Query: bio::tools::run::trnascanse
OS: debian
Section: 3pm
Format: Original Unix Latex Style Formatted with HTML and a Horizontal Scroll Bar
Bio::Tools::Run::tRNAscanSE(3pm) User Contributed Perl Documentation Bio::Tools::Run::tRNAscanSE(3pm)NAMEBio::Tools::Run::tRNAscanSE - Wrapper for local execution of tRNAscan-SESYNOPSISmy $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);DESCRIPTIONWrapper module for tRNAscan-SE. tRNAscan-SE is open source and available at http://selab.wustl.edu/cgi-bin/selab.pl?mode=software#trnascan/ <http://selab.wustl.edu/cgi- bin/selab.pl?mode=software#trnascan/>.FEEDBACKMailing 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 - Mark Johnson Email: mjohnson-at-watson-dot-wustl-dot-eduAPPENDIXThe 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: gets/sets the program name Returns: string Args : string program_dir Title : program_dir Usage : $factory->program_dir() Function: gets/sets the program dir Returns: string Args : string new Title : new Usage : $tRNAscanSE->new(@params) Function: creates a new tRNAscanSE factory Returns: Bio::Tools::Run::tRNAscanSE Args : run Title : run Usage : $obj->run($seq_file) Function: Runs tRNAscan-SE Returns : A Bio::Tools::tRNAscanSE object Args : An array of Bio::PrimarySeqI objects _run Title : _run Usage : $obj->_run() Function: Internal(not to be used directly) Returns : An instance of Bio::Tools::tRNAscanSE Args : file name _write_seq_file Title : _write_seq_file Usage : obj->_write_seq_file($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 perl v5.12.3 2011-06-18 Bio::Tools::Run::tRNAscanSE(3pm)
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