[Bioperl-l] WGS sequences through Bio::DB::GenBank
cjfields at uiuc.edu
Wed Mar 1 23:04:08 EST 2006
Thanks, Brian. I was actually typing this up when you responded.
Okay, to answer my own question somewhat (and to confirm your answer), there
IS no direct way; efetch doesn't complete these files, so the best way is
with a query. I'm posting this so anybody searching the mail list with the
same question will maybe find this. The NCBI help desk basically told me to
use a query like so:
which needs to be parsed for the individual contigs. I tried the same query
using Bio::DB::Query::GenBank and got it to work.
As for NCBIHelper, I'll give it a look and try adding this in but it won't
be until next week.
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign
> -----Original Message-----
> From: Brian Osborne [mailto:osborne1 at optonline.net]
> Sent: Wednesday, March 01, 2006 9:55 PM
> To: Chris Fields
> Subject: Re: [Bioperl-l] WGS sequences through Bio::DB::GenBank
> No, NCBIHelper.pm doesn't handle the WGS block, presumably this is where
> should be coded. The approach would be very similar to that used for the
> CONTIG block, piece the sequence together by retrieving the CONTIG
> information specified by the WGS_SCAFLD entries.
> Brian O.
> On 2/28/06 9:41 PM, "Chris Fields" <cjfields at uiuc.edu> wrote:
> > I know that a recent post showed that you could retrieve CONTIG
> > from GenBank files fairly easily:
> > http://bioperl.org/pipermail/bioperl-l/2006-February/020891.html
> > I'm driving myself a bit buggy looking for this, and I may be blind to
> > but can the same be done with WGS files? I've tried Bio::DB::GenBank
> and a
> > few other Bio::DB* modules to see if it's been implemented but haven't
> > any luck yet. I may try getting around it using
> > but just trying to find a more direct route.
> > Christopher Fields
> > Postdoctoral Researcher - Switzer Lab
> > Dept. of Biochemistry
> > University of Illinois Urbana-Champaign
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
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