[Bioperl-l] Sigcleave module problem

[Sanjeev Pillai]

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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