problem with Bioperl get_sequence ('swiss', "acc#");

[Bohr]

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.

[Chris Fields]

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@...
> 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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[Bohr]

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:

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
> [e-mail]
> 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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