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

Chad Matsalla chad at dieselwurks.com
Fri Jun 10 01:40:00 EDT 2005


I have a genbank file that I would like to convert to GFF so that I can
view it in a GBrowse. I would also like to use the normal Bio::DB::GFF
(memory adaptor) interface to work with this data.

I took a genbank entry (in this case t/data/AE003644_Adh-genomic.gb) and
ran the bp_genbank2gff.pl program like this:
/usr/bin/bp_genbank2gff.pl --stdout --file
t/data/AE003644_Adh-genomic.gb > csm.gff3

Now, I want to get the segment represented by AE003644.

If this was gff2, I would successfully get that like this - I've chosen
the gffv2 file t/data/biodbgff/test.gff

my $db2 = Bio::DB::GFF->new( -adaptor => 'memory', -file => 't/data/biodbgff/test.gff' );
my $segment2 = $db2->segment(-name => 'Contig1');
my @features = $segment2->features();
print("There are this many features on Contig1 (".scalar(@features).")\n");

However, with gff3 I'm not able to get the segment. ($segment is undef)

Am I missing something? Can someone push me in the right direction?

I also want to use gff from genbank2gff in gbrowse - I can't seem to get
the thing to appear and I assume it's related to this. Is this an issue
with the reference class?
AE003644  Genbank   region    1    263309    .    .    .  ID=AE003644;Alias=AE002690,AE014134

Chad Matsalla

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