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)