debian man page for bio::tools::pseudowise

Bio::Tools::Pseudowise(3pm)				User Contributed Perl Documentation			       Bio::Tools::Pseudowise(3pm)

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://redmine.open-bio.org/projects/bioperl/

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 v5.14.2							    2012-03-02					       Bio::Tools::Pseudowise(3pm)