Mercurial > repos > mcharles > rapsosnp
view rapsodyn/PileupVariant.pl @ 0:442a7c88b886 draft
Uploaded
author | mcharles |
---|---|
date | Wed, 10 Sep 2014 09:18:15 -0400 |
parents | |
children | 3f7b0788a1c4 |
line wrap: on
line source
#!/usr/bin/perl use strict; my $inputfile = $ARGV[0]; open(IF, $inputfile) or die("Can't open $inputfile\n"); #Extraction des variants my $nb_line=0; while (my $line=<IF>){ my $test = $line; $test =~ s/\$//g; #the read start at this position $test =~ s/\^.//g; #the read end at this position followed by quality char my @field = split(/\s+/,$test); if ($field[4]=~/[ATGCN]/i){ print $line; } } close(IF);