def test_func_write_FASTA(self):
test_array = convert_to_obj_array(
["> alirocumab", "AAAAAAKKKKK", "> secondone", "TTTTTTTT"])
if not os.path.exists((get_test_dir() + "/outputs")):
os.mkdir(get_test_dir() + "/outputs")
write_fasta(get_test_dir() + "/outputs/test-write.txt", test_array)
output_file = get_test_dir() + "/outputs/tidied-test-write.txt"
try:
path_exists = os.path.exists(output_file)
self.assertEqual(1, path_exists)
finally:
os.remove(output_file)
def test_class_method_ProcessFASTA_get_fasta_gold_standard(self):
test_processfasta = ProcessFasta(
get_test_dir() + "/inputs/test_gold_standard.txt", False, False)
test_processfasta.get_fasta()
valid_array = test_processfasta.validate_fasta()
self.assertEqual("> alirocumab", valid_array[0].id)
self.assertEqual("MVKVYAPASSANMSVGFDVLGAAVTPVDGALLGDVVTVEAAETF",
valid_array[0].sequence)
def test_func_read_fasta_excess_whitespace_multi(self):
input_array = read_fasta(get_test_dir() +
"/inputs/test_excess_whitespace_multi.txt")
test_array = remove_whitespace(input_array)
ref_array = [
"> alirocumab1", "MVKVYAPASSANMSVGFDVLGAA", "> alirocumab2",
"MVKVYAPASSANMSVGFDVLGAA", "> alirocumab3",
"MVKVYAPASSANMSVGFDVLGAA"
]
self.assertEqual(ref_array, test_array)
def test_class_method_ProcessFASTA_get_fasta_excess_whitespace_multi(self):
test_processfasta = ProcessFasta(
get_test_dir() + "/inputs/test_excess_whitespace_multi.txt", False,
False)
test_processfasta.get_fasta()
valid_array = test_processfasta.validate_fasta()
self.assertEqual("> alirocumab1", valid_array[0].id)
self.assertEqual("MVKVYAPASSANMSVGFDVLGAA", valid_array[0].sequence)
self.assertEqual("> alirocumab2", valid_array[1].id)
self.assertEqual("MVKVYAPASSANMSVGFDVLGAA", valid_array[1].sequence)
self.assertEqual("> alirocumab3", valid_array[2].id)
self.assertEqual("MVKVYAPASSANMSVGFDVLGAA", valid_array[2].sequence)
def test_func_read_fasta(self):
test_array = read_fasta(get_test_dir() + "/inputs/test_gold_short.txt")
ref_array = ["> alirocumab", "MVKVYAPASSANMSVGFDVL", "GAAVTPVDG"]
self.assertEqual(ref_array, test_array)
def test_class_method_ProcessFASTA_get_fasta_ID_only_single(self):
fasta_array = read_fasta(get_test_dir() +
"/inputs/test_ID_only_single.txt")
with self.assertRaisesRegex(Exception, "Unpaired ID and sequence"):
convert_to_obj_array(fasta_array)
def test_func_read_fasta_empty(self):
with self.assertRaisesRegex(Exception, "No data in file"):
read_fasta(get_test_dir() + "/inputs/test_empty.txt")