Rationale For Gff3 Not Being A Part Of Bio::Seqio

Question

[rasche.eric]

Could anyone please explain the rationale behind gff3 being part of the Bio::Tools rather than being another sequence parser? Or is this just a module that no one has implemented yet and still needs to be written?

[Neilfws]

It helps if you tell us which language/library you're talking about. I assume Bioperl?

[Joachim]

I really wish that changing tags was still possible. That way it would be much easier to address these problems.

[Istvan Albert]

you can change the tags by editing the post

[Neilfws]

I really wish that adding tags used auto-suggest. Might go some way to preventing people inventing a new tag for every question.

[Istvan Albert]

I'll try to add that next week on the coding sprint

[Joachim]

Sorry, but I don't see how. I can edit my answer, where I have no control over tags of the question. Everything else appears non-editable to me.

[Istvan Albert]

ok, forgot to mention that only the original author and moderators may edit a post and thus change the tags

Answer 1

[Joachim]

Are you perhaps just looking at the wrong module? GFF3 is supported by Bio::FeatureIO, which lets you access the GFF3 file contents in various ways (http://doc.bioperl.org/bioperl-live/Bio/FeatureIO.html).

For example, I took a GFF3 file example from http://gmod.org/wiki/GFF and saved it in test.gff3 with the following contents:

##gff-version 3
ctg123 . operon          1300 15000  .  +  .  ID=operon001;Name=superOperon
ctg123 . mRNA            1300  9000  .  +  .  ID=mrna0001;Parent=operon001;Name=sonichedgehog
ctg123 . exon            1300  1500  .  +  .  Parent=mrna0001
ctg123 . exon            1050  1500  .  +  .  Parent=mrna0001
ctg123 . exon            3000  3902  .  +  .  Parent=mrna0001
ctg123 . exon            5000  5500  .  +  .  Parent=mrna0001
ctg123 . exon            7000  9000  .  +  .  Parent=mrna0001
ctg123 . mRNA           10000 15000  .  +  .  ID=mrna0002;Parent=operon001;Name=subsonicsquirrel
ctg123 . exon           10000 12000  .  +  .  Parent=mrna0002
ctg123 . exon           14000 15000  .  +  .  Parent=mrna0002

Note: The empty spaces in the GFF3 above need to be replaced by tabs.

I then created gff3.pl, which looks like:

use strict;
use Bio::FeatureIO;

# Open GFF file:
my $gff = Bio::FeatureIO->new(-file => 'test.gff3', -format => 'gff', -version => 3);

# Iterate through the file, feature-by-feature:
while(my $feature = $gff->next_feature) {
    print $feature, "\n";
}

Running perl gff3.pl goes though all the features in the GFF3 file.

Having said that, there is also a GFF3 implementation in BioRuby, which is explained with many examples here: http://thebird.nl/bioruby/BioRuby_GFF3.html

Hope that helps.

[Chris Fields]

We (Bioperl core developers) are also reworking Bio::FeatureIO to remove a lot of the cruftiness of its original implementation.