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

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/ Describe contact details here 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 : 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