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

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://bio.perl.org/MailList.html - About the mailing lists

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.bioperl.org/ Email gisoht@nus.edu.sg 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

_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