def test_reading_frame1(self):
seed = 'AAGCGGGGCATGCGAGTACA' # Amino seq: ?AGHAST (shifted one base)
coord = 'HAS'
expected_extract = 'CATGCGAGT' # Amino seq: HAS
extract = extract_target(seed, coord)
self.assertEqual(expected_extract, extract)
def test_extract(self):
seed = 'GCGGGGCATGCGAGTACA' # Amino seq: AGHAST
coord = 'HAS'
expected_extract = 'CATGCGAGT' # Amino seq: HAS
extract = extract_target(seed, coord)
self.assertEqual(expected_extract, extract)
def test_reading_frame1(self):
seed = 'AAGCGGGGCATGCGAGTACA' # Amino seq: ?AGHAST (shifted one base)
coord = 'HAS'
expected_extract = 'CATGCGAGT' # Amino seq: HAS
extract = extract_target(seed, coord)
self.assertEqual(expected_extract, extract)
def test_extract(self):
seed = 'GCGGGGCATGCGAGTACA' # Amino seq: AGHAST
coord = 'HAS'
expected_extract = 'CATGCGAGT' # Amino seq: HAS
extract = extract_target(seed, coord)
self.assertEqual(expected_extract, extract)
def extract_v3loop_ref():
ref_filename = os.path.join(os.path.dirname(__file__), 'v3loop_ref.txt')
try:
with open(ref_filename) as f:
v3loop_ref = f.read()
except FileNotFoundError:
project_config = ProjectConfig.loadDefault()
hiv_seed = project_config.getReference(G2P_SEED_NAME)
coordinate_ref = project_config.getReference(COORDINATE_REF_NAME)
v3loop_ref = extract_target(hiv_seed, coordinate_ref)
with open(ref_filename, 'w') as f:
f.write(v3loop_ref)
return v3loop_ref
def extract_v3loop_ref():
ref_filename = os.path.join(os.path.dirname(__file__), 'v3loop_ref.txt')
try:
with open(ref_filename) as f:
v3loop_ref = f.read()
except FileNotFoundError:
project_config = ProjectConfig.loadDefault()
hiv_seed = project_config.getReference(G2P_SEED_NAME)
coordinate_ref = project_config.getReference(COORDINATE_REF_NAME)
v3loop_ref = extract_target(hiv_seed, coordinate_ref)
with open(ref_filename, 'w') as f:
f.write(v3loop_ref)
return v3loop_ref