[Bioperl-l] Bug: swiss.pm doesn't parse seq_version

[Jason Stajich]

Sounds like a "missing feature" =)

AFAIK the module was only written for swissprot files.  It is  
possible there have been changes in the format that have not been  
tracked to the current code.  We'd certainly appreciate someone  
testing it out as versions evolve.  If you submit a bug to bugzilla  
with version of bioperl and example files you can track when a fix is  
in.  We of course appreciate anyone's efforts to provide a patch as  
most bugs get fixed of late when someone gets "itchy" enough to fix  
them.

-jason

On May 22, 2006, at 7:56 PM, Michael Rogoff wrote:

>
> As best as I can tell, using Bio::SeqIO to parse a uniprot file  
> ignores the
> sequence version, and calling seq_version() on the resulting  
> RichSeq object
> returns undef.
>
> It looks like swiss.pm is trying to parse the version out of the SV  
> line, which
> apparently doesn't exist any more?  The sequence version(s) are now  
> specified as
> part of the Date (DT) lines.
>
> Is this not a bug?  Is swiss.pm not designed to parse uniprot files?
>
> Thanks for any help ...
>
>
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--
Jason Stajich
Duke University
http://www.duke.edu/~jes12