[Bioperl-l] parser for GeneSeqer

[Chris Fields]

Not any word yet.  Been pretty quiet, likely b/c everybody was there
planning a roadmap for v1.6.  

Chris

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Robert Buels
> Sent: Thursday, July 06, 2006 6:11 PM
> To: bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] parser for GeneSeqer
> 
> The Annotation/Annotatable stuff was going to be talked about at the
> GMOD meeting that just happened, wasn't it?  What's the scoop on that?
> 
> Rob
> 
> 
> Chris Fields wrote:
> > If you plan on generating seqfeatures from this output you could check
> > out the Bio::Tools core modules for examples.  There are a few there
> > that take program output and convert them to Bio::SeqFeature::Generic
> > objects, including Bio::Tools:RNAMotif and Bio::Tools::tRNAscanSE.  If
> > alignments are involved you might want something like
> > Bio::SeqFeature::FeaturePair.  Not sure about using the
> > SeqFeature::Annotation or others; I thought that the some of the
> > Annotation/Annotatable stuff might be changing soon but I may be wrong.
> >
> > Chris
> >
> > On Jun 30, 2006, at 12:01 PM, Robert Buels wrote:
> >
> >> Hi all,
> >>
> >> I find myself needing a parser for GeneSeqer output, so I'm writing one
> >> (which I will submit for your consideration when it's working).  In a
> >> nutshell, GeneSeqer is a (kind of old) program for aligning a bunch of
> >> ESTs to genomic sequence, then using those alignments to predict where
> >> in the genomic sequence the genes are.  So really what you get from
> this
> >> is a bunch of hierarchical features.
> >>
> >> I don't really know where I should put it in the bioperl hierarchy
> >> though.  Probably FeatureIO?
> >>
> >> And what's the current fashion for objects it should emit?
> >> Bio::SeqFeature::Generic?  Bio::SeqFeature::Annotated?
> >>
> >> Rob
> >>
> >> --Robert Buels
> >> SGN Bioinformatics Analyst
> >> 252A Emerson Hall, Cornell University
> >> Ithaca, NY  14853
> >> Tel: 503-889-8539
> >> rmb32 at cornell.edu
> >> http://www.sgn.cornell.edu
> >>
> >>
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> > Christopher Fields
> > Postdoctoral Researcher
> > Lab of Dr. Robert Switzer
> > Dept of Biochemistry
> > University of Illinois Urbana-Champaign
> >
> >
> >
> 
> --
> Robert Buels
> SGN Bioinformatics Analyst
> 252A Emerson Hall, Cornell University
> Ithaca, NY  14853
> Tel: 503-889-8539
> rmb32 at cornell.edu
> http://www.sgn.cornell.edu
> 
> 
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