sg2vg

Prototype code for converting Global Alliance (Side Graph) Server graph to VG.

(c) 2015 Glenn Hickey. See LICENSE for details.

See also:

• vg2sg: Convert VG to Side Graph SQL
• hal2sg: Convert HAL (output by Cactus and CAMEL) to Side Graph SQL

Algorithm

Download entire graph from server into memory. Cut sequences so that all joins are incident to the first or last side of a sequence. Print resulting graph in VG JSON format to stdout.

Instructions

Dependency: libcurl needs to be installed.

Cloning: Don't forget to clone submodules:

 git clone https://github.com/glennhickey/sg2vg.git --recursive

Note Start by verifying that the unit tests all pass:

  make test

To run the converter:

  sg2vg graph-url -u | vg view -J -v - > graph.vg

graph-url URL of graph server with version attached at end

graph.vg Output VG graph. VG must be installed for vg view to work...

Options

-h, --help
-p, --pageSize     Number of records per POST request (default=1000).
-u, --upper        Write all sequences in upper case. (RECOMMENDED)
-a, --paths        Add a VG path for each input sequence.
-n, --no-paths     Don't write any paths.