---
name: "Bio::Tools::Run::Eponine"
section: "3pm"
platform: "linux"
package: "libbio-perl-run-perl"
version: "1.7.3-13"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/Bio::Tools::Run::Eponine"
---

# Bio::Tools::Run::Eponine(3pm)

Object for execution of the Eponine which is a mammalian TSS predictor

## 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
```