in `seq 1 $num_pop`</span>
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241
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="diff"> do</span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- python ./random_mut_fasta.py $genome $div_pop > ERASEME_pos_mut_pop"$p"</span></span>
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243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ python3 ./random_mut_fasta.py $genome $div_pop > ERASEME_pos_mut_pop"$p"</span></span>
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244
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="diff"> #pos random ordering</span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="diff"> sort -R ERASEME_pos_mut_pop"$p" > ERASEME_pos_mut_random_pop"$p"</span>
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="diff"><span class="p">@@ -90,7 +90,7 @@</span> for p in `seq 1 $num_pop`</span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="diff"> #homozygotes mutations</span>
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="diff"> cat ERASEME_pos_mut_random_shared_allpop"$p" ERASEME_pos_mut_random_shared_pop"$p"_s"$i" > ERASEME_pos_mut_random_spe_pop"$p"_and_s"$i"</span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="diff"> #mutation inducing</span>
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- python ./targeted_mut_fasta_corrected.py "$genome" ERASEME_pos_mut_random_spe_pop"$p"_and_s"$i"</span></span>
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ python3 ./targeted_mut_fasta_corrected.py "$genome" ERASEME_pos_mut_random_spe_pop"$p"_and_s"$i"</span></span>
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="diff"> mv "$genome"_mut ERASEME_"$genome"_pop"$p"_s"$i"_withhetero.fasta</span>
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="diff"> #homozygote and heterozygote mutations</span>
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="diff"> nb_line2=`grep "." -c ERASEME_pos_mut_random_shared_pop"$p"_s"$i"`</span>
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="diff"><span class="p">@@ -99,7 +99,7 @@</span> for p in `seq 1 $num_pop`</span>
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="diff"> head -n +"$nb_homo" ERASEME_pos_mut_random_shared_pop"$p"_s"$i" > ERASEME_pos_mut_random_shared_pop"$p"_s"$i"_homo</span>
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="diff"> #population mutationq</span>
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="diff"> cat ERASEME_pos_mut_random_shared_allpop"$p" ERASEME_pos_mut_random_shared_pop"$p"_s"$i"_homo > ERASEME_pos_mut_random_spe_pop"$p"_and_s"$i"_homo</span>
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- python ./targeted_mut_fasta_corrected.py "$genome" ERASEME_pos_mut_random_spe_pop"$p"_and_s"$i"_homo</span></span>
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ python3 ./targeted_mut_fasta_corrected.py "$genome" ERASEME_pos_mut_random_spe_pop"$p"_and_s"$i"_homo</span></span>
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="diff"> mv "$genome"_mut ERASEME_"$genome"_pop"$p"_s"$i"_homo.fasta</span>
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="diff"> #READS SIMULATION</span>
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="diff"> mutareads_forward ERASEME_"$genome"_pop"$p"_s"$i"_withhetero.fasta pop"$p"_ind"$i"_allele1_err_reads $read_s $read_l 0.01 0 0</span>
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/simulations/targeted_mut_fasta_corrected.py</span></span>
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/simulations/targeted_mut_fasta_corrected.py</span></span>
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="diff"> # -*- coding: utf-8 -*-</span>
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="diff"> # </span>
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/from_phased_alleles_to_clusters.sh</span></span>
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<td class="diff-line-num new new_line" data-linenumber="274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/from_phased_alleles_to_clusters.sh</span></span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="diff"><span class="p">@@ -13,7 +13,7 @@</span> filename=$(basename -- "$file")</span>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="diff"> path=$(dirname "${file}")</span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="diff"> </span>
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278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="diff"> # FIND THE PATH CONTAINING THE SCRIPT: </span>
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<td class="diff-line-num new new_line" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-EDIR=$( python -c "import os.path; print(os.path.dirname(os.path.realpath(\"${BASH_SOURCE[0]}\")))" ) </span></span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+EDIR=$( python3 -c "import os.path; print(os.path.dirname(os.path.realpath(\"${BASH_SOURCE[0]}\")))" ) </span></span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="diff"> echo $EDIR</span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="diff"> </span>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="diff"> edge_coverage_threshold=0</span>
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<td class="diff-line-num new new_line" data-linenumber="284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="diff"><span class="p">@@ -77,4 +77,4 @@</span> then</span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="diff"> exit 1</span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="diff"> fi</span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-echo "Connected components (clusters of variants) from file $file are in $path/connected_components_${filename}"</span></span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="diff"><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span> No newline at end of file</span>
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+echo "Connected components (clusters of variants) from file $file are in $path/connected_components_${filename}"</span></span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/redundancy_removal_discosnp.py</span></span>
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/redundancy_removal_discosnp.py</span></span>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/bin/python</span></span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="diff"> # -*- coding: utf-8 -*-</span>
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="diff"> ###################################</span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="diff"> # from kissnp output: </span>
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<td class="diff-line-num new new_line" data-linenumber="299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/run_VCF_creator.sh</span></span>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/run_VCF_creator.sh</span></span>
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<td class="diff-line-num new new_line" data-linenumber="301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="diff"><span class="p">@@ -212,10 +212,10 @@</span> if [ -z "$samfile" ];then</span>
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<td class="diff-line-num new new_line" data-linenumber="302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="diff"> exit 1</span>
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<td class="diff-line-num new new_line" data-linenumber="303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="diff"> else</span>
