[Bioperl-l] parser for GeneSeqer

[Hilmar Lapp]

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
>>
>>
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>
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-- 
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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