[Bioperl-l] Downloading refseq genomes in batch

Juan Jovel jovel_juan at hotmail.com
Tue Apr 3 17:02:26 EDT 2012


Hi Shalab
You can try use Bio::DB::GenBank, but I believe the NCBI does not like people doing many remote lookups. I would advise you download the whole database you are interested in, and then you parse it locally.
Cheers, Juan
> Date: Tue, 3 Apr 2012 14:15:16 -0400
> From: shalabh.sharma7 at gmail.com
> To: carandraug+dev at gmail.com
> CC: Bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] Downloading refseq genomes in batch
> 
> Hi Came,
>               Thanks for your reply.
> I tried to get UID from genome names but i cant find on EUtilities.
> I have taxa id for those genomes, can i download genomes with taxa id in
> batch ?
> 
> Thanks
> Shalabh
> 
> 
> On Tue, Apr 3, 2012 at 11:53 AM, Carnë Draug <carandraug+dev at gmail.com>wrote:
> 
> > On 3 April 2012 16:34, shalabh sharma <shalabh.sharma7 at gmail.com> wrote:
> > > Hi All,
> > >         I am trying to download refseq genomes in batch. But instead of
> > > accession number i have genome names (=~ 500).
> > > Is there any way i can download them using some bioperl module ?
> >
> > If you have their name/official symbol, then searching on the database
> > should nly return one hit, therefore one UID. Make the search, get
> > that number, and use it for download. The EUtilities module should do
> > that.
> >
> > Carnë
> >
> 
> 
> 
> -- 
> Shalabh Sharma
> Scientific Computing Professional Associate (Bioinformatics Specialist)
> Department of Marine Sciences
> University of Georgia
> Athens, GA 30602-3636
> 
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