Bio::Tools::PseudowiseUser Contributed Perl DocumentaBio::Tools::Pseudowise(3)NAMEBio::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
perl v5.14.1 2011-07-22 Bio::Tools::Pseudowise(3)
