[Bioperl-l] Tag handling on SeqFeature::Generic

[Hilmar Lapp]

> -----Original Message-----
> From: Jason Stajich [mailto:jason@cgt.mc.duke.edu]
> Sent: Wednesday, August 28, 2002 7:32 AM
> To: Marco Aurelio Valtas Cunha
> Cc: Bioperl
> Subject: Re: [Bioperl-l] Tag handling on SeqFeature::Generic
[...]
> 
> > I felling that using SeqFeature::Generic is wrong. But I'm really
> > confused with Tools:GFF and SeqFeature::Generic in both 
> modules you can
> 
> To clarify:
> 
> Bio::Tools::GFF is probably badly named -- it is just and Input/Output
> mechanism for Bio::SeqFeatureI objects and GFF format.

In fact internally calling $seqfeature->gff_string() delegates to an instance of Bio::Tools::GFF to do the job. So there's really no difference between the output.

Bio::Tools::GFF is indeed badly named -- it should be in a Bio::SeqFeatureIO directory to be consistent with Bioperl's other IO module layouts.

Marco, if you want comments on how you accomplished the job in your script you should post the script, or its relevant parts.

	-hilmar