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




        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);


        Wrapper module for the pfscan program


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AUTHOR - Balamurugan Kumarasamy



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

        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

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

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