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Bio::Tools::Run::Eponine.3pm

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://bugzilla.open-bio.org/
 
 

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