[Bioperl-l] A failure to fetch a sequence

Chris Fields cjfields at uiuc.edu
Wed Sep 13 20:12:56 EDT 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. 

Christopher Fields
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
> 
> GET
> http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?retmode=text&rett
> ype=gbwithparts&db=nucleotide&tool=bioperl&id=X61622&retstart=0&usehistory
> =n
> 
> The response ends with no sequence data:
> 
> ORIGIN
> //
> 
> 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
> 
> 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
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



More information about the Bioperl-l mailing list