[Bioperl-l] Sigcleave module problem

[Sanjeev Pillai]

Hi Chris,
Thanks for responding.

The amino acid sequence that I'm using is a simple raw
sequence file by name seq.aa which is as follows:

MLELLPTAVEGVSQAQITGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFGEAEAPEPSAGDGAAATSD

The perl script that I wrote is also very simple,
(straight from the docs site) as I was wanting to test
it first.

#!/usr/local/bin/perl -w

use Bio::Tools::Sigcleave;

$sigcleave_object =
Bio::Tools::Sigcleave->new('-file'=>'seq.aa',         

                      			       '-threshold'=>'3.5',
                      			       '-desc'=>'test
sigcleave protein seq',
                      			       '-type'=>'AMINO');

%raw_results      = $sigcleave_object->signals;
$formatted_output = $sigcleave_object->pretty_print;


Thanks again for your time and attention.
Regards
Sanjeev

--- chris dagdigian <dag@sonsorol.org> wrote:
> 
> 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
> Office: 617-666-6454, Mobile: 617-877-5498, Fax:
> 425-699-0193
> Yahoo IM: craffi
> 


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