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<td class="diff-line-num new new_line" data-linenumber="304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- python $PATH_VCF_creator/VCF_creator.py -s $discoSNPs -o $vcffile #-n $n</span></span>
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<td class="diff-line-num new new_line" data-linenumber="306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ python3 $PATH_VCF_creator/VCF_creator.py -s $discoSNPs -o $vcffile #-n $n</span></span>
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<td class="diff-line-num new new_line" data-linenumber="307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="diff"> if [ $? -ne 0 ]</span>
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<td class="diff-line-num new new_line" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="diff"> then</span>
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<td class="diff-line-num new new_line" data-linenumber="309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- echo "there was a problem with the VCF creation (command was \"python $PATH_VCF_creator/VCF_creator.py -s $discoSNPs -o $vcffile\""</span></span>
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<td class="diff-line-num new new_line" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ echo "there was a problem with the VCF creation (command was \"python3 $PATH_VCF_creator/VCF_creator.py -s $discoSNPs -o $vcffile\""</span></span>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="diff"> exit 1</span>
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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="diff"> fi</span>
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<td class="diff-line-num new new_line" data-linenumber="313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="diff"> echo -e "... Creation of the vcf file : done ...==> $vcffile"</span>
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<td class="diff-line-num new new_line" data-linenumber="314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="diff"><span class="p">@@ -259,9 +259,9 @@</span> if [ -z "$samfile" ];then</span>
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<td class="diff-line-num new new_line" data-linenumber="315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="diff"> discoSNPsbis=$(basename $discoSNPs .fa)"bis.fasta"</span>
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<td class="diff-line-num new new_line" data-linenumber="316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="diff"> if [ $map_with_extensions -eq 1 ];then</span>
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<td class="diff-line-num new new_line" data-linenumber="318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- python $PATH_VCF_creator/keep_extensions_disco_file.py $discoSNPs $discoSNPsbis</span></span>
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<td class="diff-line-num new new_line" data-linenumber="319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ python3 $PATH_VCF_creator/keep_extensions_disco_file.py $discoSNPs $discoSNPsbis</span></span>
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<td class="diff-line-num new new_line" data-linenumber="320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="diff"> else</span>
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<td class="diff-line-num new new_line" data-linenumber="321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
321
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- python $PATH_VCF_creator/remove_extensions_disco_file.py $discoSNPs $discoSNPsbis</span></span>
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<td class="diff-line-num new new_line" data-linenumber="322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
322
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ python3 $PATH_VCF_creator/remove_extensions_disco_file.py $discoSNPs $discoSNPsbis</span></span>
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323
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="diff"> fi</span>
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324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="diff"> if [ -z "$discoSNPsbis" ];then</span>
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325
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="diff"> echo "...Error with the script remove_extensions_disco_file.py..."</span>
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<td class="diff-line-num new new_line" data-linenumber="326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="diff"><span class="p">@@ -320,10 +320,10 @@</span> else</span>
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327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="diff"> fi</span>
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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="diff"> fi</span>
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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-python $PATH_VCF_creator/VCF_creator.py -s $samfile -o $vcffile </span></span>
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<td class="diff-line-num new new_line" data-linenumber="331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+python3 $PATH_VCF_creator/VCF_creator.py -s $samfile -o $vcffile </span></span>
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<td class="diff-line-num new new_line" data-linenumber="332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="diff"> if [ $? -ne 0 ]</span>
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333
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="diff"> then</span>
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<td class="diff-line-num new new_line" data-linenumber="334" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
334
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- echo "there was a problem with the VCF creation (command was \"python $PATH_VCF_creator/VCF_creator.py -s $samfile -o $vcffile \""</span></span>
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<td class="diff-line-num new new_line" data-linenumber="335" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
335
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ echo "there was a problem with the VCF creation (command was \"python3 $PATH_VCF_creator/VCF_creator.py -s $samfile -o $vcffile \""</span></span>
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336
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="diff"> exit 1</span>
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337
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="diff"> fi</span>
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338
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="diff"> echo -e "... Creation of the vcf file: done ...==> $vcffile "</span>
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<td class="diff-line-num new new_line" data-linenumber="339" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
339
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="diff"><span class="p">@@ -332,10 +332,10 @@</span> echo -e "... Creation of the vcf file: d</span>
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340
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="diff"> if [ $igv -eq 1 ] ; then</span>
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341
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="diff"> $DIR/create_IGV_compatible_VCF.sh $vcffile</span>
