/ 
bioperl-1.0.2
/ Bio::Tools::MZEF

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://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://bio.perl.org/bioperl-bugs/

AUTHOR - Hilmar Lapp

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

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 :

_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