[Bioperl-l] Sigcleave module problem

[Richard Copley]

I think if you instantiate it with the sequence as a string, not a file, it 
works.

$sigcleave = Bio::Tools::Sigcleave->new( -seq => 'MLELLPTAVEGVS etc",
                                           -id => 'blah' );

%sig_hash = $sigcleave->signals;

Richard.

Sanjeev Pillai wrote:
> 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
>>>
>>>__________________________________________________
>>>Do You Yahoo!?
>>>Got something to say? Say it better with Yahoo!
>>>
>>Video Mail 
>>
>>>http://mail.yahoo.com
>>>_______________________________________________
>>>Bioperl-l mailing list
>>>Bioperl-l@bioperl.org
>>>http://bioperl.org/mailman/listinfo/bioperl-l
>>>
>>>
>>
>>-- 
>>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
>>
>>
> 
> 
> __________________________________________________
> Do You Yahoo!?
> Got something to say? Say it better with Yahoo! Video Mail 
> http://mail.yahoo.com
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l
> 
> 


-- 
  Richard Copley
  EMBL
  Meyerhofstr.1
  69012 Heidelberg
  Germany
  Tel: +49 6221 387 534
  FAX: +49 6221 387 517