Summary

Bio::SeqIO::game -- a class for parsing and writing game-XML

Package variables

Included modules

Inherit

Bio::SeqIO

Synopsis

 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.
This modules is not used directly

Methods

Methods description

 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

Methods code

sub _initialize {

    my ($self, @args) = @_;
    $self->SUPER::_initialize(@args);

}

sub next_seq {

    my $self   = shift;
    
    my $seq_l  = $self->_getseqs;
    my $annseq = shift @{$seq_l};
    my $seq    = $annseq->[0];
    my $feats  = $annseq->[1];
    
    for ( @{$feats} ) {
	$seq->add_SeqFeature( $_ );
    }

    return $seq;

}

sub write_seq {

    my ($self, $seq) = @_;
    my $writer = Bio::SeqIO::game::gameWriter->new($seq);
    my $xml = $writer->write_to_game;
    $self->_print($xml);

}

sub _getseqs {

    my $self = shift;
    if ( defined $self->{seq_l} ) {
        return $self->{seq_l};
    }
    else {
	my $fh = $self->_fh;
	my $text = join '', <$fh>;
	$text || $self->throw("Input file is empty or does not exist");
	my $source = $text =~ /type>(source|origin|\bregion\b)<\/type/gm ? 1 : 0;
        my $handler = Bio::SeqIO::game::gameHandler->new;
	$handler->{has_source} = $source if $source;
	$handler->{verbose} = 1 if $self->verbose;
        my $parser  = XML::Parser::PerlSAX->new( Handler => $handler );
        my $game    = $parser->parse( $text );
	$self->{seq_l} = $game->load;
    }

}

sub _hide_dna {

    my $self = shift;
    
    my $annseqs = $self->_getseqs;

    for ( @{$annseqs} ) {
        my $seq = $_->[0];
        $seq->seq('');
    }
    return 0;

}

General documentation

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/MailList.shtml      - About the mailing lists

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 email or the web:

  bioperl-bugs@bioperl.org
  http://bugzilla.bioperl.org/

Email smckay@bcgsc.bc.ca

The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _