[Bioperl-l] parser for GeneSeqer

[Robert Buels]

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
>>
>>
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>
> 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