Bio::Network IO
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Summary
Bio::Network::IO - Class for reading and writing biological network data.
Package variables
No package variables defined.
Inherit
Bio::Root::IO
Synopsis
This is a modules for reading and writing protein-protein interaction
and creating networks from this data.
  # Read protein interaction data in some format
my $io = Bio::Network::IO->new(-file => 'bovine.xml',
-format => 'psi25' );
my $network = $io->next_network;
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::Network::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
newDescriptionCode
next_networkDescriptionCode
write_networkDescriptionCode
thresholdDescriptionCode
verboseDescriptionCode
_load_format_moduleDescriptionCode
_initialize_ioDescriptionCode
_get_standard_nameDescriptionCode
Methods description
newcode    nextTop
 Name       : new
Usage : $io = Bio::Network::IO->new(-file => 'myfile.xml',
-format => 'psi25');
Returns : A Bio::Network::IO stream initialised to the appropriate format.
Args : Named parameters:
-file => $filename
-format => format
-threshold => a confidence score for the interaction, optional
-source => optional database name (e.g. "intact")
-verbose => optional, set to 1 to get commentary
next_networkcodeprevnextTop
 Name       : next_network
Usage : $gr = $io->next_network
Returns : A Bio::Network::ProteinNet object.
Args : None
write_networkcodeprevnextTop
 Name       : write_network
Usage : $gr = $io->write_network($net).
Args : A Bio::Network::ProteinNet object.
Returns : None
thresholdcodeprevnextTop
 Name       : get or set a threshold
Usage : $io->threshold($val)
Returns : The threshold
Args : A number or none
verbosecodeprevnextTop
 Name       : get or set verbosity
Usage : $io->verbose(1)
Returns : The verbosity setting
Args : 1 or none
_load_format_modulecodeprevnextTop
 Title   : _load_format_module
Usage : INTERNAL Bio::Network::IO stuff
Function: Loads up (like use) a module at run time on demand
Returns :
Args :
_initialize_iocodeprevnextTop
 Title   : _initialize_io
Usage : *INTERNAL Bio::Network::IO stuff*
Function:
Returns :
Args :
_get_standard_namecodeprevnextTop
 Title   : _get_standard_name
Usage :
Function: Returns some standard name for a database, uses global
%DBNAMES
Returns :
Args :
Methods code
newdescriptionprevnextTop
sub new {
	my ($caller, @args) = @_;
	my $class = ref($caller) || $caller;
	if ($class =~ /Bio::Network::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 undef unless ($class->_load_format_module($format)); 
		return "Bio::Network::IO::$format"->new(@args);
	}
}
next_networkdescriptionprevnextTop
sub next_network {
   my ($self, $gr) = @_;
   $self->throw("Sorry, you cannot read from a generic Bio::Network::IO object.");
}
write_networkdescriptionprevnextTop
sub write_network {
   my ($self, $gr) = @_;
   $self->throw("Sorry, you can't write from a generic Bio::NetworkIO object.");
}
thresholddescriptionprevnextTop
sub threshold {
   my $self = shift;
   $self->{_th} = @_ if @_;
   return $self->{_th};
}
verbosedescriptionprevnextTop
sub verbose {
   my $self = shift;
   $self->{_verbose} = @_ if @_;
   return $self->{_verbose};
}
_load_format_moduledescriptionprevnextTop
sub _load_format_module {
	my ($self, $format) = @_;
	my $module = "Bio::Network::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::Network::IO system please see the Bio:Network::IO docs. END ; } return $ok;
}
_initialize_iodescriptionprevnextTop
sub _initialize_io {
	my ($self, @args) = @_;
	$self->SUPER::_initialize_io(@args);
	my ($th,$verbose) = $self->_rearrange( [qw(THRESHOLD VERBOSE)], @args);
	$self->{'_th'} = $th;
	$self->{'_verbose'} = $verbose;
	return $self;
}
_get_standard_namedescriptionprevnextTop
sub _get_standard_name {
	my ($self,$name) = @_;
	$DBNAMES{$name};
}

1;

__END__
}
General documentation
$net = $io->next_networkTop
The next_network method does not imply that multiple networks are
contained in a file, this is to maintain a consistent nomenclature
with Bioperl methods like $seqio->next_seq and $alnio->next_aln.
$io->write_network($network)Top
UNIMPLEMENTED.
REQUIREMENTSTop
To read from PSI XML you will need the XML::Twig module,
available from CPAN.
FEEDBACKTop
Mailing ListsTop
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 Top
 
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 BugsTop
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/
AUTHORSTop
Brian Osborne bosborne at alum.mit.edu
Richard Adams richard.adams@ed.ac.uk