NAME
Bio::Network::IO - Class for reading and writing biological network data.
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
The main methods are:
$net = $io->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->next_seq and $alnio->next_aln.
$io->write_network($network)
UNIMPLEMENTED.
REQUIREMENTS
To read from PSI XML you will need the XML::Twig module, available from CPAN.
FEEDBACK
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 the bugs and their resolution. Bug reports can be submitted via the web:
http://bugzilla.open-bio.org/
AUTHORS
Brian Osborne bosborne at alum.mit.edu Richard Adams richard.adams@ed.ac.uk
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
next_network
Name : next_network
Usage : $gr = $io->next_network
Returns : A Bio::Network::ProteinNet object.
Args : None
write_network
Name : write_network
Usage : $gr = $io->write_network($net).
Args : A Bio::Network::ProteinNet object.
Returns : None
threshold
Name : get or set a threshold
Usage : $io->threshold($val)
Returns : The threshold
Args : A number or none
verbose
Name : get or set verbosity
Usage : $io->verbose(1)
Returns : The verbosity setting
Args : 1 or none
_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 :
_initialize_io
Title : _initialize_io
Usage : *INTERNAL Bio::Network::IO stuff*
Function:
Returns :
Args :
_get_standard_name
Title : _get_standard_name
Usage :
Function: Returns some standard name for a database, uses global
%DBNAMES
Returns :
Args :