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)
def test_type_generator_valid(self):
profiles = Profiles(os.path.join(data_dir, 'initial_profiles.txt'),
False)
p = GATProfile(False,
fragments=['1', '7\'', '6\'', '4\'', '5\'', '3', '2\''])
tg = TypeGenerator(profiles, p, False, prefix='GS')
self.assertEqual(2, tg.calculate_orientationless_order())
self.assertEqual('GS2.122', tg.calculate_type())
def test_type_generator_valid_seen(self):
profiles = Profiles(os.path.join(data_dir, 'initial_profiles.txt'),
False)
p = GATProfile(False, fragments=['1', '2', '3', '5', '4', '6', '7'])
tg = TypeGenerator(profiles, p, False, True, prefix='GS')
self.assertEqual(2, tg.calculate_orientationless_order())
self.assertEqual('GREEN', tg.quality)
self.assertEqual('GS2.0', tg.calculate_type())
def calc_type(self):
profile_db = Profiles(os.path.join(self.db_dir, 'profile.txt'))
split_fragments = self.fragments.split('-')
input_profile = GATProfile(fragments=split_fragments)
tg = TypeGenerator(profile_db, input_profile)
return tg.calculate_type()
def test_profiles(self):
p = Profiles(os.path.join(data_dir, 'profile.txt'), False)
self.assertEqual(7, len(p.gats))
self.assertEqual("1 2 3 4 5 6 7", str(p.gats[0]))
p.gats[0].fragments = p.gats[0].invert_fragments()
self.assertEqual("1' 7' 6' 5' 4' 3' 2'", str(p.gats[0]))
self.assertEqual(5, p.dnaA_fragment_number)
def run(self):
# load the profiles
p = Profiles(os.path.join(self.db_dir, 'profile.txt'))
d = Database(self.db_dir)
for i in self.input_files:
output_type = self.run_analysis(i, p, d)
self.output_results(i, output_type)
if self.top_blast_hits is not None:
with open(self.top_blast_hits, "a+") as output_fh:
for h in self.top_results:
output_fh.write(str(h)+"\n")
def type_generator(self):
profile_db = Profiles(os.path.join(self.db_dir, 'profile.txt'),
self.verbose)
split_fragments = self.fragments.split('-')
input_profile = GATProfile(
self.verbose,
fragments=split_fragments,
dnaA_fragment_number=profile_db.dnaA_fragment_number,
dif_fragment_number=profile_db.dif_fragment_number)
input_profile.orientate_for_dnaA()
is_profile_valid = self.validate_profile(profile_db, input_profile)
tg = TypeGenerator(profile_db, input_profile, self.verbose,
is_profile_valid)
return tg
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")
def run(self):
# load the profiles
if self.verbose:
print("Loading profiles:\t" + os.path.join(self.db_dir, 'profile.txt'))
p = Profiles(os.path.join(self.db_dir, 'profile.txt'), self.verbose)
if self.verbose:
print("Loading database:\t" + self.db_dir)
d = Database(self.db_dir, self.verbose)
for i in self.input_files:
if self.verbose:
print("Beginning analysis of input file:\t" + i)
output_type = self.run_analysis(i, p, d)
self.output_results(i, output_type)
if self.top_blast_hits is not None:
with open(self.top_blast_hits, "a+") as output_fh:
for h in self.top_results:
output_fh.write(str(h)+"\n")