from PianaGraph import *
from PianaDBaccess import *
from PianaGraphBuilder import *
import cPickle

piana_access = PianaDBaccess(dbname="pianaDB_simple_dummy", dbhost="bass")
cPickle.dump(piana_access, file("piana_access.pickle", "wb"), -1)
pickle_access = cPickle.load(file("piana_access.pickle", "rb"))
pickle_access.get_methodID("y2h")
pickle_access.get_protein_taxonomy_ids(proteinPiana_value= 2)


piana_graph = PianaGraph("1", piana_access)
piana_builder = PianaGraphBuilder(piana_access_object=piana_access, depth=1, list_protein_codes=[1], code_type_name="proteinPiana", species_name_value="all", list_source_dbs="all", list_source_methods="all")
piana_graph.build_graph(piana_builder)


cPickle.dump(piana_graph, file("piana_graph.pickle", "wb"), -1)
pickle_graph = cPickle.load(file("piana_graph.pickle", "rb"))

pickle_graph.output_interactions_table(protein_type_name="proteinPiana", output_target=sys.stdout, mode="all")



To visualize pickled graphs
---------------------------

execute python

import cPickle
g = cPickle.load(file("/home/raragues/phd/piana/code/execs/temp/gold_standard.patchgroup_graph", "rb"))
g.output_dot_file(output_target= file("gold_standard.dot", "w"))

herzl> cat gold_standard.dot | neato -Tgif -o gold_standard.gif

xview gold_standard.gif


or you can alternatively use piana.py option load-network and then print-network followed by the neato call
