Bio::Network::IO - Class for reading and writing biological network data.
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;
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.
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.
To read from PSI 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.
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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:
Brian Osborne bosborne at alum.mit.edu Richard Adams firstname.lastname@example.org
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
Name : next_network Usage : $gr = $io->next_network Returns : A Bio::Network::ProteinNet object. Args : None
Name : write_network Usage : $gr = $io->write_network($net). Args : A Bio::Network::ProteinNet object. Returns : None
Name : get or set a threshold Usage : $io->threshold($val) Returns : The threshold Args : A number or none
Name : get or set verbosity Usage : $io->verbose(1) Returns : The verbosity setting Args : 1 or none
Title : _load_format_module Usage : INTERNAL Bio::Network::IO stuff Function: Loads up (like use) a module at run time on demand Returns : Args :
Title : _initialize_io Usage : *INTERNAL Bio::Network::IO stuff* Function: Returns : Args :
Title : _get_standard_name Usage : Function: Returns some standard name for a database, uses global %DBNAMES Returns : Args :