Bio::Graph::IO(3pm)

Bio::Graph::IO - Class for reading /writing biological graph data.

  # This is a class for reading /writing biological data that can
  # be represented by graphs e.g., protein interaction data.

  # e.g., a graph reformatter..
  my $graph_in = Bio::Graph::IO->new(-file =>'myfile.dat',
                                     -format=>'dip' );
  my $graph = $graph_in->next_graph();
  my $graph_out = Bio::Graph::IO->new(-file =>'outfile.dat',
                                      -format=>'psixml') ;
  $graph_out->write_graph($graph);

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::Graph::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:
$graph = $io->next_graph() The next_graph method does not imply that multiple graphs are contained in a file, more to maintain the consistency of nomenclature with the $seqio->next_seq() and $alnio->next_aln() methods.
$io->write_graph($graph) (not implemented yet). Writes the graph data to file in requested format. To read or write from XML you will need the XML::Twig module available from CPAN.
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new

 Name       : new
 Usage      : $io = Bio::Graph::IO->new(-file => 'myfile.dat', 
                                        -format => 'dip');
 Returns    : A Bio::Graph::IO stream initialised to the appropriate format.
 Args       : Named parameters: 
              -file      => $filename
              -format    => format
              -threshold => a confidence score for the interaction, optional

next_graph

 Name       : next_graph
 Usage      : $gr = $io->next_graph().
 Returns    : A Bio::Graph::ProteinGraph object.
 Args       : None

write_graph

 Name       : write_graph
 Usage      : $gr = $io->write_graph($graph).
 Args       : A Bio::Graph object.
 Returns    : None

_load_format_module

 Title   : _load_format_module
 Usage   : *INTERNAL BioGraphIO stuff*
 Function: Loads up (like use) a module at run time on demand
 Returns :
 Args    :