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
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Usage : $pseudowise->analysis_method(); Purpose : Inherited method. Overridden to ensure that the name matches /pseudowise/i. Returns : String Argument : n/a
Title : next_prediction Usage : while($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 :
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
To install LocalConfig, copy and paste the appropriate command in to your terminal.
cpanm
cpanm LocalConfig
CPAN shell
perl -MCPAN -e shell install LocalConfig
For more information on module installation, please visit the detailed CPAN module installation guide.