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root/gclib/scripts/gff2geneloc.pl
Revision: 24
Committed: Tue Jul 26 21:46:39 2011 UTC (8 years, 2 months 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     }

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svn:executable *