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

[Michael Rogoff]

I have a patch that seems to work but I'm not familiar with the proper method to
"provide" it.  How do I go about that?

The patch is pretty simple, it just parses the sequence version out of the date
line where it now hides:

         #date
         elsif( /^DT\s+(.*)/ ) {
           my $date = $1;
+
+          if ($date =~ /sequence version (\d+)/i) {
+              $params{'-seq_version'} ||= $1;
+          }
+
           $date =~ s/\;//;
           $date =~ s/\s+$//;
           push @{$params{'-dates'}}, $date;
         }

By the way, what is the difference between Bio::Seq::version and
Bio::Seq::RichSeq::seq_version?


> -----Original Message-----
> From: Jason Stajich [mailto:jason.stajich at duke.edu] 
> Sent: Monday, May 22, 2006 6:37 PM
> To: Michael Rogoff
> Cc: bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] Bug: swiss.pm doesn't parse seq_version
> 
> 
> 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 ...
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> --
> Jason Stajich
> Duke University
> http://www.duke.edu/~jes12
> 
> 
>