def testRunSBiDer(directory_path, user_query, indirect=False):
# Access database
database_file = directory_path + "/SBiDer.db"
conn, cur = db.db_open(database_file)
# Dictionary of fragmented user inputs that satisfy user query
logic_dictionary = parser.parse_logic(cur, user_query)
# Dictionaries of: Operon <-> InputSpecies, Operon <-> OutputSpecies, and Operon <-> Repressor
input_dictionary, output_dictionary = db.make_ope_id_spe_id_dics(cur)
repressor_dictionary = db.make_ope_id_rep_spe_id_dic(cur)
#rint("** input dictionary")
#BiDer_helper.printplus(input_dictionary)
#rint("** output dictionary")
#BiDer_helper.printplus(output_dictionary)
#rint("** repressor dictionary")
#BiDer_helper.printplus(repressor_dictionary)
# Build operon path for each fragmented user input, which satisfies user query
all_operon_path = []
for input_species, output_species_list in logic_dictionary.items():
operon_path_per_start_species = [input_species]
for output_species in output_species_list:
operon_path_list = searcher.get_sbider_path(
input_dictionary, repressor_dictionary, output_dictionary,
list(input_species), output_species, indirect)
operon_path_per_start_species.extend(operon_path_list)
all_operon_path.append(operon_path_per_start_species)
return all_operon_path == [[('21', '22'), ['72-3'], ['82-1']]]
def test_searcher_indirect_2(self):
"""testing the following query ahl and laci = gfp for the indirect traverse"""
conn, cur = db.db_open("sbider.db")
user_query = "ahl and laci = gfp"
logic_dictionary = parse.parse_logic(cur, user_query)
input_dictionary, output_dictionary = db.make_ope_id_spe_id_dics(cur)
repressor_dictionary = db.make_ope_id_rep_spe_id_dic(cur)
self.operon_path_list = search.get_sbider_path(input_dictionary,
repressor_dictionary,
output_dictionary,
['13', '22'],
['11'],
True)
for operon_path in self.operon_path_list:
current_species = ['13', '22']
input_species_set = set(current_species)
output_species_set = set(current_species)
for operon in operon_path:
input_species = helper.uniquely_merge_list_of_lists(input_dictionary[operon])
output_species = helper.uniquely_merge_list_of_lists(output_dictionary[operon])
for species in input_species:
if species in output_species_set:
input_species_set.add(species)
for species in output_species:
output_species_set.add(species)
self.assertEquals(input_species_set.issubset(output_species_set), True)
db.db_close(conn,cur)
def test_searcher_indirect_2(self):
"""testing the following query ahl and laci = gfp for the indirect traverse"""
conn, cur = db.db_open("sbider.db")
user_query = "ahl and laci = gfp"
logic_dictionary = parse.parse_logic(cur, user_query)
input_dictionary, output_dictionary = db.make_ope_id_spe_id_dics(cur)
repressor_dictionary = db.make_ope_id_rep_spe_id_dic(cur)
self.operon_path_list = search.get_sbider_path(input_dictionary,
repressor_dictionary,
output_dictionary,
['13', '22'], ['11'],
True)
for operon_path in self.operon_path_list:
current_species = ['13', '22']
input_species_set = set(current_species)
output_species_set = set(current_species)
for operon in operon_path:
input_species = helper.uniquely_merge_list_of_lists(
input_dictionary[operon])
output_species = helper.uniquely_merge_list_of_lists(
output_dictionary[operon])
for species in input_species:
if species in output_species_set:
input_species_set.add(species)
for species in output_species:
output_species_set.add(species)
self.assertEquals(
input_species_set.issubset(output_species_set), True)
db.db_close(conn, cur)
def test_searcher_direct(self):
"""testing the following query lara and arac to gfp for the direct traverse"""
conn, cur = db.db_open("sbider.db")
user_query = "lara and arac = gfp"
logic_dictionary = parse.parse_logic(cur, user_query)
input_dictionary, output_dictionary = db.make_ope_id_spe_id_dics(cur)
repressor_dictionary = db.make_ope_id_rep_spe_id_dic(cur)
self.operon_path_list = search.get_sbider_path(input_dictionary,repressor_dictionary,\
output_dictionary, ['2', '38'], ['11'], False)
for operon_path in self.operon_path_list:
current_species = ['2', '38']
for operon in operon_path:
self.assertEquals(current_species in input_dictionary[operon], True)
current_species = output_dictionary[operon][0]
db.db_close(conn,cur)
def test_searcher_direct(self):
"""testing the following query lara and arac to gfp for the direct traverse"""
conn, cur = db.db_open("sbider.db")
user_query = "lara and arac = gfp"
logic_dictionary = parse.parse_logic(cur, user_query)
