[Bioperl-l] GFF method in Bio::SeqFeatureI

Matthew Pocock mrp@sanger.ac.uk
Tue, 20 Feb 2001 15:13:58 +0000

>> <heresy>Could you not produce a GFF module that looks very similar to 
>> the SeqIO stuff that consumes text and is a factory for features? It can 
>> also have the methods for producing GFF. GFF is a file format, and is in 
>> no way integral to SeqFeatureI.</heresy>
> Sounds great! When do we expect code matthew?
Checked in Bio::Tools::GFF that implements Bio::SeqAnalysisParserI and 
has the method write_feature. It is un-documented, and the GFF2 parser 
can't parse the GFF2 output it generates. I just coppied code from 
Generic & SeqFeatureI. I think the t/GFF.t needs completely re-writing 
to be a propper test-harness program.

Somebody take this off my hands before nasty things happen!

>> Matthew