[Bioperl-l] A failure to fetch a sequence

smarkel at scitegic.com smarkel at scitegic.com
Wed Sep 13 18:14:59 EDT 2006


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


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