Bio::Das::ProServer::SourceAdaptor::Transport::sif

NAME

Bio::Das::ProServer::SourceAdaptor::Transport::sif

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VERSION

$LastChangedRevision: 688 $

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SYNOPSIS

my $hInteractions = $oTransport->query('interactorA'); my $hInteractions = $oTransport->query('interactorA', 'interactorB');

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DESCRIPTION

A data transport exposing interactions stored in a SIF file, along with attributes stored in Cytoscape attribute files. Access is via the 'query' method.

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FILE FORMAT

Each line of a Simple Interaction Format (SIF) file describes one or more binary interactions, and takes the form: nodeA lineType nodeB [nodeC ...]

This example describes a protein-protein interaction between interactorA and interactorB: interactorA pp interactorB

This example describes three separate interactions, each involving interactorA: interactorA pp interactorB interactorC interactor D

Node attribute files may be used to add DAS 'detail' elements to interactors: description interactorA = An example interactor interactorB = Another example of an interactor ...

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

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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

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SUBROUTINES/METHODS

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.

DESTROY : object destructor - disconnect filehandles

  Generally not directly invoked, but if you really want to:
  $transport->DESTROY();

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DIAGNOSTICS

Run ProServer with the -debug flag.

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SEE ALSO

Cytoscape - SIF
Cytoscape - Attributes

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DEPENDENCIES

Carp
Bio::Das::ProServer::SourceAdaptor::Transport::file

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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).

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INCOMPATIBILITIES

None reported.

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AUTHOR

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

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LICENSE AND COPYRIGHT

Copyright (c) 2008 EMBL-EBI

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 Bio::Das::ProServer::SourceAdaptor::Transport::sif