Bio::Tools::Genscan.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

NAME

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

SYNOPSIS

    use Bio::Tools::Genscan;
 
    $genscan = Bio::Tools::Genscan->new(-file => 'result.genscan');
    # filehandle:
    $genscan = Bio::Tools::Genscan->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 = $genscan->next_prediction()) {
        # $gene is an instance of Bio::Tools::Prediction::Gene, which inherits
        # off Bio::SeqFeature::Gene::Transcript.
        #
        # $gene->exons() returns an array of 
        # Bio::Tools::Prediction::Exon objects
        # all exons:
        @exon_arr = $gene->exons();
 
        # initial exons only
        @init_exons = $gene->exons('Initial');
        # internal exons only
        @intrl_exons = $gene->exons('Internal');
        # terminal exons only
        @term_exons = $gene->exons('Terminal');
        # singleton exons: 
        ($single_exon) = $gene->exons();
    }
 
    # essential if you gave a filename at initialization (otherwise the file
    # will stay open)
    $genscan->close();
 
 

DESCRIPTION

The Genscan module provides a parser for Genscan gene structure prediction output. It parses one gene prediction into a Bio::SeqFeature::Gene::Transcript- derived object.

This module also implements the Bio::SeqAnalysisParserI interface, and thus can be used wherever such an object fits. 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

APPENDIX

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

analysis_method

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

next_feature

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

_has_cds

  Title   : _has_cds()
  Usage   : $obj->_has_cds()
  Function: Whether or not the result contains the predicted CDSs, too.
  Example :
  Returns : TRUE or FALSE
 
 

_read_fasta_seq

  Title   : _read_fasta_seq()
  Usage   : ($id,$seqstr) = $obj->_read_fasta_seq();
  Function: Simple but specialised FASTA format sequence reader. Uses
            $self->_readline() to retrieve input, and is able to strip off
            the traling description lines.
  Example :
  Returns : An array of two elements.