/ 
BioPerl-Run-1.007001
River stage one • 2 direct dependents • 2 total dependents
/ Bio::Tools::Run::Eponine

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