Provided by: libbio-perl-perl_1.7.6-3_all bug

NAME

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

SYNOPSIS

          $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)
          $estscan->close();

DESCRIPTION

       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 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 - Hilmar Lapp

       Email hlapp@gmx.net (or hilmar.lapp@pharma.novartis.com)

APPENDIX

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

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

   next_feature
        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    :

   next_prediction
        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    :

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

   _fasta_stream
        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    :