[Bioperl-l] A failure to fetch a sequence
cjfields at uiuc.edu
Thu Sep 14 00:12:56 UTC 2006
I've run several tests today which rely on Bio::DB::GenBank and they all
seem to be passing. Using your URL directly in a browser gets the proper
sequence back as well, so it was likely a 'burp' on NCBI's end. Are you
still having any problems?
BTW, 'gbwithparts' is set by default for the return format to always grab
full sequence records (ones w/o CONTIG information) as that's what most
users want. You can change that if needed to 'gb','fasta', etc.
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of smarkel at scitegic.com
> Sent: Wednesday, September 13, 2006 5:15 PM
> To: goshng at gmail.com; bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] A failure to fetch a sequence
> We just had a customer report this today. It looks like the URL
> used by BioPerl no longer results in the sequence data being returned.
> Our test case is
> The response ends with no sequence data:
> Changing the rettype to "gb" doesn't change the result. Using a
> rettype of "fasta" does return the correct FASTA entry.
> Our regressions ran fine last night, so it looks like the change
> was today at NCBI.
> Scott Markel, Ph.D.
> Principal Bioinformatics Architect email: smarkel at scitegic.com
> SciTegic Inc. mobile: +1 858 205 3653
> 10188 Telesis Court, Suite 100 voice: +1 858 799 5603
> San Diego, CA 92121 fax: +1 858 279 8804
> USA web: http://www.scitegic.com
> > -----Original Message-----
> > From: bioperl-l-bounces at lists.open-bio.org
> > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of
> > Sang Chul Choi
> > Sent: Wednesday, 13 September 2006 13:03
> > To: bioperl-l at bioperl.org
> > Subject: [Bioperl-l] A failure to fetch a sequence
> > Hi,
> > I want to fetch a sequence and I tested the following simple code:
> > use Bio::DB::GenBank;
> > $gb = new Bio::DB::GenBank;
> > $seq = $gb->get_Seq_by_id('MUSIGHBA1'); # Unique ID print
> > $seq->display_id, "\n"; print $seq->seq, "\n";
> > Output:
> > -----------------------
> > MUSIGHBA1
> > -----------------------
> > I could get the sequence information but not the sequence itself.
> > I felt like my fetching work was blocked by NCBI server
> > because I have run many jobs to fetch DNA and protein sequences using
> > get_Seq_by_*** method. If my fetching job was blocked, what
> > else could I do for fetching sequences? Can I download
> > datafile and parse it locally?
> > Thank you,
> > Sang Chul
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