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