[Bioperl-l] reading gff3?
cain.cshl at gmail.com
Thu Mar 12 19:23:45 EDT 2009
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 Cain, Ph. D.
scott at scottcain dot net
Ontario Institute for Cancer Research
216 392 3087
On Mar 12, 2009, at 6:42 PM, "Smithies, Russell" <Russell.Smithies at agresearch.co.nz
> 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?
> Russell Smithies
> Bioinformatics Applications Developer
> T +64 3 489 9085
> E russell.smithies at agresearch.co.nz
> Invermay Research Centre
> Puddle Alley,
> New Zealand
> T +64 3 489 3809
> F +64 3 489 9174
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