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

[Jason Stajich]

On Tue, 20 Feb 2001, Matthew Pocock wrote:

> >> <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!
I've updated the tests to do a better job testing.
Added a close() method to Bio::Tools::GFF.
> 
> > 
> > 
> >> Matthew
> 
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Jason Stajich
jason@chg.mc.duke.edu
Center for Human Genetics
Duke University Medical Center 
http://www.chg.duke.edu/