[Bioperl-l] Downloading refseq genomes in batch

shalabh sharma shalabh.sharma7 at gmail.com
Thu Apr 5 10:40:06 EDT 2012


Hi All,
        Thanks for all the suggestions.
Thanks a lot Chris, i am using your method to pull out genomes. Its working
fine.

Thanks
Shalabh


On Tue, Apr 3, 2012 at 5:19 PM, Fields, Christopher J <cjfields at illinois.edu
> wrote:

> 500 sequences isn't too bad for a remote lookup (I have run about ~20K
> myself).  It's much easier if you can grab them as a batch, e.g. run
> esearch for the IDs, use efetch with the webenv/key to grab the sequences.
>  NCBI is more worried about the number of requests made, the length of time
> between requests, and the time of day requests are made.
>
> In fact, I recall updating EUtilities recently so it can use a POST, so
> you can grab ~2000 seqs at a time w/o having to iterate through them.
>
> chris
>
> On Apr 3, 2012, at 4:02 PM, Juan Jovel wrote:
>
> >
> > 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
> >>
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>


-- 
Shalabh Sharma
Scientific Computing Professional Associate (Bioinformatics Specialist)
Department of Marine Sciences
University of Georgia
Athens, GA 30602-3636



More information about the Bioperl-l mailing list