[Bioperl-l] A failure to fetch a sequence

smarkel at scitegic.com smarkel at scitegic.com
Wed Sep 13 20:42:45 EDT 2006


Chris,

Runs fine here, too, now.

Scott
 

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org 
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of 
> Chris Fields
> Sent: Wednesday, 13 September 2006 17:13
> To: Scott Markel; goshng at gmail.com; bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] A failure to fetch a sequence
> 
> 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 


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