- AUTHOR - Sheldon McKay
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.
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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