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

[Tao Zhu]

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)