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view snpEff_2_1a/snpEff_2_1a/scripts/data/rice5/mRnaAddParent.pl @ 3:c052639fa666 default tip
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author | pcingola |
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date | Fri, 20 Apr 2012 11:22:59 -0400 |
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#!/usr/bin/perl #------------------------------------------------------------------------------- # Add 'Parent' option in mRNA lines # # Pablo Cingolani #------------------------------------------------------------------------------- while( $l = <STDIN> ) { chomp $l; @t = split /\t/,$l; $type = $t[2]; # Is it an mRNA? if( $type eq 'mRNA' ) { # Parse ID in options $opts = $t[8]; if( $opts =~ /ID=(.*?)-\d+;/ ) { $pid = $1; $pid =~ tr/t/g/; # Add 'Parent' option $l .= ";Parent=$pid"; } } print "$l\n"; }