Langue: en

Version: 2010-04-29 (fedora - 01/12/10)

Section: 3 (Bibliothèques de fonctions)


Bio::Tools::Run::tRNAscanSE - Wrapper for local execution of tRNAscan-SE


   my $factory = Bio::Tools::Run::tRNAscanSE->new('-program' => 'tRNAscan-SE');
   # Pass the factory Bio::Seq objects
   # returns a Bio::Tools::tRNAscanSE object
   my $factory = $factory->run($seq);
   my $factory = $factory->run(@seq);


Wrapper module for tRNAscan-SE.

tRNAscan-SE is open source and available at <>.


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.                  - General discussion  - About the mailing lists


Please direct usage questions or support issues to the mailing list:

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:

AUTHOR - Mark Johnson

  Email: mjohnson-at-watson-dot-wustl-dot-edu


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: gets/sets the program name
  Returns:  string
  Args    : string


  Title   : program_dir
  Usage   : $factory->program_dir()
  Function: gets/sets the program dir
  Returns:  string
  Args    : string


  Title   : new
  Usage   : $tRNAscanSE->new(@params)
  Function: creates a new tRNAscanSE factory
  Returns:  Bio::Tools::Run::tRNAscanSE
  Args    :


  Title   :   run
  Usage   :   $obj->run($seq_file)
  Function:   Runs tRNAscan-SE
  Returns :   A Bio::Tools::tRNAscanSE object
  Args    :   An array of Bio::PrimarySeqI objects


  Title   :   _run
  Usage   :   $obj->_run()
  Function:   Internal(not to be used directly)
  Returns :   An instance of Bio::Tools::tRNAscanSE 
  Args    :   file name


  Title   :   _write_seq_file
  Usage   :   obj->_write_seq_file($seq) or obj->_write_seq_file(@seq)
  Function:   Internal(not to be used directly)
  Returns :   Name of a temp file containing program output
  Args    :   One or more Bio::PrimarySeqI objects