[Bioperl-l] reading gff3?

Kevin Brown Kevin.M.Brown at asu.edu
Thu Mar 12 19:19:54 EDT 2009


http://bioperl.org/cgi-bin/deob_interface.cgi?Search=Search&module=Bio%3A%3AFeatureIO%3A%3Agff&sort_order=by+method&search_string=Bio%3A%3AFeatureIO%3A%3Agff

Method: fasta_mode

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?
> 
> Thanx,
> 
> --Russell 
> 
> 
> Russell Smithies 
> Bioinformatics Applications Developer 
> T +64 3 489 9085 
>russell.smithies at agresearch.co.nz 
> Invermay  Research Centre 
> Puddle Alley, 
> Mosgiel, 
> New Zealand 
> T  +64 3 489 3809   
> F  +64 3 489 9174  
> www.agresearch.co.nz 
> 
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