| Revision 15555 (by maj, 2009/02/21 22:06:54) |
adding FEEDBACK:Support section to pod |
# $Id: IO.pm 15555 2009-02-21 22:06:54Z maj $
#
# BioPerl module for Bio::Network::IO
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Network::IO - Class for reading and writing biological network data.
=head1 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;
=head1 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.
=head1 METHODS
The main methods are:
=head2 $net = $io-E<gt>next_network
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-E<gt>next_seq and $alnio-E<gt>next_aln.
=head2 $io-E<gt>write_network($network)
UNIMPLEMENTED.
=head1 REQUIREMENTS
To read from PSI XML you will need the XML::Twig module,
available from CPAN.
=head1 FEEDBACK
=head2 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
=head2 Support
Please direct usage questions or support issues to the mailing list:
L<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.
=head2 Reporting Bugs
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/
=head1 AUTHORS
Brian Osborne bosborne at alum.mit.edu
Richard Adams richard.adams@ed.ac.uk
=cut
package Bio::Network::IO;
use strict;
use base 'Bio::Root::IO';
use vars qw(%DBNAMES);
# these values are used to standardize database names
%DBNAMES = (
DIP => "DIP", # found in DIP files
SWP => "UniProt", # found in DIP files
PIR => "PIR", # found in DIP files
GI => "GenBank" # found id DIP files
);
=head2 new
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 => $filename
-format => format
-threshold => a confidence score for the interaction, optional
-source => optional database name (e.g. "intact")
-verbose => optional, set to 1 to get commentary
=cut
sub new {
my ($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);
}
}
=head2 next_network
Name : next_network
Usage : $gr = $io->next_network
Returns : A Bio::Network::ProteinNet object.
Args : None
=cut
sub next_network {
my ($self, $gr) = @_;
$self->throw("Sorry, you cannot read from a generic Bio::Network::IO object.");
}
=head2 write_network
Name : write_network
Usage : $gr = $io->write_network($net).
Args : A Bio::Network::ProteinNet object.
Returns : None
=cut
sub write_network {
my ($self, $gr) = @_;
$self->throw("Sorry, you can't write from a generic Bio::NetworkIO object.");
}
=head2 threshold
Name : get or set a threshold
Usage : $io->threshold($val)
Returns : The threshold
Args : A number or none
=cut
sub threshold {
my $self = shift;
$self->{_th} = @_ if @_;
return $self->{_th};
}
=head2 verbose
Name : get or set verbosity
Usage : $io->verbose(1)
Returns : The verbosity setting
Args : 1 or none
=cut
sub verbose {
my $self = shift;
$self->{_verbose} = @_ if @_;
return $self->{_verbose};
}
=head2 _load_format_module
Title : _load_format_module
Usage : INTERNAL Bio::Network::IO stuff
Function: Loads up (like use) a module at run time on demand
Returns :
Args :
=cut
sub _load_format_module {
my ($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 $ok;
}
=head2 _initialize_io
Title : _initialize_io
Usage : *INTERNAL Bio::Network::IO stuff*
Function:
Returns :
Args :
=cut
sub _initialize_io {
my ($self, @args) = @_;
$self->SUPER::_initialize_io(@args);
my ($th,$verbose) = $self->_rearrange( [qw(THRESHOLD VERBOSE)], @args);
$self->{'_th'} = $th;
$self->{'_verbose'} = $verbose;
return $self;
}
=head2 _get_standard_name
Title : _get_standard_name
Usage :
Function: Returns some standard name for a database, uses global
%DBNAMES
Returns :
Args :
=cut
sub _get_standard_name {
my ($self,$name) = @_;
$DBNAMES{$name};
}
1;
__END__
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