SYNOPSISThis module is not used directly, use SeqIO.
my $in = Bio::SeqIO->new ( -file => 'file.xml',
-format => 'game',
-verbose => 1 );
my $seq = $in->next_seq;
DESCRIPTIONBio::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.
Mailing ListsUser 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.
[email protected] - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
SupportPlease direct usage questions or support issues to the mailing list:
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 BugsReport 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:
AUTHOR - Sheldon McKayEmail [email protected]
APPENDIXThe 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