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

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

perl v5.24.1			  2017-07-08	     Bio::Tools::Pseudowise(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Jason Stajich | APPENDIX

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