[Bioperl-l] genbank2gff and how do I use gff3 with Bio::DB::GFF?

Chad Matsalla chad at dieselwurks.com
Tue Jun 14 22:53:02 EDT 2005

On Tue, 14 Jun 2005, Scott Cain wrote:
> Sorry I haven't reproduced your results; I've been dragged down by other
> matters.  If I can recap to make sure I have it right:
> bp_genbank2gff.pl will correctly generate gff2

I don't know how to ask it to produce gff2. As far as I can tell from
the source it generates v3 only and under default use it produces gff3.
And the gff3 it produces returns undef to the segment() call in [1].

> bp_genbank2gff3.pl will correctly generate gff3

Yes, it generates gff that I can successfully bind to using code I
provided earlier and included here[1].

I'm not at all a gff expert so I was hoping for someone else[2] to tell
me the difference between the gff3 produced by genbank2gff and
genbank2gff3. Whew, that's a mouthfull to say out loud.

> If I have that right, I would be reluctant to pitch bp_genbank2gff.pl as
> there are still plenty of people (that is, the overwhelming majority)
> that use gff2.  I nearly certain (without even looking) that they could
> be documented better.

I'd be pleased for information on how to make either script produce
gff2. Am I missing something?

> What would be really great would be if you could submit this as a bug on
> bioperl's bugzilla, so I won't forget about it.  I have a few software
> releases I really want to get out in the next week or so, so I know I
> won't get to it real soon.

I'd love to report a bug but I'm not clear on what I'm reporting. Is it
that the gff3 produced by genbank2gff is incomplete in some way? Or is
it that the gff3 produced by genbank2gff requires some special technique
to use as in [1]? Or is it that genbank2gff should be producing gff2?

Thanks for your advice on how to treat this! These scripts provide a
great start to working with these systems.

Chad Matsalla

my $db2 = Bio::DB::GFF->new( -adaptor => 'memory', -file => './t/data/AE003644_Adh-genomic.gff' );
my $segment2 = $db2->segment(-name => 'AE003644');
my @features = $segment2->features();
print("There are this many features on AE003644 (".scalar(@features).")\n");

[2] wink wink, nudge nudge

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