[Bioperl-l] Bio::SeqIO::swiss species parsing bug?

Chris Fields cjfields at uiuc.edu
Fri Aug 17 13:20:21 EDT 2007


On Aug 17, 2007, at 12:03 PM, David Gonzalez wrote:

> 	Hi,
>
> 	I had a problem with a swissprot file in which the genus and species
> were being left undefined, and I believe it could be a bug in the
> swiss.pm module.
>
>
> 	When I tried to parse the file with Bio::SeqIO, I got the following
> error messages:
>
> Use of uninitialized value in pattern match (m//) at
> /sw/lib/perl5/5.8.6/Bio/SeqIO/swiss.pm line 965, <GEN0> line 12.
> Use of uninitialized value in string eq at
> /sw/lib/perl5/5.8.6/Bio/SeqIO/swiss.pm line 967, <GEN0> line 12.
> ...
> 	I am using the fink installed bioperl:
> 	bioperl-pm586   1.4-5   Perl module for biology
>
> 	I don't know if this has  been reported/solved in the newer  
> versions of
> bioperl.
>
> 	David
>
> -- 
> David Gonzalez Knowles
> Smurfit Institute of Genetics
> Trinity College
> Dublin

That looks like bioperl 1.4, which is several years old.  You should  
update to the latest official release (1.5.2), then see if the  
problem persists.

chris


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