Bio::Tools::Run::Profile.3pm

Langue: en

Version: 2009-11-04 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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://bugzilla.open-bio.org/
 
 

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