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

NAME

       Bio::Tools::Geneid - Results of one geneid run

SYNOPSIS

	 use Bio::Tools::Geneid;
	 my $gid = Bio::Tools::Geneid(-file => "geneid.out");

	 while (my $gene = $gid->next_prediction)
	 {
	   my @transcripts = $gene->transcripts;
	     foreach my $t (@transcripts)
	     {
	       my @exons = $t->exons;
	       foreach my $e (@exons)
	       {
		 printf("Exon %d..%d
", $e->start, $e->end);
	       }
	     }
	 }

DESCRIPTION

       This is the parser for the output of geneid by Enrique Blanco and Roderic Guigo (IMIM-UPF). See http://www1.imim.es/software/geneid. It
       relies on native geneid output format internally and will work with geneid versions 1.0 and 1.1. Currently this module supports only the
       default mode of operation which is to predict exons and assemble an optimal gene prediction.

       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 - Keith James
	Email: kdj@sanger.ac.uk

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 = "<geneid.out");
		  $obj->new(-fh => *GI);
	Function: Constructor for geneid wrapper. Takes either a file
		: or filehandle
	Returns : L<Bio::Tools::Geneid>

   next_prediction
	Title	: next_prediction
	Usage	: while($gene = $geneid->next_prediction)
		  {
		      # do something
		  }
	Function: Returns the gene structure prediction of the geneid result
		  file. Call this method repeatedly until FALSE is returned.
	Returns : A Bio::SeqFeature::Gene::GeneStructure object
	Args	: None

   _add_exon
	Title	: _add_exon
	Usage	: $obj->_add_exon($gene, $transcript, ... exon data ...)
	Function: Adds a new exon to both gene and transcript from the data
		: supplied as args
	Example :
	Returns : Nothing

   _set_strand
	Title	: _set_strand
	Usage	: $obj->_set_strand($gene)
	Function: Sets the overall gene strand to the same strand as all
		: the exons if they are all on the same strand, or to strand 0
		: if the exons are on different strands.
	Example :
	Returns : Nothing

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

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