def test_results(self):
r = Results(os.path.join(data_dir, 'yersinia'), False)
valid_patterns = [str(p) for p in r.filter(7)]
self.assertEqual(valid_patterns, [
"1'\t7'\t6'\t5'\t3\t4\t2'", "1'\t2\t3\t4\t5\t6\t7",
"1'\t7'\t3\t4\t5\t6\t2'", "1\t7'\t3\t4\t5\t6\t2'"
])
def __init__(self, options):
self.socru_output_filename = options.socru_output_filename
self.profile_filename = options.profile_filename
self.output_file = options.output_file
shutil.copy(self.profile_filename, self.output_file)
self.profiles = Profiles(self.profile_filename)
self.results = Results(self.socru_output_filename)
class SocruUpdateProfile:
def __init__(self, options):
self.socru_output_filename = options.socru_output_filename
self.profile_filename = options.profile_filename
self.output_file = options.output_file
self.verbose = options.verbose
shutil.copy(self.profile_filename, self.output_file)
self.profiles = Profiles(self.profile_filename, self.verbose)
self.results = Results(self.socru_output_filename, self.verbose)
def run(self):
valid_profiles_not_db_checked = self.results.filter(
self.profiles.num_fragments)
valid_profiles = []
for input_profile in valid_profiles_not_db_checked:
match_found = False
for db_profile in self.profiles.gats:
if db_profile.does_the_profile_match(input_profile):
match_found = True
continue
if not match_found:
valid_profiles.append(input_profile)
with open(self.output_file, "a+") as output_fh:
for p in valid_profiles:
tg = TypeGenerator(self.profiles,
p,
self.verbose,
True,
prefix='')
# get orientationless versions of p and db
# check if there is an order number assigned, if not generate the next one.
order_to_use = tg.calculate_orientationless_order()
if order_to_use == 0:
order_to_use = self.profiles.next_order_number()
p.gat_number = str(order_to_use) + '.' + str(
p.orientation_binary())
self.profiles.gats.append(p)
novel_type = p.gat_number + "\t" + str(p)
output_fh.write(novel_type + "\n")