[Bioperl-l] reading gff3?
Kevin.M.Brown at asu.edu
Thu Mar 12 19:19:54 EDT 2009
And comment in the next_seq() method:
"access the FASTA section (if any) at the end of the GFF stream. note that this method
will return undef if not all features in the stream have been handled"
>From a quick read through the code, it seems that once you've gotten all the features, you should be able to call next_seq() to get the fasta information.
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of
> Smithies, Russell
> Sent: Thursday, March 12, 2009 3:42 PM
> To: 'BioPerl List'
> Subject: [Bioperl-l] reading gff3?
> 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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