Provided by: libbio-perl-perl_1.6.901-2_all bug


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


         use Bio::Tools::Pseudowise;

         my $parser = Bio::Tools::Pseudowise->new(-file=>"pw.out");
         while(my $feat = $parser->next_result){
             push @feat, $feat;


       Pseudowise is a pseudogene prediction program written by Ewan Birney as part of the Wise
       Package. This module is the parser for the output of the program.


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AUTHOR - Jason Stajich

       Previous committed by the Fugu Team

       Re-written by Jason Stajich jason-at-bioperl-dot-org


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

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

        Title   : next_feature
        Usage   : $seqfeature = $obj->next_feature();
        Function: Returns the next feature available in the analysis result, or
                  undef if there are no more features.
        Example :
        Returns : A Bio::SeqFeatureI implementing object, or undef if there are no
                  more features.
        Args    : none

       See Also  Bio::SeqFeatureI

        Title   : next_prediction
        Usage   : while($gene = $pseudowise->next_prediction()) {
                         # do something
        Function: Returns the gene of the Pseudowise result
                  file. Call this method repeatedly until FALSE is returned.

        Example :
        Returns : a Bio::SeqFeature::Generic
        Args    : none

       See Also Bio::SeqFeature::Generic

        Title   : _parse_predictions()
        Usage   : $obj->_parse_predictions()
        Function: Parses the prediction section. Automatically called by
                  next_prediction() if not yet done.
        Example :
        Returns :


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

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

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