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<td class="diff-line-num new new_line" data-linenumber="342" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
342
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="diff"> nameVCFIGV=$( basename $vcffile .vcf )</span>
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<td class="diff-line-num new new_line" data-linenumber="343" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
343
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- python $PATH_VCF_creator/filterOnBestDP_multiple_variant_at_same_pos.py $nameVCFIGV\_for_IGV.vcf > tmp.vcf</span></span>
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<td class="diff-line-num new new_line" data-linenumber="344" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
344
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ python3 $PATH_VCF_creator/filterOnBestDP_multiple_variant_at_same_pos.py $nameVCFIGV\_for_IGV.vcf > tmp.vcf</span></span>
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<td class="diff-line-num new new_line" data-linenumber="345" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
345
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="diff"> if [ $? -ne 0 ]</span>
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346
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="diff"> then</span>
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347
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- echo "there was a problem with the IGV VCF creation (command was \"python $PATH_VCF_creator/filterOnBestDP_multiple_variant_at_same_pos.py $nameVCFIGV\_for_IGV.vcf > tmp.vcf\""</span></span>
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<td class="diff-line-num new new_line" data-linenumber="348" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
348
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ echo "there was a problem with the IGV VCF creation (command was \"python3 $PATH_VCF_creator/filterOnBestDP_multiple_variant_at_same_pos.py $nameVCFIGV\_for_IGV.vcf > tmp.vcf\""</span></span>
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349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="diff"> exit 1</span>
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350
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="diff"> fi</span>
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351
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="diff"> echo -e "... Creation of the vcf file: done ...==> $vcffile"</span>
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352
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/simulations/random_mut_fasta.py</span></span>
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353
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/simulations/random_mut_fasta.py</span></span>
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354
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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355
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<td class="diff-line-num new new_line" data-linenumber="356" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
356
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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357
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="diff"> # -*- coding: utf-8 -*-</span>
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358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="diff"> # </span>
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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="diff"> </span>
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360
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/create_IGV_compatible_VCF.sh</span></span>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/create_IGV_compatible_VCF.sh</span></span>
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362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="diff"><span class="p">@@ -30,7 +30,7 @@</span> igvfile=$(basename $vcffile .vcf)"_for_I</span>
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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="diff"> cat $vcffile|grep "#">$igvfile</span>
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364
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="diff"> #cat $vcffile|grep -v "#"|sort -k 2n,2n -n|grep -v "^SNP"|grep -v "^INDEL">>$igvfile</span>
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365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="diff"> cat $vcffile|grep -v "#"|sort -k 1,1 -k 2,2n |grep -v "^SNP"|grep -v "^INDEL">>$igvfile # from 2 2 6</span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#python $DIR/tools/one2zeroBased_vcf.py $igvfiletemp </span></span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#python3 $DIR/tools/one2zeroBased_vcf.py $igvfiletemp </span></span>
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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="diff"> #cat VCFone2zeroBAsed.vcf >> $igvfile</span>
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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="diff"> #rm -f $igvfiletemp VCFone2zeroBAsed.vcf</span>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="diff"> echo -e "... Creation of the vcf file for IGV: done ...==> $igvfile"</span>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/k3000/K3000_gfa_to_dat.py</span></span>
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372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/k3000/K3000_gfa_to_dat.py</span></span>
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373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="diff"><span class="p">@@ -242,7 +242,7 @@</span> def main(gfa_file_name):</span>
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374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="diff"> '''</span>
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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="diff"> Creation of a DAT file from the graph_plus.gfa GFA file </span>
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376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="diff"> Usage: </span>
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377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- python ~/workspace/gatb-discosnp/scripts/k3000/K3000_gfa_to_dat.py graph_plus.gfa > graph_diploid.dat</span></span>
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378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ python3 ~/workspace/gatb-discosnp/scripts/k3000/K3000_gfa_to_dat.py graph_plus.gfa > graph_diploid.dat</span></span>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="diff"> '''</span>
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380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="diff"> # Store the information as a graph. </span>
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381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="diff"> # This enables </span>
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382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/keep_extensions_disco_file.py</span></span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/keep_extensions_disco_file.py</span></span>
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384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/bin/python</span></span>
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386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="diff"> # -*- coding: utf-8 -*-</span>
