Christopher Fields > BioPerl-1.6.923 > Bio::SeqIO::game



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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' ( 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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AUTHOR - Sheldon McKay ^



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
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