/ 
bioperl-1.2.2
/ Bio::Tools::Eponine

NAME

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

SYNOPSIS

use Bio::Tools::Run::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://bio.perl.org/MailList.html             - About the mailing lists

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 email or the web:

bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/

AUTHOR - Tania Oh

Describe contact details here

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