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388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="diff"> ###################################</span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="diff"> # change extensions in uppercase and replace relative positions of SNPs in the header</span>
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390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/remove_extensions_disco_file.py</span></span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/remove_extensions_disco_file.py</span></span>
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392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/bin/python</span></span>
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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="diff"> # -*- coding: utf-8 -*-</span>
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396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="diff"> ###################################</span>
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397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="diff"> #Removes extensions in lowercase :</span>
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398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/validation_scripts/compare_vcf_disco_pos_allele_only.py</span></span>
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399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/validation_scripts/compare_vcf_disco_pos_allele_only.py</span></span>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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403
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="diff"> # -*- coding: utf-8 -*-</span>
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404
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="diff"> # </span>
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405
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="diff"> </span>
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406
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/validation_scripts/eval_disco_one_snp_per_locus.py</span></span>
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407
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/validation_scripts/eval_disco_one_snp_per_locus.py</span></span>
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408
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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409
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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410
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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411
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="diff"> # -*- coding: utf-8 -*-</span>
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412
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="diff"> # </span>
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413
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="diff"> </span>
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414
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/k3000/K3000.py</span></span>
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415
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/k3000/K3000.py</span></span>
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416
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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417
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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418
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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419
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="diff"> # -*- coding: utf-8 -*-</span>
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420
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="diff"> #</span>
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421
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="diff"> '''</span>
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422
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/k3000/K3000_node_ids_to_node_sequences.py</span></span>
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423
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/k3000/K3000_node_ids_to_node_sequences.py</span></span>
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424
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="diff"><span class="p">@@ -152,7 +152,7 @@</span> def main():</span>
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425
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="diff"> Produces a gfa file replacing the node content from int ids of alleles to their sequence</span>
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426
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="diff"> '''</span>
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427
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="diff"> if len(sys.argv) !=3:</span>
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428
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- sys.stderr.write("Usage: python K3000_node_ids_to_node_sequences.py graph_plus.gfa compacted_facts.fa > graph_final.gfa\n")</span></span>
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429
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ sys.stderr.write("Usage: python3 K3000_node_ids_to_node_sequences.py graph_plus.gfa compacted_facts.fa > graph_final.gfa\n")</span></span>
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430
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="diff"> sys.exit(0)</span>
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431
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="diff"> sys.stderr.write("Indexing sequence positions\n")</span>
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432
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="diff"> header_to_file_position = index_sequences(sys.argv[2])</span>
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433
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/k3000/run.sh</span></span>
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434
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/k3000/run.sh</span></span>
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435
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="diff"><span class="p">@@ -11,7 +11,7 @@</span> wraith=false #$4 # set to true if you on</span>
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436
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="diff"> phased_allele_file=$1</span>
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437
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="diff"> disco_fa_file=$2</span>
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438
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="diff"> read_set_id=$3</span>
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439
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-EDIR=$( python -c "import os.path; print(os.path.dirname(os.path.realpath(\"${BASH_SOURCE[0]}\")))" ) # as suggested by Philippe Bordron </span></span>
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440
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+EDIR=$( python3 -c "import os.path; print(os.path.dirname(os.path.realpath(\"${BASH_SOURCE[0]}\")))" ) # as suggested by Philippe Bordron </span></span>
