Question

I would like to write a Perl function that gets a GFF3 filename and a range (i.e. 100000 .. 2000000). and returns a reference to an array containing all names/accessions of genes found in this range.

I guess using bioperl will make sense, but I have very little experience with it. I can write a script that parses a GFF3 by my self, but if using bioperl (or another packagae) is not too complicated – I’d rather reuse their code.

Answer 1

use Bio::Tools::GFF;

my $range_start = 100000;
my $range_end   = 200000;

my @features_in_range = ( );


my $gffio = Bio::Tools::GFF->new(-file => $gff_file, -gff_version => 3);

while (my $feature = $gffio->next_feature()) {

    ## What about features that are not contained within the coordinate range but
    ## do overlap it?  Such features won't be caught by this check.            
    if (
        ($feature->start() >= $range_start)
        &&
        ($feature->end()   <= $range_end)
       ) {

        push @features_in_range, $feature;

    }

}

$gffio->close();

DISCLAIMER: Naive implementation. I just banged that out, it’s had no testing. I won’t even guarantee it compiles.