def attempt_bc_correction(curr_bc,
all_bcs,
barcode_type = "golay_12"):
""" Gets corrected barcode and number of errors
curr_bc: current barcode sequence to attempt correction with
all_bcs: List of all barcode sequences.
barcode_type: Specified barcode, can be golay_12, hamming_8,
variable_length, or an integer specifying length.
"""
# First check for exact matches
corrected_bc = get_exact_bc_matches(curr_bc, all_bcs)
if corrected_bc:
return corrected_bc, 0
if barcode_type == "golay_12":
corrected_bc, num_errors = decode_golay_12(curr_bc)
elif barcode_type == "hamming_8":
corrected_bc, num_errors = decode_barcode_8(curr_bc)
elif barcode_type == 0:
corrected_bc, num_errors = ('', 0)
else:
corrected_bc, num_errors = correct_barcode(curr_bc, all_bcs)
return corrected_bc, num_errors
def attempt_bc_correction(curr_bc,
all_bcs,
barcode_type = "golay_12"):
""" Gets corrected barcode and number of errors
curr_bc: current barcode sequence to attempt correction with
all_bcs: List of all barcode sequences.
barcode_type: Specified barcode, can be golay_12, hamming_8,
variable_length, or an integer specifying length.
"""
# First check for exact matches
corrected_bc = get_exact_bc_matches(curr_bc, all_bcs)
if corrected_bc:
return corrected_bc, 0
if barcode_type == "golay_12":
corrected_bc, num_errors = decode_golay_12(curr_bc)
elif barcode_type == "hamming_8":
corrected_bc, num_errors = decode_barcode_8(curr_bc)
elif barcode_type == 0:
corrected_bc, num_errors = ('', 0)
else:
corrected_bc, num_errors = correct_barcode(curr_bc, all_bcs)
return corrected_bc, num_errors
def test_correct_barcode(self):
""" correct_barcode should correctly assign barcode to 2nd possibility,
2 errors
"""
original = "ATTTTTTTTTCG"
recieved = "ATTTTTTTTTTT"
possibilities = ["TGTATTCGTGTA", "ATTTTTTTTTCG", "TGTAGGCGTGTA", "TGTAGAAGTGTA", "TGTAGGCGTATA", "TGTAAAAAAAAA"]
decoded, num_errors = barcode.correct_barcode(recieved, possibilities)
self.assertEqual(decoded, original)
self.assertEqual(num_errors, 2)
def test_correct_barcode(self):
""" correct_barcode should correctly assign barcode to 2nd possibility,
2 errors
"""
original = 'ATTTTTTTTTCG'
recieved = 'ATTTTTTTTTTT'
possibilities = ['TGTATTCGTGTA','ATTTTTTTTTCG','TGTAGGCGTGTA',
'TGTAGAAGTGTA','TGTAGGCGTATA','TGTAAAAAAAAA']
decoded, num_errors = barcode.correct_barcode(recieved, possibilities)
self.assertEqual(decoded, original)
self.assertEqual(num_errors, 2)
def test_correct_barcode(self):
""" correct_barcode should correctly assign barcode to 2nd possibility,
2 errors
"""
original = 'ATTTTTTTTTCG'
recieved = 'ATTTTTTTTTTT'
possibilities = ['TGTATTCGTGTA', 'ATTTTTTTTTCG', 'TGTAGGCGTGTA',
'TGTAGAAGTGTA', 'TGTAGGCGTATA', 'TGTAAAAAAAAA']
decoded, num_errors = barcode.correct_barcode(recieved, possibilities)
self.assertEqual(decoded, original)
self.assertEqual(num_errors, 2)