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://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://bugzilla.bioperl.org/

AUTHOR - Fugu Team

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

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    :

_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