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Bio::Tools::MZEF.3pm

NAME

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

SYNOPSIS

    $mzef = Bio::Tools::MZEF->new(-file => 'result.mzef');
    # filehandle:
    $mzef = Bio::Tools::MZEF->new( -fh  => \*INPUT );
    # to indicate that the sequence was reversed prior to feeding it to MZEF
    # and that you want to have this reflected in the strand() attribute of 
    # the exons, as well have the coordinates translated to the non-reversed
    # sequence
    $mzef = Bio::Tools::MZEF->new( -file   => 'result.mzef',
                                   -strand => -1 );
 
    # 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 = $mzef->next_prediction()) {
        # $gene is an instance of Bio::Tools::Prediction::Gene
 
        # $gene->exons() returns an array of 
        # Bio::Tools::Prediction::Exon objects
        # all exons:
        @exon_arr = $gene->exons();
 
        # internal exons only
        @intrl_exons = $gene->exons('Internal');
        # note that presently MZEF predicts only internal exons!
    }
 
    # essential if you gave a filename at initialization (otherwise the file
    # will stay open)
    $mzef->close();
 
 

DESCRIPTION

The MZEF module provides a parser for MZEF gene structure prediction output.

This module inherits off Bio::Tools::AnalysisResult and therefore implements 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-at-gmx.net (or hilmar.lapp-at-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     : $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 :
 
 

_prediction

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

_add_prediction

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

_predictions_parsed

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