[Bioperl-l] Sigcleave module problem

[chris dagdigian]

Sanjeev-

That module is very old and does not conform to any of the new bioperl 
standards. It will likely be removed from bioperl in the future unless 
someone steps up and "modernizes" it. I'm willing to take a look at your 
problem but it would help me greatly if you could provide me with the 
sequence you were using that generated the error.

Regards,
Chris


Sanjeev Pillai wrote:
> Hi all,
> I'm encountering a problem when I use the Sigcleave
> module in one of my perl scripts (This module helps
> predict signal peptide cleavage regions).  When I run
> my script that uses Sigcleave and pass on an amino
> acid sequence file (raw amino acid sequence data with
> no headers), it gives me the following error messages:
> 
> Use of uninitialized value in transliteration (tr///)
> at
> /usr/local/lib/perl5/site_perl/5.6.1/Bio/Tools/Sigcleave.pm
> line 333.
> Use of uninitialized value in transliteration (tr///)
> at
> /usr/local/lib/perl5/site_perl/5.6.1/Bio/Tools/Sigcleave.pm
> line 450.
> Use of uninitialized value in concatenation (.) or
> string at
> /usr/local/lib/perl5/site_perl/5.6.1/Bio/Tools/Sigcleave.pm
> line 452.
> 
> When I checked the module and went to the specific
> lines mentioned in the error messages, I find that
> they all do the perl transliteration on $pep. I
> realize that $pep is never initialized eventhough
> earlier in the module as part of the _Analyze function
> in the constructor $pep is initialized as $self->seq.
> So for some reason, the sequence I feed the program is
> never being read. I do not want to tinker with
> anything inside the module. 
> 
> I would greatly appreciate if any of you could help me
> out here with suggestions/modifications. I'm thinking
> some of you may have encountered this problem.
> 
> Thanks a lot
> Sanjeev
> 
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-- 
Chris Dagdigian, <dag@sonsorol.org>
Life Science IT & Research Computing Freelancer
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