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441
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="diff"> if [ -z "$phased_allele_file" ]; then</span>
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442
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="diff"> echo "${red} You must provide a phased file name${reset}"</span>
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443
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="diff"> exit 1</span>
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444
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/remove_non_biallelic.py</span></span>
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445
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/remove_non_biallelic.py</span></span>
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="diff"><span class="p">@@ -3,7 +3,7 @@</span> import gzip</span>
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447
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="diff"> </span>
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448
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="diff"> if len(sys.argv)<2:</span>
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449
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="diff"> print ("This tool removes from discoSnp sorted VCF the locus which are tri-allelic or more")</span>
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450
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print ("python remove_non_diploids.py \".vcf from discoSnp\" ")</span></span>
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451
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print ("python3 remove_non_diploids.py \".vcf from discoSnp\" ")</span></span>
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="diff"> sys.exit()</span>
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/discoSnpRAD/post-processing_scripts/README.md</span></span>
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/discoSnpRAD/post-processing_scripts/README.md</span></span>
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="diff"><span class="p">@@ -7,7 +7,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="diff"> * removes variants belonging to a cluster (locus) whose size (nb of variants) is outside the given size range (options `-m` and `-M`)</span>
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="diff"> * removes variants with rank lower than a given threshold given by option `-r`</span>
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="diff"> * Usage : </span>
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- `python filter_by_cluster_size_and_rank.py -i vcf_file [-o new_vcf_file -m 0 -M 150 -r 0.4]`</span></span>
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ `python3 filter_by_cluster_size_and_rank.py -i vcf_file [-o new_vcf_file -m 0 -M 150 -r 0.4]`</span></span>
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463
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="diff"> 3. **script** `filter_vcf_by_indiv_cov_max_missing_and_maf.py`:</span>
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="diff"> * replaces individual genotypes that have DP less than the value given by option `-c` by missing genotype `./.`</span>
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="diff"><span class="p">@@ -15,14 +15,14 @@</span></span>
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="diff"> * removes variants (vcf lines) that have a minor allele frequency smaller than the value given by option `-f` </span>
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="diff"> * outputs only SNP variants if option `-s`. </span>
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="diff"> * Usage : </span>
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- `python filter_vcf_by_indiv_cov_max_missing_and_maf.py -i vcf_file -o new_vcf_file [-c min_cov -m max_missing -f maf -s] `</span></span>
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ `python3 filter_vcf_by_indiv_cov_max_missing_and_maf.py -i vcf_file -o new_vcf_file [-c min_cov -m max_missing -f maf -s] `</span></span>
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="diff"> 3. **script** `filter_paralogs.py`:</span>
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="diff"> * identifies variants (vcf lines) that have a fraction of heterozygous genotypes greater than `x` (not counting missing genotypes)</span>
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="diff"> * removes variants (vcf lines) that belong to a cluster having a fraction of such variants greater than `y`</span>
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="diff"> * Example : `x=0.1` and `y= 0.5` and if we consider a cluster to represent a locus. This filter removes loci that have more than 50% of the SNPs that have each more than 10% of heterozygous genotypes.</span>
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="diff"> * Usage : </span>
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- `python filter_paralogs.py -i vcf_file -o new_vcf_file [-x 0.1 -y 0.5]`</span></span>
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ `python3 filter_paralogs.py -i vcf_file -o new_vcf_file [-x 0.1 -y 0.5]`</span></span>
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="diff"> ## Scripts for STRUCTURE analyses :</span>
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="diff"><span class="p">@@ -30,7 +30,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="diff"> 4. **script** `1SNP_by_cluster.py`</span>
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="diff"> * selects one SNP per cluster (the one with less missing genotypes)</span>
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="diff"> * Usage : </span>
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- `python 1SNP_per_cluster.py -i vcf_file -o new_vcf_file`</span></span>
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ `python3 1SNP_per_cluster.py -i vcf_file -o new_vcf_file`</span></span>
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="diff"> 5. **script** `vcf2structure.sh` </span>
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="diff"> * changes the vcf format to a Structure format (input of the software Structure)</span>
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="diff"><span class="p">@@ -55,13 +55,13 @@</span> Here is the full pipeline to map the res</span>
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="diff"> sh [DISCO_DIR]/scripts/run_VCF_creator.sh -G dm6_masked.fa -p myDiscoSnpRADResult_raw_filtered.fa -e -o temp.vcf</span>
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="diff"> # Adding clustering information (and minimal filtering on cluster size)</span>
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-python add_cluster_info_to_mapped_vcf.py -m temp.vcf -u myDiscoSnpRADResult_clustered.vcf -o myDiscoSnpRADResult_mapped.vcf</span></span>
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+python3 add_cluster_info_to_mapped_vcf.py -m temp.vcf -u myDiscoSnpRADResult_clustered.vcf -o myDiscoSnpRADResult_mapped.vcf</span></span>
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="diff"> # final vcf is myDiscoSnpRADResult_mapped.vcf</span>
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="diff"> ```</span>
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="diff"> Additionnally, in a validation context, if one wants to compare variant positions between two such vcf files, the following command will output recall and precision metrics:</span>