input_dictionary, output_dictionary = db.make_ope_id_spe_id_dics(cur)
repressor_dictionary = db.make_ope_id_rep_spe_id_dic(cur)
self.operon_path_list = search.get_sbider_path(input_dictionary,repressor_dictionary,\
output_dictionary, ['2', '38'], ['11'], False)
for operon_path in self.operon_path_list:
current_species = ['2', '38']
for operon in operon_path:
self.assertEquals(current_species in input_dictionary[operon],
True)
current_species = output_dictionary[operon][0]
db.db_close(conn, cur)
def build_sbider_network(directory_path, user_query, indirect=False):
print("** build_sbider_network")
# Access database
database_file = directory_path + "/SBiDer.db"
conn, cur = db.db_open(database_file)
# Dictionary of fragmented user inputs that satisfy user query
logic_dictionary = parser.parse_logic(cur, user_query)
# Dictionaries of: Operon <-> InputSpecies & Operon <-> OutputSpecies
input_dictionary, output_dictionary = db.make_ope_id_spe_id_dics(cur)
print("** input dictionary")
SBiDer_helper.printplus(input_dictionary)
print("** output dictionary")
SBiDer_helper.printplus(output_dictionary)
# Dictionary of: Operon <-> Repressor
repressor_dictionary = db.make_ope_id_rep_spe_id_dic(cur)
print("** repressor dictionary")
SBiDer_helper.printplus(repressor_dictionary)
# Build operon path for each fragmented user input, which satisfies user query
all_operon_path = []
for input_species, output_species_list in logic_dictionary.items():
operon_path_per_start_species = [input_species]
for output_species in output_species_list:
operon_path_list = searcher.get_sbider_path(input_dictionary,
repressor_dictionary,
output_dictionary,
list(input_species),
output_species,
indirect)
operon_path_per_start_species.extend(operon_path_list)
all_operon_path.append(operon_path_per_start_species)
# Create JSON file needed to display the found genetic circuit
path_json = grapher.create_subnetwork_json_string(cur, operon_path_per_start_species, database_file)
return path_json
def build_sbider_network(user_query, indirect=False):
database_file = \
"/cellar/users/hyeerna/Dropbox/Project/20140601_sbider/UCSD_IGEM/SBiDer/SBiDer_Database/sbider.db"
conn, cur = db.db_open(database_file)
logic_dictionary = parser.parse_logic(cur, user_query)
print "build_sbider_network: logic_dictionary", logic_dictionary
input_dictionary, output_dictionary = db.make_ope_id_spe_id_dicts(cur)
all_operon_path_list_per_start_species = []
file_name_idx = 1
for input_species, output_species_list in logic_dictionary.items():
operon_path_list_per_start_species = [input_species]
for output_species in output_species_list:
print "\t Path:", input_species, "--->", output_species, "="
operon_path_list = searcher.get_sbider_path(input_dictionary,
output_dictionary,
list(input_species),
output_species,
indirect)
operon_path_list_per_start_species.extend(operon_path_list)
for operon_path in operon_path_list:
print "\t\t build_sbider_network: operon_path =>", operon_path
all_operon_path_list_per_start_species.append(operon_path_list_per_start_species)
file_name = "test_json_file_%d.json" % file_name_idx
grapher.create_subnetwork_json(cur, operon_path_list_per_start_species, file_name)
file_name_idx += 1
def testRunSBiDer(directory_path, user_query, indirect=False):
# Access database
database_file = directory_path + "/SBiDer.db"
conn, cur = db.db_open(database_file)
# Dictionary of fragmented user inputs that satisfy user query
logic_dictionary = parser.parse_logic(cur, user_query)
# Dictionaries of: Operon <-> InputSpecies, Operon <-> OutputSpecies, and Operon <-> Repressor
input_dictionary, output_dictionary = db.make_ope_id_spe_id_dics(cur)
repressor_dictionary = db.make_ope_id_rep_spe_id_dic(cur)
#rint("** input dictionary")
#BiDer_helper.printplus(input_dictionary)
#rint("** output dictionary")
#BiDer_helper.printplus(output_dictionary)
#rint("** repressor dictionary")
#BiDer_helper.printplus(repressor_dictionary)
# Build operon path for each fragmented user input, which satisfies user query
all_operon_path = []
for input_species, output_species_list in logic_dictionary.items():
operon_path_per_start_species = [input_species]
for output_species in output_species_list:
operon_path_list = searcher.get_sbider_path(input_dictionary,
repressor_dictionary,
output_dictionary,
list(input_species),
output_species,
indirect)
operon_path_per_start_species.extend(operon_path_list)
all_operon_path.append(operon_path_per_start_species)
return all_operon_path == [[('21', '22'), ['72-3'], ['82-1']]]