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); or my $factory = $factory->run(@seq);
Wrapper module for tRNAscan-SE.
tRNAscan-SE is open source and available at http://selab.wustl.edu/cgi-bin/selab.pl?mode=software#trnascan/.
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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