def test_golay_module1(self):
"""switching the last base, decode() should recover the original barcode
"""
sent = golay.encode([0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0])
rec = sent[:-1] + 'C' # possible error here
decoded, errors = golay.decode(rec)
self.assertEqual(decoded, sent)
self.assertLessThan(errors, 1.5)
rec = sent[:-1] + 'T' # possible error here
decoded, errors = golay.decode(rec)
self.assertEqual(decoded, sent)
self.assertLessThan(errors, 1.5)
def test_golay_module1(self):
"""switching the last base, decode() should recover the original barcode
"""
sent = golay.encode([0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0])
rec = sent[:-1] + 'C' # possible error here
decoded, errors = golay.decode(rec)
self.assertEqual(decoded, sent)
self.assertLessThan(errors, 1.5)
rec = sent[:-1] + 'T' # possible error here
decoded, errors = golay.decode(rec)
self.assertEqual(decoded, sent)
self.assertLessThan(errors, 1.5)
def test_decode(self):
""" decode should decode barcodes from tutorial"""
barcodes = ['AGCACGAGCCTA',
'AACTCGTCGATG',
'ACAGACCACTCA',
'ACCAGCGACTAG',
'AGCAGCACTTGT',
'AACTGTGCGTAC',
'ACAGAGTCGGCT',
'ACCGCAGAGTCA',
'ACGGTGAGTGTC', ]
for bc in barcodes:
self.assertEqual(golay.decode(bc), (bc, 0))
for bc in barcodes:
err_bc = 'C' + bc[1:]
self.assertEqual(golay.decode(err_bc), (bc, 2))
def test_decode(self):
""" decode should decode barcodes from tutorial"""
barcodes = ['AGCACGAGCCTA',
'AACTCGTCGATG',
'ACAGACCACTCA',
'ACCAGCGACTAG',
'AGCAGCACTTGT',
'AACTGTGCGTAC',
'ACAGAGTCGGCT',
'ACCGCAGAGTCA',
'ACGGTGAGTGTC',]
for bc in barcodes:
self.assertEqual(golay.decode(bc),(bc,0))
for bc in barcodes:
err_bc = 'C'+bc[1:]
self.assertEqual(golay.decode(err_bc),(bc,2))
def test_golay600_2bit_errors(self):
""" A->C, G->T errors should be 2 bit errors for all 600 barcodes """
for bc in golay600:
if bc.count('A') == 0:
continue # only check those with A's
err_bc = bc.replace('A', 'C', 1)
corr, num_errs = golay.decode(err_bc)
self.assertEqual(corr, bc)
self.assertEqual(num_errs, 2)
for bc in golay600:
if bc.count('G') == 0:
continue # only check those with A's
err_bc = bc.replace('G', 'T', 1)
corr, num_errs = golay.decode(err_bc)
self.assertEqual(corr, bc)
self.assertEqual(num_errs, 2)
def test_golay600_2bit_errors(self):
""" A->C, G->T errors should be 2 bit errors for all 600 barcodes """
for bc in golay600:
if bc.count('A') == 0:
continue # only check those with A's
err_bc = bc.replace('A', 'C', 1)
corr, num_errs = golay.decode(err_bc)
self.assertEqual(corr, bc)
self.assertEqual(num_errs, 2)
for bc in golay600:
if bc.count('G') == 0:
continue # only check those with A's
err_bc = bc.replace('G', 'T', 1)
corr, num_errs = golay.decode(err_bc)
self.assertEqual(corr, bc)
self.assertEqual(num_errs, 2)
def test_golay_matches_old_code(self):
""" decode should behave as micah's code did, i.e., same golay encoding
this requires
DEFAULT_NT_TO_BITS = { "A":"11", "C":"00", "T":"10", "G":"01"}
"""
NT_TO_BITS = {"A": "11", "C": "00", "T": "10", "G": "01"}
original = 'GCATCGTCAACA'
rec = 'GCATCGTCCACA'
corr, nt_errs = golay.decode(rec, NT_TO_BITS)
self.assertEqual(corr, original)
self.assertEqual(nt_errs, 2)
def test_golay_matches_old_code(self):
""" decode should behave as micah's code did, i.e., same golay encoding
this requires
DEFAULT_NT_TO_BITS = { "A":"11", "C":"00", "T":"10", "G":"01"}
"""
NT_TO_BITS = {"A": "11", "C": "00", "T": "10", "G": "01"}
original = 'GCATCGTCAACA'
rec = 'GCATCGTCCACA'
corr, nt_errs = golay.decode(rec, NT_TO_BITS)
self.assertEqual(corr, original)
self.assertEqual(nt_errs, 2)
def test_golay600_codes(self):
""" all 600 codes should be left uncorrected, 0 errors"""
for bc in golay600:
corr, num_errs = golay.decode(bc)
self.assertEqual(corr, bc)
self.assertEqual(num_errs, 0)
def test_golay600_codes(self):
""" all 600 codes should be left uncorrected, 0 errors"""
for bc in golay600:
corr, num_errs = golay.decode(bc)
self.assertEqual(corr, bc)
self.assertEqual(num_errs, 0)
