[Bioperl-l] parser for GeneSeqer

[Chris Fields]

Oh well.  There's always BOSC...

Chris

> -----Original Message-----
> From: Hilmar Lapp [mailto:hlapp at gmx.net]
> Sent: Thursday, July 06, 2006 6:42 PM
> To: Chris Fields
> Cc: 'Robert Buels'; bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] parser for GeneSeqer
> 
> Uhm - roadmap - I guess yes, but more that of the Golden State, or
> other states on the way, for Jason.
> 
> On Jul 6, 2006, at 7:28 PM, Chris Fields wrote:
> 
> > 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
> >>
> >>
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> > _______________________________________________
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> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> 
> --
> ===========================================================
> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
> ===========================================================
> 
> 
>