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);


  wrapper module for Signalp program


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 Based on the EnsEMBL module Bio::EnsEMBL::Pipeline::Runnable::Protein::Signalp
 originally written by Marc Sohrmann (
 Written in BioPipe by Balamurugan Kumarasamy <>
 Contributions by David Vilanova (
                  Shawn Hoon (
# Please direct questions and support issues to <> 
 Cared for by the Fugu Informatics team (


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


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


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


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


 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


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


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


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


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