[Bioperl-l] problem with Bioperl get_sequence ('swiss', "acc#");
juheymann at yahoo.com
Wed May 9 22:38:42 UTC 2007
Thank you for pointing that out! I installed 1.5.2 via Build.pl. The scripts
work as expected now.
Chris Fields wrote:
> 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:
>> I installed bioperl under OSX Tiger via Fink. I tested the
>> 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
>> View this message in context: http://www.nabble.com/problem-with-
>> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
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