def manual_barcodes_test(self):
bc_list = list(self.barcodes)
for i in range(len(self.barcodes)):
bc1 = num2dna(bc_list[i], self.bc_len)
for j in range(i+1, len(self.barcodes)):
bc2 = num2dna(bc_list[j], self.bc_len)
dist = editmeasures.free_divergence(bc1, bc2)
if dist < self.max_err:
log.error('!'*10 + ' FAIL ' + '!'*10)
log.error('Distance {} between {} and {}.'.format(dist, bc1, bc2))
return
log.info('Barcodes Pass Manual Check')
def iterator_test(self, iterator='self'):
log.info('Generating self set...')
if iterator == 'self':
self_set = set(self)
elif iterator == 'parallel_num':
self_set = set(
seqtools.num2dna(seq, len(self.c))
for seq in self.parallel_num_iterator())
else:
raise ValueError('Invalid iterator to test: {}'.format(iterator))
log.info('Generating brute force set...')
bf_set = set(''.join(tup)
for tup in itertools.product(bases, repeat=len(self.c))
if self.min_r <= editmeasures.free_divergence(
self.c, ''.join(tup)) <= self.r)
log.info('Comparing...')
if self_set == bf_set:
log.info('PASS')
else:
log.error('#### FAIL ####')
log.error('{} missing seqs, {} extra seqs'.format(
len(bf_set - self_set), len(self_set - bf_set)))