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


          $estscan = Bio::Tools::ESTScan->new(-file => 'result.estscan');
          # filehandle:
          $estscan = Bio::Tools::ESTScan->new( -fh  => \*INPUT );

          # parse the results
          # note: this class is-a Bio::Tools::AnalysisResult which implements
          # Bio::SeqAnalysisParserI, i.e., $genscan->next_feature() is the same
          while($gene = $estscan->next_prediction()) {
              # $gene is an instance of Bio::Tools::Prediction::Gene
              foreach my $orf ($gene->exons()) {
                  # $orf is an instance of Bio::Tools::Prediction::Exon
                  $cds_str = $orf->predicted_cds();

          # essential if you gave a filename at initialization (otherwise the file
          # will stay open)


       The ESTScan module provides a parser for ESTScan coding region
       prediction output.

       This module inherits off Bio::Tools::AnalysisResult and therefore
       implements the Bio::SeqAnalysisParserI interface.  See


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       Bioperl modules. Send your comments and suggestions preferably to one
       of the Bioperl mailing lists.  Your participation is much appreciated.
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       Please direct usage questions or support issues to the mailing list:

       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.

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       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

AUTHOR - Hilmar Lapp

       Email (or


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

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

        Title   : next_feature
        Usage   : while($orf = $estscan->next_feature()) {
                         # do something
        Function: Returns the next gene structure prediction of the ESTScan 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.

        Example :
        Returns : A Bio::Tools::Prediction::Gene object.
        Args    :

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

                  So far, this method DOES NOT work for reverse strand predictions,
                  even though the code looks like.
        Example :
        Returns : A Bio::Tools::Prediction::Gene object.
        Args    :

        Title   : close
        Usage   : $result->close()
        Function: Closes the file handle associated with this result file.
                  Inherited method, overridden.
        Example :
        Returns :
        Args    :

        Title   : _fasta_stream
        Usage   : $result->_fasta_stream()
        Function: Gets/Sets the FASTA sequence IO stream for reading the contents of
                  the file associated with this MZEF result object.

                  If called for the first time, creates the stream from the filehandle
                  if necessary.
        Example :
        Returns :
        Args    :

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