Mercurial > repos > mcharles > rapsosnp

comparison rapsodyn/PileupVariant.pl @ 0:442a7c88b886 draft

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Uploaded
author mcharles
date Wed, 10 Sep 2014 09:18:15 -0400
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children 3f7b0788a1c4
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-1:000000000000 0:442a7c88b886
1 #!/usr/bin/perl
2 use strict;
3
4 my $inputfile = $ARGV[0];
5 open(IF, $inputfile) or die("Can't open $inputfile\n");
6
7 #Extraction des variants
8 my $nb_line=0;
9 while (my $line=<IF>){
10 my $test = $line;
11 $test =~ s/\$//g; #the read start at this position
12 $test =~ s/\^.//g; #the read end at this position followed by quality char
13 my @field = split(/\s+/,$test);
14
15 if ($field[4]=~/[ATGCN]/i){
16 print $line;
17 }
18 }
19 close(IF);