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Bio::Tools::Run::tRNAsUserEContributed Perl DocuBio::Tools::Run::tRNAscanSE(3)
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://selab.wustl.edu/cgi-bin/selab.pl?mode=software#trnascan/
<http://selab.wustl.edu/cgi-bin/selab.pl?mode=software#trnascan/>.
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@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://bugzilla.open-bio.org/
AUTHOR - Mark Johnson
Email: mjohnson-at-watson-dot-wustl-dot-edu
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
perl v5.14.1 2011-07-21 Bio::Tools::Run::tRNAscanSE(3)
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