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. "\n";
                 }
         }

        # 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