[Bioperl-l] Re: [Bioperl-guts-l] Notification: incoming/1183

[Heikki Lehvaslaiho]

Sanjeev,

Our apologies. Sigcleave module has not been maintained for a long time.

Bioperlers,

It really needs to be updated to current BioPerl standards. Chris Dagdigian
is the primary author, but anyone else wants to have a go, I am sure Chris
does not mind. Any volunteers?


Sanjeev,

You were misled by the synopsis which shows a 'file' attribute to the new().
However, 'file' is not implemented and you have to pass the sequence as a
string. See the test file t/Sigcleave.t . (It really should take a bioperl
sequence object and throw an error if anything else than protein sequence is
given to it.) Also, pretty-print() method does not work. (The output could
be an array of Bio::LocatableSeq objects.)


Here is your script modified so that you get results printed out:

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

use Bio::Tools::Sigcleave;

$pseq = "
MLELLPTAVEGVSQAQITGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYA
ITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVD
ADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKA
ESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVG
FGLILLRSRAIFGEAEAPEPSAGDGAAATSD";
$pseq =~ s/\W//g;

$sigcleave_object = new Bio::Tools::Sigcleave
  (-seq=>$pseq,
   -threshold=>'3.5',
   -desc=>'test sigcleave protein seq',
   -type=>'AMINO');

%raw_results = $sigcleave_object->signals;

use Data::Dumper;
print Dumper(\%raw_results);
-------------------------------------------------------------

Again, the alternative is to use the EMBOSS program sigcleave
and access it from Bio::Factory::EMBOSS.
See:
http://www.uk.embnet.org/Software/EMBOSS/Apps/sigcleave.html

Yours,
	-Heikki



bioperl-bugs@bioperl.org wrote:
> 
> JitterBug notification
> 
> new message incoming/1183
> 
> Message summary for PR#1183
>         From: spillai2@yahoo.com
>         Subject: PRIVATE: problem with the Sigcleave module
>         Date: Tue, 7 May 2002 14:40:13 -0400
>         0 replies       0 followups
> 
> ====> ORIGINAL MESSAGE FOLLOWS <====
> 
> >From spillai2@yahoo.com Tue May  7 14:40:13 2002
> Received: from localhost (localhost [127.0.0.1])
>         by pw600a.bioperl.org (8.12.2/8.12.2) with ESMTP id g47IeDdo020237
>         for <bioperl-bugs@pw600a.bioperl.org>; Tue, 7 May 2002 14:40:13 -0400
> Date: Tue, 7 May 2002 14:40:13 -0400
> Message-Id: <200205071840.g47IeDdo020237@pw600a.bioperl.org>
> From: spillai2@yahoo.com
> To: bioperl-bugs@bioperl.org
> Subject: PRIVATE: problem with the Sigcleave module
> 
> Full_Name: Sanjeev Pillai
> Module: Sigcleave
> Version: 1.0
> PerlVer: 5.6.1
> OS: Linux
> Submission from: linnaeus.mendelbio.com (206.86.87.3)
> 
> Dear Sir/Madam,
> I cannot get the Sigcleave module to work. I'm cant even get the test code given
> with the documentation to work!
> 
> The following are the errors I'm getting and it looks like the sequence I'm
> supplying is not even being read:
> 
> Use of uninitialized value in transliteration (tr///) at
> /usr/local/lib/perl5/site_perl/5.6.1/Bio/Tools/Sigcleave.pm line 333.
> 
> My code is as follows:
> 
> #!/usr/local/bin/perl -w
> 
> use Bio::Tools::Sigcleave;
> 
> $sigcleave_object = new Bio::Tools::Sigcleave(-file=>'seq.aa',
>                                               -threshold=>'3.5',
>                                               -desc=>'test sigcleave protein
> seq',
>                                               -type=>'AMINO');
> 
> %raw_results      = $sigcleave_object->signals;
> 
> print %raw_results, "\n";
> 
> The file seq.aa is a raw amino acid sequence file as follows:
> 
> MLELLPTAVEGVSQAQITGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFGEAEAPEPSAGDGAAATSD
> 
> Please let me know what I'm doing wrong!
> 
> -Sanjeev
> 
> _______________________________________________
> Bioperl-guts-l mailing list
> Bioperl-guts-l@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-guts-l

-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________