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Bio::Tools::Pseudowise.3pm

NAME

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

SYNOPSIS

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

DESCRIPTION

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.

http://www.sanger.ac.uk/software/wise2

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 - Jason Stajich

Previous committed by the Fugu Team

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

APPENDIX

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

analysis_method

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

next_feature

  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

next_prediction

  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

_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