Provided by: libbio-perl-perl_1.7.2-3_all bug

NAME

       Bio::Tools::Eponine - Results of one Eponine run

SYNOPSIS

        use Bio::Tools::Eponine;
        use strict;
           my $seq = "/data/seq.fa";
           my $threshold  = "0.999";
           my @params = ( -seq => $seq,
                          -threshold => $threshold);

          my $factory = Bio::Tools::Run::Eponine->new(@params);
            # run eponine against fasta
               my $r = $factory->run_eponine($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->seq_id. "\n";
                      }
              }

DESCRIPTION

       Parser for Eponine, a probabilistic transcription start site detector optimized for
       mammalian genomic sequence. This module inherits off Bio::Tools::AnalysisResult and
       therefore implements Bio::SeqAnalysisParserI (see Bio::Tools::AnalysisResult and
       Bio::SeqAnalysisParserI).

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:

         https://github.com/bioperl/bioperl-live/issues

AUTHOR - Tania Oh

       <gisoht-at-nus.edu.sg>

APPENDIX

       The rest of the documentation details each of the object methods. Internal methods are
       usually preceded with a _

   analysis_method
        Usage     : $mzef->analysis_method();
        Purpose   : Inherited method. Overridden to ensure that the name matches
                    /mzef/i.
        Returns   : String
        Argument  : n/a

   next_feature
        Title   : next_feature
        Usage   : while($gene = $mzef->next_feature()) {
                         # do something
                  }
        Function: Returns the next gene structure prediction of the MZEF result
                  file. Call this method repeatedly until FALSE is returned.

                  The returned object is actually a SeqFeatureI implementing object.
                  This method is required for classes implementing the
                  SeqAnalysisParserI interface, and is merely an alias for
                  next_prediction() at present.

                  Note that with the present version of MZEF there will only be one
                  object returned, because MZEF does not predict individual genes
                  but just potential internal exons.
        Example :
        Returns : A Bio::Tools::Prediction::Gene object.
        Args    :

   next_prediction
        Title   : next_prediction
        Usage   : while($gene = $mzef->next_prediction()) {
                         # do something
                  }
        Function: Returns the next gene structure prediction of the MZEF result
                  file. Call this method repeatedly until FALSE is returned.

                  Note that with the present version of MZEF there will only be one
                  object returned, because MZEF does not predict individual genes
                  but just potential internal exons.
        Example :
        Returns : A Bio::Tools::Prediction::Gene object.
        Args    :

   _parse_predictions
        Title   : _parse_predictions()
        Usage   : $obj->_parse_predictions()
        Function: Parses the prediction section. Automatically called by
                  next_prediction() if not yet done.
        Example :
        Returns :

   create_feature
           Title   :   create_feature
           Usage   :   obj->create_feature($feature)
           Function:   Returns an array of features
           Returns :   Returns an array of features
           Args    :   none

   _prediction
        Title   : _prediction()
        Usage   : $gene = $obj->_prediction()
        Function: internal
        Example :
        Returns :

   _predictions_parsed
        Title   : _predictions_parsed
        Usage   : $obj->_predictions_parsed
        Function: internal
        Example :
        Returns : TRUE or FALSE