debian man page for bio::seqio::game

Bio::SeqIO::game(3pm)					User Contributed Perl Documentation				     Bio::SeqIO::game(3pm)

NAME
       Bio::SeqIO::game -- a class for parsing and writing game-XML

SYNOPSIS
       This module is not used directly, use SeqIO.

	use Bio::SeqIO;

	my $in = Bio::SeqIO->new ( -file    => 'file.xml',
				   -format  =>	'game',
				   -verbose => 1 );

	my $seq = $in->next_seq;

DESCRIPTION
       Bio::SeqIO::game will parse game XML (version 1.2) or write game XML from a Bio::SeqI implementing object.  The XML is readable by the
       genome annotation editor 'Apollo' (www.gmod.org).  It is not backwards compatible with the previous version of game XML.  The XML format
       currently used by Apollo contains a single 'main' annotated sequence, so we will only get a single annotated sequence in the stream when
       parsing a game-XML record.

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 of the bugs and their resolution.

       Bug reports can be submitted via the web:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Sheldon McKay
       Email mckays@cshl.edu

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

   next_seq
	Title	: next_seq
	Usage	: my $seq = $seqio->next_seq;
	Function: get the main sequence object
	Returns : a Bio::Seq::RichSeq object
	Args	: none

   write_seq
	Title	: write_seq
	Usage	: $seqio->write_seq($seq)
	Function: writes a sequence object as game XML
	Returns : nothing
	Args	: a Bio::SeqI compliant object

   _getseqs
	Title	: _getseqs
	Usage	: $self->_getseqs
	Function: An internal method to invoke the PerlSAX XML handler and get
		  the sequence objects
	Returns : an reference to an array with sequence object and annotations
	Args	: none

   _hide_dna
	Title	: _hide_dna
	Usage	: $seqio->_hide_dna
	Function: Hide the DNA for really huge sequences
	Returns : nothing
	Args	: none

perl v5.14.2							    2012-03-02						     Bio::SeqIO::game(3pm)