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

Robert Buels rmb32 at cornell.edu
Fri Jun 30 15:32:11 EDT 2006


Aha!  Isn't it amazing what gets revealed when you just get off your 
butt and ask on the mailing list.

I'll look at that code straightaway.  The concept is quite attractive to 
me, since GenomeThreader is the next program that I'm going to be 
integrating into my analysis stuff.  Unfortunately, (I am under the 
impression that) my GeneSeqer parser is almost finished.

This brings us to the next question, what about parsing the 
GenomeThreader XML?  Would be lovely to have a Bioperl interface for 
that.  Is there some code floating about for that too?

Rob

Michael E Sparks wrote:
> 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
>>>       
>
>
>
>   

-- 
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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