Summary

Bio::Graph::IO - Class for reading /writing biological graph data.

Package variables

Inherit

Bio::Root::IO

Synopsis

  # This is a class for reading /writing biological data that can
  # be represented by graphs e.g., protein interaction data.

  # e.g., a graph reformatter..
  my $graph_in = Bio::Graph::IO->new(-file =>'myfile.dat',
                                     -format=>'dip' );
  my $graph = $graph_in->next_graph();
  my $graph_out = Bio::Graph::IO->new(-file =>'outfile.dat',
                                      -format=>'psixml') ;
  $graph_out->write_graph($graph);

Description

This class is analagous to the SeqIO and AlignIO classes. To read in a
file of a particular format, file and format are given as key/value
pairs as arguments. The Bio::Graph::IO checks that the appropriate
module is available and loads it.
At present only the DIP tab delimited format and PSI XML format are supported

Methods

Methods description

 Name       : new
 Usage      : $io = Bio::Graph::IO->new(-file => 'myfile.dat', 
                                        -format => 'dip');
 Returns    : A Bio::Graph::IO stream initialised to the appropriate format.
 Args       : Named parameters: 
              -file      => $filename
              -format    => format
	      -threshold => a confidence score for the interaction, optional

 Name       : next_graph
 Usage      : $gr = $io->next_graph().
 Returns    : A Bio::Graph::ProteinGraph object.
 Args       : None

 Name       : write_graph
 Usage      : $gr = $io->write_graph($graph).
 Args       : A Bio::Graph object.
 Returns    : None

 Title   : _load_format_module
 Usage   : *INTERNAL BioGraphIO stuff*
 Function: Loads up (like use) a module at run time on demand
 Returns :
 Args    :

Methods code

sub new {

	my ($caller, @args) = @_;
	my $class           = ref($caller) || $caller;
	if ($class =~ /Bio::Graph::IO::(\S+)/){
		my $self = $class->SUPER::new(@args);
		$self->_initialize_io(@args);
		return $self;
	} else {
		my %param = @args;
		@param{ map { lc $_ } keys %param } = values %param;
		if (!exists($param{'-format'})) {
			Bio::Root::Root->throw("Must specify a valid format!");
		} 
		my $format = $param{'-format'};
		$format    = "\L$format";	
		return unless ($class->_load_format_module($format)); 
		return "Bio::Graph::IO::$format"->new(@args);
	}

}

sub next_graph {

   my ($self, $gr) = @_;
   $self->throw("Sorry, you cannot read from a generic Bio::Graph::IO object.");

}

sub write_graph {

   my ($self, $gr) = @_;
   $self->throw("Sorry, you can't write from a generic Bio::GraphIO object.");

}

sub _load_format_module {

my ($self, $format) = @_;
    my $module = "Bio::Graph::IO::" . $format;
    my $ok;

    eval {
	$ok = $self->_load_module($module);
    };
    if ( $@ ) {
    print STDERR <<END
$self: $format cannot be found
Exception $@
For more information about the Bio::Graph::IO system please see the Bio:Graph::IO docs.
END
  ;
  }
  return $ok;

}

sub _initialize_io {

	my ($self, @args) = @_;
	$self->SUPER::_initialize_io(@args);
	my ($th) = $self->_rearrange( [qw(THRESHOLD)], @args);
	$self->{'_th'} = $th;
	return $self;

}

General documentation

The next_graph method does not imply that multiple graphs are
contained in a file, more to maintain the consistency of nomenclature
with the $seqio->next_seq() and $alnio->next_aln() methods.

Writes the graph data to file in requested format.

To read or write from XML you will need the XML::Twig module available
from CPAN.

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

Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the
web:

  http://bugzilla.open-bio.org/

Email richard.adams@ed.ac.uk