Bio::Tools::Run::Eponine(3pm)				User Contributed Perl Documentation			     Bio::Tools::Run::Eponine(3pm)

NAME

       Bio::Tools::Run::Eponine - Object for execution of the Eponine which is a mammalian TSS predictor

SYNOPSIS

	 use Bio::Tools::Run::Eponine;
	 use strict;
	 my $seq = "/data/seq.fa";
	 my $threshold	= "0.999";
	 my @params = ( '-seq' => $seq,
			'-threshold' => $threshold,
			'-epojar'  => '/usr/local/bin/eponine-scan.jar',
			 '-java'  => '/usr/local/bin/java');

	 my $factory = Bio::Tools::Run::Eponine->new(@params);
	 # run eponine against fasta
	 my $r = $factory->run($seq);
	 my $parser = Bio::Tools::Eponine->new($r);

	 while (my $feat = $parser->next_prediction){
		 #$feat contains array of SeqFeature
		 foreach my $orf($feat){
			 print $orf->seqname. "
";
		 }
	 }

	# Various additional options and input formats are available.  See
	# the DESCRIPTION section for details.

DESCRIPTION

       wrapper for eponine, a mammalian TSS predictor.

       The environment variable EPONINEDIR must be set to point at either the directory which contains eponine-scan.jar or directly at the jar
       which eponine-scan classfiles. NOTE: EPONINEDIR must point at the real file not a symlink.

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://redmine.open-bio.org/projects/bioperl/

AUTHOR

       Email gisoht@nus.edu.sg

APPENDIX

       The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

   java
	   Title   :   java
	   Usage   :   $obj->java('/usr/opt/java130/bin/java');
	   Function:   Get/set method for the location of java VM
	   Args    :   File path (optional)

   epojar
	   Title   :   epojar
	   Usage   :   $obj->epojar('/some/path/to/eponine-scan.jar');
	   Function:   Get/set method for the location of the eponine-scan executable JAR
	   Args    :   Path (optional)

   threshold
	Title	: threshold
	Usage	: my $threshold = $self->threshold
	Function: Get/Set the threshold for Eponine
	Returns : string
	Args	: b/w 0.9 and  1.0

   run
	Title	: run
	Usage	: my @genes = $self->run($seq)
	Function: runs Eponine and creates an array of features
	Returns : An Array of SeqFeatures
	Args	: A Bio::PrimarySeqI

   predict_TSS
	Title	: predict_TSS
	Usage	: Alias for run()

   _setinput()
	Title	: _setinput
	Usage	: Internal function, not to be called directly
	Function: writes input sequence to file and return the file name
	Example :
	Returns : string
	Args	:

   _run_eponine
	   Title   :  run_eponine
	   Usage   :   $obj->_run_eponine()
	   Function:   execs the Java VM to run eponine
	   Returns :   none
	   Args    :   none

perl v5.12.3							    2011-06-18					     Bio::Tools::Run::Eponine(3pm)