Mercurial > repos > dereeper > pangenome_explorer
view Perl/remove_duplicates_in_gff.pl @ 5:4157f435fa89 draft
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author | dereeper |
---|---|
date | Thu, 30 May 2024 12:11:25 +0000 |
parents | e42d30da7a74 |
children |
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#!/usr/bin/perl use strict; my $file = $ARGV[0]; my $out = $ARGV[1]; my %h; open(F,$file); while(<F>){ my @infos = split(/\t/,$_); if ($infos[2] eq 'CDS' && /Name=([^;]*);/){ my $id = $1; $h{$id}++; } } close(F); my %dup; foreach my $id(keys(%h)){ my $n = $h{$id}; if ($n > 1){ $dup{$id} = 1; } } open(O,">$out"); open(F,$file); while(<F>){ my @infos = split(/\t/,$_); if ($infos[2] eq 'CDS' && /Name=([^;]*);/){ my $id = $1; if ($dup{$id}){next;} } if ($infos[2] eq 'mRNA' && /Parent=([^;]*);/){ my $id = $1; if ($dup{$id}){next;} } if ($infos[2] eq 'gene' && /ID=([^;]*);/){ my $id = $1; if ($dup{$id}){next;} } if ($infos[2] eq 'exon' && /Parent=([^;]*);/){ my ($id,$extension) = split(/\./,$1); if ($dup{$id}){next;} } print O $_; } close(F); close(O);