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


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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: johnsonm-at-gmail-dot-com


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