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="diff"> ```</span>
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-python [DISCO_DIR]/scripts/validation_scripts/compare_vcf_disco_pos_allele_only.py truth.vcf myDiscoSnpRADResult_mapped.vcf</span></span>
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+python3 [DISCO_DIR]/scripts/validation_scripts/compare_vcf_disco_pos_allele_only.py truth.vcf myDiscoSnpRADResult_mapped.vcf</span></span>
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<pre style="margin: 0;">+<span id="LC505" class="line" lang="diff"> ```</span>
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC508" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/discoSnpRAD/post-processing_scripts/filter_by_cluster_size_and_rank.py</span></span>
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/discoSnpRAD/post-processing_scripts/filter_by_cluster_size_and_rank.py</span></span>
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="diff"><span class="p">@@ -1,5 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC513" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="diff"> # -*- coding: utf-8 -*-</span>
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/doc/discoSnp_user_guide.txt</span></span>
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/doc/discoSnp_user_guide.txt</span></span>
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="diff"><span class="p">@@ -201,7 +201,7 @@</span> chromosome 117 3 C</span>
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="diff"> See documentation specific to VCF_creator for more information: doc/vcf_creator_user_guide.pdf</span>
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521
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="diff"> Output Analyze</span>
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="diff"> From a fasta format to a csv format: If you wish to analyze the results in a tabulated format: </span>
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# python output_analyses/discoSnp++_to_csv.py discoSnp++_output.fa </span></span>
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<pre style="margin: 0;">+<span id="LC524" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# python3 output_analyses/discoSnp++_to_csv.py discoSnp++_output.fa </span></span>
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<pre style="margin: 0;">+<span id="LC525" class="line" lang="diff"> will output a .csv tabulated file containing on each line the content of 4 lines of the .fa, replacing the '|' character by comma ',' and removing the CX_</span>
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526
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="diff"> Exemples of close SNPs and indels</span>
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527
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<pre style="margin: 0;">+<span id="LC527" class="line" lang="diff"> Exemple of a multiple SNP:</span>
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<pre style="margin: 0;">+<span id="LC528" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/run_discoSnp++.sh</span></span>
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<pre style="margin: 0;">+<span id="LC529" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/run_discoSnp++.sh</span></span>
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="diff"><span class="p">@@ -65,7 +65,7 @@</span> verbose=1</span>
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<pre style="margin: 0;">+<span id="LC531" class="line" lang="diff"> stop_after_kissnp=0</span>
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<pre style="margin: 0;">+<span id="LC532" class="line" lang="diff"> e=""</span>
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<pre style="margin: 0;">+<span id="LC533" class="line" lang="diff"> #EDIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )</span>
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534
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<pre style="margin: 0;">+<span id="LC534" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#EDIR=$( python -c "import os.path; print(os.path.dirname(os.path.realpath(\"${BASH_SOURCE[0]}\")))" ) # as suggested by Philippe Bordron </span></span>
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535
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<pre style="margin: 0;">+<span id="LC535" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#EDIR=$( python3 -c "import os.path; print(os.path.dirname(os.path.realpath(\"${BASH_SOURCE[0]}\")))" ) # as suggested by Philippe Bordron </span></span>
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536
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<pre style="margin: 0;">+<span id="LC536" class="line" lang="diff"> EDIR="/usr"</span>
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537
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="diff"> </span>
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539
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/discoSnpRAD/post-processing_scripts/add_cluster_info_to_mapped_vcf.py</span></span>
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540
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<pre style="margin: 0;">+<span id="LC540" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/discoSnpRAD/post-processing_scripts/add_cluster_info_to_mapped_vcf.py</span></span>
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541
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<pre style="margin: 0;">+<span id="LC541" class="line" lang="diff"><span class="p">@@ -1,5 +1,4 @@</span></span>
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542
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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543
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="diff"> # -*- coding: utf-8 -*-</span>
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="diff"> import sys</span>
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/discoSnpRAD/post-processing_scripts/filter_paralogs.py</span></span>
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549
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/discoSnpRAD/post-processing_scripts/filter_paralogs.py</span></span>
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<pre style="margin: 0;">+<span id="LC550" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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551
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<pre style="margin: 0;">+<span id="LC551" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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552
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<pre style="margin: 0;">+<span id="LC552" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<pre style="margin: 0;">+<span id="LC553" class="line" lang="diff"> # -*- coding: utf-8 -*-</span>
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<pre style="margin: 0;">+<span id="LC554" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC555" class="line" lang="diff"> </span>
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556
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/discoSnpRAD/post-processing_scripts/filter_vcf_by_indiv_cov_max_missing_and_maf.py</span></span>
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557
