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Bio::Tools::Run::Eponine(3) User Contributed Perl Documentation Bio::Tools::Run::Eponine(3)

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. NOTE: EPONINEDIR must point at the real file not a symlink.

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

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.

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/

Email gisoht@nus.edu.sg

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
2022-04-13 perl v5.32.1

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