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

BioPerl documentation Contained in the BioPerl distribution.

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NAME

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

SYNOPSIS

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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;

DESCRIPTION

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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.

FEEDBACK

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Mailing Lists

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

Support

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.

Reporting Bugs

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://redmine.open-bio.org/projects/bioperl/

AUTHOR - Sheldon McKay

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Email mckays@cshl.edu

APPENDIX

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

next_seq

 Title   : next_seq
 Usage   : my $seq = $seqio->next_seq;
 Function: get the main sequence object
 Returns : a Bio::Seq::RichSeq object
 Args    : none

write_seq

 Title   : write_seq
 Usage   : $seqio->write_seq($seq)
 Function: writes a sequence object as game XML
 Returns : nothing
 Args    : a Bio::SeqI compliant object

_getseqs

 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

_hide_dna

 Title   : _hide_dna
 Usage   : $seqio->_hide_dna
 Function: Hide the DNA for really huge sequences
 Returns : nothing 
 Args    : none
BioPerl documentation Contained in the BioPerl distribution. 
#
# BioPerl module for Bio::SeqIO::game
#
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
#
# Cared for by Sheldon McKay <mckays@cshl.edu>
#
# You may distribute this module under the same terms as perl itself
#

# POD documentation - main docs before the code


package Bio::SeqIO::game;

use Bio::SeqIO::game::gameHandler;
use Bio::SeqIO::game::gameWriter;

use base qw(Bio::SeqIO);

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;
}


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