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

[Chris Fields]

This patch works only for the recent change in swissprot seq format  
for sequence versions on the DT line.  I checked it out vs the test  
data provided with bioperl (t\data\swiss.dat).  I did manage to get  
it working for both old and new using a modification to your patch  
but there's another issue; using $seq->get_dates, which should only  
show dates, shows the entire line (date and version info).  Jason  
mentioned that there needs to be a better way to address this which  
I'm looking into.

Chris

On May 22, 2006, at 8:51 PM, Michael Rogoff wrote:

> 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
>>
>>
>>
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign