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

[Bohr]

Thank you for the feedback and the suggestion.

I installed 1.5.2 via Build.pl and the results were the same e.g. embl and
genbank worked fine, swissprot failed

Here is the output:

MSG: acc (CALX_YEAST) does not exist
---------------------------------------------------

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Did not provide a valid Bio::PrimarySeqI object
STACK: Error::throw
STACK: Bio::Root::Root::throw /sw/lib/perl5/5.8.6/Bio/Root/Root.pm:328
STACK: Bio::SeqIO::fasta::write_seq
/sw/lib/perl5/5.8.6/Bio/SeqIO/fasta.pm:181

Before contemplating too much:
Here my question: how do I verify the update to 1.5.2? (I ran ./Build test
and that came back positive.) And what else could have gone wrong here?

What might be a clever way to troubleshoot this?




---------------------------------------------------------------------------

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:
> 
> http://www.bioperl.org/wiki/Bptutorial
> 
> chris
> 
> 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.
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
> 
> 
> 
> _______________________________________________
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> Bioperl-l at lists.open-bio.org
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> 
> 

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