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Bio::Tools::GenomewiseUser Contributed Perl DocumentaBio::Tools::Genomewise(3)

NAME
       Bio::Tools::Genomewise -	Results	of one Genomewise run

SYNOPSIS
	 use Bio::Tools::Genomewise;
	 my $gw	= Bio::Tools::Genomewise(-file=>"genomewise.out");

	 while (my $gene = $gw->next_prediction){
	     my	@transcripts = $gene->transcripts;
	     foreach my	$t(@transcripts){
	       my @exons =  $t->exons;
	       foreach my $e(@exons){
		   print $e->start." ".$e->end."\n";
	       }
	     }
	 }

DESCRIPTION
       This is the parser for the output of Genewise. It takes either a	file
       handle or a file	name and returns a
       Bio::SeqFeature::Gene::GeneStructure object.  You will need to specify
       the proper target sequence id on	the object with	the
       $feature->seq_id($seqid).

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 - Fugu Team, Jason Stajich
	Email: fugui-at-worf.fugu-sg.org
	       jason-at-bioperl-dot-org

APPENDIX
       The rest	of the documentation details each of the object	methods.
       Internal	methods	are usually preceded with a _

   new
	Title	: new
	Usage	: $obj->new(-file=>"genewise.out");
		  $obj->new(-fh=>\*GW);
	Function: Constructor for genomewise wrapper. Takes either a file or filehandle
	Example	:
	Returns	: L<Bio::Tools::Genomewise>

   _get_strand
	Title	: _get_strand
	Usage	: $obj->_get_strand
	Function: takes	start and end values, swap them	if start>end and returns end
	Example	:
	Returns	:$start,$end,$strand

   score
	Title	: score
	Usage	: $obj->score
	Function: get/set for score info
	Example	:
	Returns	: a score value

   _prot_id
	Title	: _prot_id
	Usage	: $obj->_prot_id
	Function: get/set for protein id
	Example	:
	Returns	:a protein id

   _target_id
	Title	: _target_id
	Usage	: $obj->_target_id
	Function: get/set for genomic sequence id
	Example	:
	Returns	:a target id

   next_prediction
	Title	: next_prediction
	Usage	: while($gene =	$genewise->next_prediction()) {
			 # do something
		  }
	Function: Returns the gene structure prediction	of the Genomewise result
		  file.	Call this method repeatedly until FALSE	is returned.

	Example	:
	Returns	: a Bio::SeqFeature::Gene::GeneStructure object
	Args	:

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

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Fugu Team, Jason Stajich | APPENDIX

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