[Bioperl-l] Parsing Genbank

[Mark A. Jensen]

Hi Brandi-
If $cds is a Bio::SeqFeature::Generic, that's weird (I believe); if its an 
ordinary Bio::Seq, that's normal.
Can you elaborate by posting your code?
cheers,
MAJ
----- Original Message ----- 
From: "Brandi Cantarel" <bcantarel at som.umaryland.edu>
To: <bioperl-l at lists.open-bio.org>
Sent: Wednesday, December 02, 2009 1:36 PM
Subject: [Bioperl-l] Parsing Genbank


> Hi all,
> I am not sure if this is normal, but when I use SEQIO to parse genbank files, 
> it changes the coordinates of things on the minus strand.
>
>
> For example, I have a sequence that has a CDS on the minus strand at it is 
> from 911 to 974.  The sequence is 974 nt.
>
> x $cds->start
> 1
> x $cds->end
> 64
>
> How can I get the original coordinates?  Is there a command for that or will I 
> have to just do the math?
>
> Feature or Bug?
>
>
> ~~~~~~~~~~~~~~~~~~~~
> Brandi Cantarel, PhD
> Bioinformatics Analyst
> Institute for Genome Sciences
> School of Medicine
> University of Maryland, Baltimore
>
>
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