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://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:
https://github.com/bioperl/bioperl-live/issues
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