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Bio::Tools::Run::Signalp.3pm

NAME

Bio::Tools::Run::Signalp

SYNOPSIS

   Build a Signalp factory
 
   my $factory = Bio::Tools::Run::Signalp->new();
   # Pass the factory a Bio::Seq object
   # @feats is an array of Bio::SeqFeature::Generic objects
   my @feats = $factory->run($seq);
 
 

DESCRIPTION

   wrapper module for Signalp program
 
 

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.

   bioperl-l@bioperl.org                  - General discussion
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
 
 

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:

   http://bugzilla.open-bio.org/
 
 

AUTHOR

  Based on the EnsEMBL module Bio::EnsEMBL::Pipeline::Runnable::Protein::Signalp
  originally written by Marc Sohrmann (ms2@sanger.ac.uk)
  Written in BioPipe by Balamurugan Kumarasamy <savikalpa@fugu-sg.org>
  Contributions by David Vilanova (david.vilanova@urbanet.ch)
                   Shawn Hoon (shawnh@fugu-sg.org)
 # Please direct questions and support issues to <bioperl-l@bioperl.org> 
 #
  Cared for by the Fugu Informatics team (fuguteam@fugu-sg.org)
 
 

APPENDIX

  The rest of the documentation details each of the object
  methods. Internal methods are usually preceded with a _
 
 

program_name

  Title   : program_name
  Usage   : $factory>program_name()
  Function: holds the program name
  Returns:  string
  Args    : None
 
 

program_dir

  Title   : program_dir
  Usage   : $factory->program_dir(@params)
  Function: returns the program directory, obtained from ENV variable.
  Returns:  string
  Args    :
 
 

new

  Title   : new
  Usage   : my $factory= Bio::Tools::Run::Signalp->new();
  Function: creates a new Signalp factory
  Returns:  Bio::Tools::Run::Signalp
  Args    :
 
 

predict_protein_features

  Title   :   predict_protein_features()
  Usage   :   DEPRECATED. Use $factory->run($seq) instead
  Function:   Runs Signalp and creates an array of featrues
  Returns :   An array of Bio::SeqFeature::Generic objects
  Args    :   A Bio::PrimarySeqI
 
 

run

  Title   :   run()
  Usage   :   my $feats = $factory->run($seq)
  Function:   Runs Signalp 
  Returns :   An array of Bio::SeqFeature::Generic objects
  Args    :   A Bio::PrimarySeqI
 
 

_input

  Title   :   _input
  Usage   :   $factory->_input($seqFile)
  Function:   get/set for input file
  Returns :
  Args    :
 
 

_run

  Title   :   _run
  Usage   :   $factory->_run()
  Function:   Makes a system call and runs signalp
  Returns :   An array of Bio::SeqFeature::Generic objects
  Args    :
 
 

_writeSeqFile

  Title   :   _writeSeqFile
  Usage   :   $factory->_writeSeqFile($seq)
  Function:   Creates a file from the given seq object
  Returns :   A string(filename)
  Args    :   Bio::PrimarySeqI