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Bio::Tools::Run::tRNAscanSE

NAME

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

SYNOPSIS

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);

DESCRIPTION

Wrapper module for tRNAscan-SE.

tRNAscan-SE is open source and available at <http://lowelab.ucsc.edu/software/>.

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 AT bioperl DOT 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 AT bioperl DOT 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: johnsonm-at-gmail-dot-com

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: 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

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