repost - Re: [Bioperl-l] Huh? Bioperl Seq objects and strands

[Ewan Birney]

On Tue, 19 Sep 2000, Mark Wilkinson wrote:

> Just to re-post this question as it seems to be either (a) a bug, or (b) an
> unusual desire by the person who wrote the parser...

It is a "feature".

> Can *anyone* explain the rationale behind this?  If others agree that the
> status-quo is not a "good idea", then can we "fix" it?
> 

There is no good idea about this. It is simply a bug. 

> Thanks for your time,
> 
> Mark Wilkinson
> 
> 
> David Block wrote:
> 
> > Hi experienced bioperlers,
> >
> > We're trying to map a Bio::SeqI compliant object onto a Tk Map.  We're
> > very close (code within days for this part), but we're fighting with the
> > Seq object's definitions of gene, exon, and CDS.
> >
> > We loaded up a Bio::Seq object from GenBank using SeqIO.  Top-level
> > features for genes on the -1 strand have the tags
> > gene  strand 1
> > gene_span strand 0
> > intron strand -1
> > exon strand -1
> > etc...
> >
> > How can we tell which top-level features with strand 1 are actually strand
> > -1 without looking at sub-features?  We would like to be able to decide so
> > we can map the gene on the correct side of the axis.

This is a bug

> >
> > Also, why are introns and exons top-level features of a sequence, when
> > they are also (obviously) sub-features of a gene?
> >

This is an issue with GenBank/EMBL being mapped into a more interpretable
format. 

GenBank/EMBL sometimes puts introns/exons separate from the CDS lines.
Quite often they *disagree* with the CDS lines. What are we meant to do in
these cases.


> > Shouldn't it be (top-level features only):
> > gene strand -1
> > gene_span strand 0
> >
> > and that gene's subfeatures:
> > intron strand -1
> > exon strand -1
> >
> > Thanx,
> >
> > Dave "Huh?" Block, with commentary by Mark "I Dunno???" Wilkinson
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
> 
> --
> ---
> Dr. Mark Wilkinson
> Bioinformatics Group
> National Research Council of Canada
> Plant Biotechnology Institute
> 110 Gymnasium Place
> Saskatoon, SK
> Canada
> 
> 
> 
> _______________________________________________
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> Bioperl-l@bioperl.org
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> 

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