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

[Mark Wilkinson]

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

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.
>
> Also, why are introns and exons top-level features of a sequence, when
> they are also (obviously) sub-features of a gene?
>
> 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
>
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--
---
Dr. Mark Wilkinson
Bioinformatics Group
National Research Council of Canada
Plant Biotechnology Institute
110 Gymnasium Place
Saskatoon, SK
Canada