Provided by: libbio-perl-run-perl_1.7.1-3_all bug




         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