[Bioperl-l] What's wrong with the script about module Bio::SeqFeature::Gene::GeneStructure

[Jason Stajich]

You have to instantiate the gene structure and copy the exon objects into the substructure. Unless you have specific methods in the GeneStructure I would just pull out the data from the generic objects. 

See the genbank to gff script and the Unflattener for ways to more simply destruct the mRNA feature into gene->mRNA->CDS,Exons 

If you are just wanting to count Exons 
You can see example on slide 27 or so. 

http://jason.open-bio.org/Bioperl_Tutorials/ProgrammingBiology2008/ProgBiology_BioPerl_I.pdf

Sent from my iPhone-please excuse typos

--
Jason Stajich

On Mar 19, 2011, at 2:49 AM, Tao Zhu <tzhu at mail.bnu.edu.cn> wrote:

> But I think an "mRNA" feature should have exons. For example:
> 
> 
>     mRNA            complement(join(1031434..1031901,1031940..1032269,
>                     1032329..1032418,1032472..1032489))
>                     /locus_tag="SPCC825.05c"
>                     /transcript_id="NM_001023047.1"
>                     /db_xref="GI:68021105"
>                     /db_xref="GeneID:2539459"
> 
> Such mRNA should have 4 exons and 3 introns, right? And I just want to
> calculate the lengths of every exons and introns quickly.
> 
> Besides, in the document of module Bio::SeqFeature::Gene::GeneStructure,
> it writes like these:
> 
> @exons = $gene->exons();
> @introns = $gene->introns();
> @utr_sites = $gene->utrs();
> 
> Then where does the object "$gene" come from? I've searched through all
> the google sites but found nothing.
> 
> 在 2011-03-18五的 15:05 +0000，Frank Schwach写道： 
>> maybe I'm missing the point here but I think an "mRNA" feature should
>> not be a Bio::SeqFeature::Gene::GeneStructure and it should not have
>> exons - it would not make sense biologically.
>> 
>> Frank
>> 
>> 
>> On Fri, 2011-03-18 at 21:57 +0800, Tao Zhu wrote:
>>> Yes. But in the document
>>> http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/SeqFeature/Gene/GeneStructure.html
>>> It says that module Bio::SeqFeature::Gene::GeneStructure can inherit
>>> Bio::SeqFeature::Generic. I wonder how to do such inheritance.
> 
> 
> -- 
> Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
> 100875, China
> Email: tzhu at mail.bnu.edu.cn
> Website: http://bnuzt.org (mainly written in Chinese)
> 
> 
> 
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