Provided by: libbio-perl-run-perl_1.7.2-4_all bug

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://redmine.open-bio.org/projects/bioperl/

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