How Can I Get Sequences From A Gff3 File?

Question

[David B]

As you know, GFF3 files can contain FASTA sequences after the feature table.

How do I extract a specific FASTA sequence given it's ID?

my $gffio = Bio::Tools::GFF->new(
    -file =>
        "/path/to/file.gff",
    -gff_version => 3
);

print Dumper $gffio->get_seqs();

but it's seems null, although the GFF3 has sequences and is also valid. I am abke to parse the features themselves (using $gffio->next_feature()), but not the sequences ($gffio->get_seqs());

Answer 1

[brentp]

For some (undocumented) reason, the bioperl gff parser wants you to iterate through all the features before getting the sequences. Of course it's likely this limitation is because the sequences appear at the end, but it's not explained to be the case as far as I could see.

I was able to get your example to work by adding:

while($gffio->next_feature()){ }

to the line before the print.

[David B]

Thanks, this seems to work, but the other option to get sequences - $gffio->seq_id_by_h() - (documented here) does not... very strange.