[Bioperl-l] Fwd: FW: parser for GeneSeqer

Michael E Sparks mespar1 at iastate.edu
Fri Jun 30 15:20:29 EDT 2006


Hi Rob,

For what it's worth, I wrote a fair amount of code for parsing GeneSeqer output.
 You may want to have a look here: http://www.public.iastate.edu/~mespar1/gthxml/

There is a perl script--GSQ2XML.pl--to convert GeneSeqer plain text output into
an XML format also used by the GenomeThreader spliced alignment program, whose
schema is specified in a RELAX NG document, GenomeThreader.rng.txt.  The file
0README in the above directory will give you an overview of what tools I've made
available.  Hope you find it useful!

Regards,
Michael

--
Thanks,
Michael E Sparks
Graduate Assistant, Brendel Lab
2128 Molecular Biology Building
Iowa State University
Ames, IA 50011-3260
1-515-294-4063
http://www.public.iastate.edu/~mespar1/


Forwarded Message:
> To: <plantgdb at iastate.edu>
> From: "Shannon D Schlueter" <sds at iastate.edu>
> Subject: FW: [Bioperl-l] parser for GeneSeqer
> Date: Fri, 30 Jun 2006 13:01:46 -0500
> -----
> >Date: Fri, 30 Jun 2006 10:01:38 -0700
> >From: Robert Buels <rmb32 at cornell.edu>
> >User-Agent: Thunderbird 1.5.0.2 (X11/20060516)
> >To: bioperl-l at bioperl.org
> >Subject: [Bioperl-l] parser for GeneSeqer
> >Sender: bioperl-l-bounces at lists.open-bio.org
> >
> >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
> 





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