gclib/scripts/gff2geneloc.pl

#!/usr/bin/perl
use strict;
while (<>) {
 next unless m/\tmRNA\t/;
 my @t=split("\t");
 my ($id)=(m/ID=([\|\w\.]+)/);
 $id=~s/\.[a-z]+\d+$//;
 my ($score)=(m/score=([\d\.]+)/i);
 my ($cov)=(m/Cov=([\d\.]+)/i);
 my $pid=$t[5];
 my $covpid=int(($pid*$cov)/100);
 #my ($geneid)=(m/(GeneID:\d+)/);
 print join("\t", $id, $score, $pid, $cov, $covpid, # $geneid,
            $t[0], $t[3], $t[4], $t[6])."\n";
}
Revision:	24
Committed:	Tue Jul 26 21:46:39 2011 UTC (13 years ago) by gpertea
File size:	405 byte(s)
Log Message:
Line	User	Rev	File contents
1	gpertea	23	#!/usr/bin/perl
2			use strict;
3			while (<>) {
4			next unless m/\tmRNA\t/;
5			my @t=split("\t");
6			my ($id)=(m/ID=([\\|\w\.]+)/);
7			$id=~s/\.[a-z]+\d+$//;
8			my ($score)=(m/score=([\d\.]+)/i);
9			my ($cov)=(m/Cov=([\d\.]+)/i);
10			my $pid=$t[5];
11			my $covpid=int(($pid*$cov)/100);
12			#my ($geneid)=(m/(GeneID:\d+)/);
13			print join("\t", $id, $score, $pid, $cov, $covpid, # $geneid,
14			$t[0], $t[3], $t[4], $t[6])."\n";
15			}