view release on metacpan or  search on metacpan

lib/Bio/Das/ProServer/SourceAdaptor/Transport/sif.pm  view on Meta::CPAN

  ...

Edge attribute files may be used to add DAS 'detail' elements to interactions:
  score
  interactorA pp interactorB = 2.43
  interactorX pp interactorY = 5.1
  ...

=head1 CONFIGURATION AND ENVIRONMENT

Configured as part of each source's ProServer 2 INI file:

  [mysif]
  ... source configuration ...
  transport  = sif
  filename   = /data/interactions.sif
  attributes = /data/node-attribute.noa ; /data/edge-attributes.eda

=head1 SUBROUTINES/METHODS

=head2 query : Retrieves interactions for one or two interactors

  Retrieves interactions involving interactorA:
  $hInteractions = $oTransport->query('interactorA');
  
  Retrieves an interaction involving both interactorA and interactorB:
  $hInteractions = $oTransport->query('interactorA', 'interactorB');
  
  The returned hash is of the structure expected by ProServer.

=head2 DESTROY : object destructor - disconnect filehandles

  Generally not directly invoked, but if you really want to:

  $transport->DESTROY();

=head1 DIAGNOSTICS

Run ProServer with the -debug flag.

=head1 SEE ALSO

=over

=item L<Cytoscape - SIF|http://www.cytoscape.org/cgi-bin/moin.cgi/Cytoscape_User_Manual/Network_Formats>

=item L<Cytoscape - Attributes|http://www.cytoscape.org/cgi-bin/moin.cgi/Cytoscape_User_Manual/Attributes>

=back

=head1 DEPENDENCIES

=over

=item L<Carp|Carp>

=item L<Bio::Das::ProServer::SourceAdaptor::Transport::file|Bio::Das::ProServer::SourceAdaptor::Transport::file>

=back

=head1 BUGS AND LIMITATIONS

The Simple Interaction Format is very simple, and therefore only supports a
limited range of DAS annotation details. It also only handles binary
interactions (i.e. those with exactly two interactors).

=head1 INCOMPATIBILITIES

None reported.

=head1 AUTHOR

Andy Jenkinson <andy.jenkinson@ebi.ac.uk>

=head1 LICENSE AND COPYRIGHT

Copyright (c) 2008 EMBL-EBI

=cut