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<pre style="margin: 0;">+<span id="LC557" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/discoSnpRAD/post-processing_scripts/filter_vcf_by_indiv_cov_max_missing_and_maf.py</span></span>
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558
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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559
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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560
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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561
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<pre style="margin: 0;">+<span id="LC561" class="line" lang="diff"> # -*- coding: utf-8 -*-</span>
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562
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="diff"> </span>
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563
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<pre style="margin: 0;">+<span id="LC563" class="line" lang="diff"> ''' ***********************************************</span>
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564
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<pre style="margin: 0;">+<span id="LC564" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/run_discoSnp++_storagefile.sh</span></span>
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565
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<pre style="margin: 0;">+<span id="LC565" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/run_discoSnp++_storagefile.sh</span></span>
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566
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="diff"><span class="p">@@ -55,7 +55,7 @@</span> remove=1</span>
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567
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<pre style="margin: 0;">+<span id="LC567" class="line" lang="diff"> verbose=1</span>
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568
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="diff"> e=""</span>
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569
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<pre style="margin: 0;">+<span id="LC569" class="line" lang="diff"> #EDIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )</span>
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570
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<pre style="margin: 0;">+<span id="LC570" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-EDIR=$( python -c "import os.path; print(os.path.dirname(os.path.realpath(\"${BASH_SOURCE[0]}\")))" ) # as suggested by Philippe Bordron </span></span>
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571
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+EDIR=$( python3 -c "import os.path; print(os.path.dirname(os.path.realpath(\"${BASH_SOURCE[0]}\")))" ) # as suggested by Philippe Bordron </span></span>
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572
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<pre style="margin: 0;">+<span id="LC572" class="line" lang="diff"> </span>
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573
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<pre style="margin: 0;">+<span id="LC573" class="line" lang="diff"> if [ -d "$EDIR/build/" ] ; then # VERSION SOURCE COMPILED</span>
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574
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<pre style="margin: 0;">+<span id="LC574" class="line" lang="diff"> read_file_names_bin=$EDIR/build/bin/read_file_names</span>
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575
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<pre style="margin: 0;">+<span id="LC575" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/discoSnpRAD/post-processing_scripts/1SNP_per_cluster.py</span></span>
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576
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<pre style="margin: 0;">+<span id="LC576" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/discoSnpRAD/post-processing_scripts/1SNP_per_cluster.py</span></span>
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577
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<pre style="margin: 0;">+<span id="LC577" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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578
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<pre style="margin: 0;">+<span id="LC578" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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579
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<pre style="margin: 0;">+<span id="LC579" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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580
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<pre style="margin: 0;">+<span id="LC580" class="line" lang="diff"> # -*- coding: utf-8 -*-</span>
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581
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<pre style="margin: 0;">+<span id="LC581" class="line" lang="diff"> </span>
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582
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<pre style="margin: 0;">+<span id="LC582" class="line" lang="diff"> </span>
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583
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<pre style="margin: 0;">+<span id="LC583" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/discoSnpRAD/run_discoSnpRad.sh</span></span>
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584
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/discoSnpRAD/run_discoSnpRad.sh</span></span>
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585
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<pre style="margin: 0;">+<span id="LC585" class="line" lang="diff"><span class="p">@@ -75,7 +75,7 @@</span> verbose=1</span>
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586
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<pre style="margin: 0;">+<span id="LC586" class="line" lang="diff"> short_read_connector_path=""</span>
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587
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<pre style="margin: 0;">+<span id="LC587" class="line" lang="diff"> option_phase_variants=""</span>
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588
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<pre style="margin: 0;">+<span id="LC588" class="line" lang="diff"> #EDIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )</span>
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589
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<pre style="margin: 0;">+<span id="LC589" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-EDIR=$( python -c "import os.path; print(os.path.dirname(os.path.realpath(\"${BASH_SOURCE[0]}\")))" ) # as suggested by Philippe Bordron </span></span>
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590
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<pre style="margin: 0;">+<span id="LC590" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+EDIR=$( python3 -c "import os.path; print(os.path.dirname(os.path.realpath(\"${BASH_SOURCE[0]}\")))" ) # as suggested by Philippe Bordron </span></span>
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591
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<pre style="margin: 0;">+<span id="LC591" class="line" lang="diff"> </span>
