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 )