NAME

       Bio::Tools::Run::Profile

SYNOPSIS

        Build a Profile factory
        # $paramfile is the full path to the seg binary file

        my @params = ('DB',$dbfile,'PROGRAM',$paramfile);
        my $factory = Bio::Tools::Run::Profile->new($param);

        # Pass the factory a Bio::PrimarySeqI object
        # @feats is an array of Bio::SeqFeature::Generic objects
        my @feats = $factory->run($seq);

DESCRIPTION

        Wrapper module for the pfscan 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 - Balamurugan Kumarasamy

        Email: fugui@worf.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 $factory= Bio::Tools::Run::Profile->new($param);
        Function: creates a new Profile factory
        Returns:  Bio::Tools::Run::Profile
        Args    :

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

   run
        Title   :   run
        Usage   :   my @feats = $factory->run($seq)
        Function:   Runs Profile
        Returns :   An array of L<Bio::SeqFeature::FeaturePair> 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 pfscan
        Returns :   An array of L<Bio::SeqFeature::FeaturePair> 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