def test_consume_seq() :
db = d.deBruijnGraph( 4 )
db.consume_seq( 'atatat' )
assert db.graph.has_key( 'atat' )
# this graph should be a ring
assert db.graph[ 'atat' ]['down'].has_key( 'tata' )
assert db.graph[ 'tata' ]['up'].has_key( 'atat' )
assert db.graph[ 'tata' ]['down'].has_key( 'atat' )
def test_create_graph_object() :
db = d.deBruijnGraph( 4 )
def test_add_edge() :
db = d.deBruijnGraph( 4 )
db.add_edge( 'atat', 'tata', 1, 1, )
assert db.graph.has_key( 'atat' )
assert db.graph[ 'atat' ]['down'].has_key( 'tata' )
#!/usr/bin/env python
import debruijnator
import xmlrpclib
import os, sys
os.system( 'ubigraph_server &' )
os.system( 'sleep 1' )
# Create a server object.
server_url = 'http://127.0.0.1:20738/RPC2'
server = xmlrpclib.Server(server_url)
G = server.ubigraph
db = debruijnator.deBruijnGraph( 32 )
db.consume_fasta( sys.argv[1] )
for key in db.graph.keys() :
G.new_vertex_w_id( db.graph.keys().index( key ) )
# G.set_vertex_attribute( db.graph.keys().index(key), 'label', key )
for key1 in db.graph.keys() :
for key2 in map( db.graph.keys().index, db.graph[key1]['down'].keys() ) :
G.new_edge( db.graph.keys().index(key1), key2 )
