[Bioperl-l] WGS sequences through Bio::DB::GenBank

[Chris Fields]

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:

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=nucleotide&term
=AAOH00000000[accn]+AND+wgs_contig[prop]

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.  

Christopher Fields
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
> 
> Chris,
> 
> No, NCBIHelper.pm doesn't handle the WGS block, presumably this is where
> it
> 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
> sequences
> > 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
> it,
> > 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
> had
> > any luck yet.  I may try getting around it using
> Bio::DB::Query::GenBank,
> > but just trying to find a more direct route.
> >
> > Christopher Fields
> > Postdoctoral Researcher - Switzer Lab
> > Dept. of Biochemistry
> > University of Illinois Urbana-Champaign
> >
> >
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