Mercurial > repos > mcharles > rapsosnp
annotate rapsodyn/PileupVariant.pl @ 5:b0cbb9d21aa9 draft
Uploaded
| author | mcharles |
|---|---|
| date | Mon, 22 Sep 2014 10:19:53 -0400 |
| parents | 442a7c88b886 |
| children | 3f7b0788a1c4 |
| rev | line source |
|---|---|
| 0 | 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); |