bio::tools::genewise(3pm) [debian man page]

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

NAME

       Bio::Tools::Genewise - Results of one Genewise run

SYNOPSIS

	 use Bio::Tools::Genewise;
	 my $gw = Bio::Tools::Genewise(-file=>"genewise.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."
";
	       }
	     }
	 }

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.

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 - Fugu Team, Jason Stajich
	Email: fugui@worf.fugu-sg.org
	Email: jason-at-bioperl.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 genewise wrapper. Takes either a file or filehandle
	Example :
	Returns : Bio::Tools::Genewise object

       See Bio::Tools::Genewise

   _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
	Returns : a score value

   _prot_id
	Title	: _prot_id
	Usage	: $obj->_prot_id
	Function: get/set for protein id
	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 Genewise result
		  file. Call this method repeatedly until FALSE is returned.

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

       See Bio::SeqFeature::Gene::GeneStructure

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