Bio::SeqIO::game -- a class for parsing and writing game-XML
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;
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.
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
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.
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://github.com/bioperl/bioperl-live/issues
Email mckays@cshl.edu
The rest of the documentation details each of the object methods. Internal
methods are usually preceded with a _
Title : next_seq
Usage : my $seq = $seqio->next_seq;
Function: get the main sequence object
Returns : a Bio::Seq::RichSeq object
Args : none
Title : write_seq
Usage : $seqio->write_seq($seq)
Function: writes a sequence object as game XML
Returns : nothing
Args : a Bio::SeqI compliant object
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
Title : _hide_dna
Usage : $seqio->_hide_dna
Function: Hide the DNA for really huge sequences
Returns : nothing
Args : none