[Bioperl-l] problem with Bioperl get_sequence ('swiss', "acc#");

Chris Fields cjfields at uiuc.edu
Tue May 8 21:53:04 UTC 2007

The Fink BioPerl distribution is 1.5.1.  You'll need to update to v  
1.5.2 due to changes on the various remote servers (NCBI, UniProt,  
etc) accessed via bioperl.

As a note, the bptutorial.pl has been moved to the bioperl wiki:



On May 8, 2007, at 1:37 PM, Bohr wrote:

> Hi,
> I installed bioperl under OSX Tiger via Fink. I tested the  
> installation
> using the test tutorial via: perl -w bptutorial.pl 5
> The script failed indicating that the file to retrieve was missing. To
> identify the problem, I used a script using 'get_sequence' that will
> retrieve a file from 'genbank' or 'embl'. Both succeeded. If I  
> replace it
> with 'swiss' or 'swissprot' and substitute the ID with the  
> identical ID as
> in the tutorial, I am recreating the problem found with  
> bptutorial.pl. Other
> ID's do the same.
> Any pointers on the origin of this finding would be greatly  
> appreciated.
> -- 
> View this message in context: http://www.nabble.com/problem-with- 
> Bioperl-get_sequence-%28%27swiss%27%2C-%22acc-%22%29-- 
> tf3711391.html#a10381379
> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign

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