Bio::Network::IO::dip_tab - class for parsing interaction data in DIP tab-delimited format
Do not use this module directly, use Bio::Network::IO. For example:
my $io = Bio::Network::IO->new(-format => 'dip_tab', -file => 'data.dip'); my $network = $io->next_network;
The Database of Interacting Proteins (DIP) is a protein interaction database (see http://dip.doe-mbi.ucla.edu/dip/Main.cgi). The species-specific subsets of the DIP database are provided in a simple, tab-delimited format. The tab-separated columns are:
edge DIP id node A DIP id node A optional id node A SwissProt id node A PIR id node A GenBank GI id node B DIP id node B optional id node B SwissProt id node B PIR id node B GenBank GI id
The source or namespace of the optional id in columns 3 and 8 varies from species to species, and optional ids are frequently absent.
The first version of this format prepended the identifier with a database name, e.g.:
DIP:4305E DIP:3048N PIR:B64526 SWP:P23487 GI:2313123 ...
The version as of 1/2006 has no database identifiers:
DIP:4305E DIP:3048N B64526 P23487 2313123 ...
This module parses both versions.
The naming system is analagous to the SeqIO system, although usually next_network() will be called only once per file.
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
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.
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/
Brian Osborne bosborne at alum.mit.edu Richard Adams richard.adams@ed.ac.uk
Name : next_network Purpose : parses a DIP file and returns a Bio::Network::ProteinNet object Usage : my $g = $graph_io->next_network(); Arguments : none Returns : a Bio::Network::ProteinNet object
Name : write_network Purpose : write graph out in dip format Arguments: a Bio::Network::ProteinNet object Returns : void Usage : $out->write_network($gr);
Name : _add_db_links Purpose : create DBLink annotations, add to an Annotation Collection object Arguments: an array of ids Returns : an Annotation::Collection object Usage :
Name : _fix_id Purpose : Arguments: Returns : Usage :
To install Bio::Network::IO, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Network::IO
CPAN shell
perl -MCPAN -e shell install Bio::Network::IO
For more information on module installation, please visit the detailed CPAN module installation guide.