Handy parse of GFF files

parseGff.pl

#!/usr/bin/env perl

# List of IDs - one per line
my $list = shift; 
# File with potential IDs, it can be GFF but also othersH
my $gff = shift;


my @ids;
open( LIST, $list ) || die "Cannot open $list";

while( <LIST> ) {

	my ($id) = $_=~/^(\S+)/;

	push( @ids, $id );
}

close( LIST );


foreach my $id ( @ids ) {

	my $geneid = $id;

	$geneid=~s/P\d+\s*$//g;

	open (GFF, $gff );

	while( <GFF> ) {

		if ( $_=~$geneid ) {
			print;
		}
	}

	close( GFF );


}