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