Bio::Graph::IO::psi_xml - access and manipulate PSI XML graphs
Do not use this module directly, use Bio::Graph::IO, for example:
my $graph_io = Bio::Graph::IO->new(-format => 'psi_xml', -file => 'data.xml');
PSI XML is a format to describe protein-protein interactions and interaction networks. The following databases support PSI XML:
http://www.bind.ca
http://dip.doe-mbi.ucla.edu/
http://www.hprd.org
http://www.ebi.ac.uk/intact
http://cbm.bio.uniroma2.it/mint/
Notes on PSI XML from various databases can be found in the Bioperl Wiki at http://bioperl.org/wiki/Module:Bio::Graph::IO::psi_xml
Documentation for PSI XML can be found at http://psidev.sourceforge.net.
The naming system is analagous to the SeqIO system, although usually next_network() will be called only once per file.
name : next_network purpose : to construct a protein interaction graph from xml data usage : my $gr = $io->next_network(); arguments : void returns : A Bio::Graph::ProteinGraph object
name : _proteinInteractor purpose : parses protein information into Bio::Seq::RichSeq objects returns : void usage : internally called by next_network(), arguments : none.
name : _addEdge purpose : adds a new edge to a graph usage : do not call, called by next_network returns : void
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.