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Bio::Tools::Geneid(3) User Contributed Perl DocumentationBio::Tools::Geneid(3)

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\n", $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://github.com/bioperl/bioperl-live/issues

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

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Keith James | APPENDIX

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