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