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592
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<pre style="margin: 0;">+<span id="LC592" class="line" lang="diff"> if [ -d "$EDIR/../build/" ] ; then # VERSION SOURCE COMPILED</span>
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593
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="diff"> read_file_names_bin=$EDIR/../build/bin/read_file_names</span>
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594
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="diff"><span class="p">@@ -556,7 +556,7 @@</span> fi</span>
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595
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<pre style="margin: 0;">+<span id="LC595" class="line" lang="diff"> echo -e "${yellow}\t############################################################"</span>
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596
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<pre style="margin: 0;">+<span id="LC596" class="line" lang="diff"> echo -e "\t#################### REDUNDANCY REMOVAL ###################"</span>
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597
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="diff"> echo -e "\t############################################################$reset"</span>
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<td class="diff-line-num new new_line" data-linenumber="598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
598
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-redundancy_removal_cmd="python $EDIR/../scripts/redundancy_removal_discosnp.py ${kissprefix}_r.fa $k $kissprefix.fa"</span></span>
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599
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<pre style="margin: 0;">+<span id="LC599" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+redundancy_removal_cmd="python3 $EDIR/../scripts/redundancy_removal_discosnp.py ${kissprefix}_r.fa $k $kissprefix.fa"</span></span>
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600
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<pre style="margin: 0;">+<span id="LC600" class="line" lang="diff"> echo $green${redundancy_removal_cmd}$cyan</span>
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601
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<pre style="margin: 0;">+<span id="LC601" class="line" lang="diff"> if [[ "$wraith" == "false" ]]; then</span>
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602
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<pre style="margin: 0;">+<span id="LC602" class="line" lang="diff"> eval ${redundancy_removal_cmd}</span>
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603
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<pre style="margin: 0;">+<span id="LC603" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/run_discoSnp++_ML.sh</span></span>
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604
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<pre style="margin: 0;">+<span id="LC604" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/run_discoSnp++_ML.sh</span></span>
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605
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<pre style="margin: 0;">+<span id="LC605" class="line" lang="diff"><span class="p">@@ -67,7 +67,7 @@</span> stop_after_kissnp=0</span>
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606
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<pre style="margin: 0;">+<span id="LC606" class="line" lang="diff"> e=""</span>
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607
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<pre style="margin: 0;">+<span id="LC607" class="line" lang="diff"> prefix_trash=`head /dev/urandom | tr -dc A-Za-z0-9 | head -c 13 ; echo ''`</span>
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608
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<pre style="margin: 0;">+<span id="LC608" class="line" lang="diff"> #EDIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )</span>
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609
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<pre style="margin: 0;">+<span id="LC609" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-EDIR=$( python -c "import os.path; print(os.path.dirname(os.path.realpath(\"${BASH_SOURCE[0]}\")))" ) # as suggested by Philippe Bordron </span></span>
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610
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<pre style="margin: 0;">+<span id="LC610" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+EDIR=$( python3 -c "import os.path; print(os.path.dirname(os.path.realpath(\"${BASH_SOURCE[0]}\")))" ) # as suggested by Philippe Bordron </span></span>
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611
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<pre style="margin: 0;">+<span id="LC611" class="line" lang="diff"> </span>
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612
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<pre style="margin: 0;">+<span id="LC612" class="line" lang="diff"> </span>
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613
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<pre style="margin: 0;">+<span id="LC613" class="line" lang="diff"> if [ -d "$EDIR/build/" ] ; then # VERSION SOURCE COMPILED</span>
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614
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<pre style="margin: 0;">+<span id="LC614" class="line" lang="diff"><span class="p">@@ -839,4 +839,4 @@</span> if [[ "$wraith" == "false" ]]; then</span>
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615
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<pre style="margin: 0;">+<span id="LC615" class="line" lang="diff"> fi</span>
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616
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<pre style="margin: 0;">+<span id="LC616" class="line" lang="diff"> echo -e " Thanks for using discoSnp++ - http://colibread.inria.fr/discoSnp/ - Forum: http://www.biostars.org/t/discoSnp/"</span>
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617
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<pre style="margin: 0;">+<span id="LC617" class="line" lang="diff"> echo -e "################################################################################################################${reset}"</span>
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<td class="diff-line-num new old_line" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="618" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
618
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<pre style="margin: 0;">+<span id="LC618" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-fi</span></span>
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<td class="diff-line-num new old_line" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
619
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<pre style="margin: 0;">+<span id="LC619" class="line" lang="diff"><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span> No newline at end of file</span>
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620
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<pre style="margin: 0;">+<span id="LC620" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+fi</span></span></pre>
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