Provided by: libbio-perl-run-perl_1.7.1-3_all bug


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


         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.


       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.


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

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

           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)

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

        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

        Title   : predict_TSS
        Usage   : Alias for run()

        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    :

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