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Bio::Tools::PseudowiseUser Contributed Perl DocumentaBio::Tools::Pseudowise(3)

       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.

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       of the Bioperl mailing lists.  Your participation is much appreciated.			- General discussion	- About	the mailing lists

       Please direct usage questions or	support	issues to the mailing list:

       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.

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       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

AUTHOR - Jason Stajich
       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
	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

perl v5.32.0			  2019-12-07	     Bio::Tools::Pseudowise(3)


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