[Bioperl-l] reading gff3?

Scott Cain cain.cshl at gmail.com
Thu Mar 12 19:23:45 EDT 2009


Hi Russell,

I'm away from my computer at the moment, but I'm pretty sure you can  
call next_seq on a Bio::FeatureIO object.

Scott

--
Scott Cain, Ph. D.
scott at scottcain dot net
Ontario Institute for Cancer Research
http://gmod.org/
216 392 3087

On Mar 12, 2009, at 6:42 PM, "Smithies, Russell" <Russell.Smithies at agresearch.co.nz 
 > wrote:

> What's the trick to reading the fasta attached to gff files?
> Bio:FeatureIO and Bio::Tools::GFF both seem to ignore it (unless I'm  
> doing it wrong)
>
> What I'm trying to do is read in a gff3 file (with attached fasta)  
> then get the sequence for the CDS features contained within.
>
> Any ideas?
>
> Thanx,
>
> --Russell
>
>
> Russell Smithies
> Bioinformatics Applications Developer
> T +64 3 489 9085
> E  russell.smithies at agresearch.co.nz
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> New Zealand
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