Bio::Tools::ESTScan(3)

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:

  http://bugzilla.open-bio.org/

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    :