| Bio::Tools::Pseudowise(3pm) | User Contributed Perl Documentation | Bio::Tools::Pseudowise(3pm) |
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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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
/pseudowise/i.
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
| 2021-08-15 | perl v5.32.1 |