/ 
FAST-1.0
River stage zero No dependents
/ FAST::Bio::SeqIO::game

NAME

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

SYNOPSIS

This module is not used directly, use SeqIO.

use FAST::Bio::SeqIO;

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

my $seq = $in->next_seq;

DESCRIPTION

FAST::Bio::SeqIO::game will parse game XML (version 1.2) or write game XML from a FAST::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 FAST::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 FAST::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