def guess_alleles(fastq_records, library, redis_db, max_hamming_dist = 2):
n_unmatched = 0
i = 0
for read in fastq_records:
rev_comp = read.get_barcode_rev_comp()
got = redis_db.get(dict_prefix + rev_comp)
#if read not in read_to_allele:
if got is None:
allele, hamming_dist = hamming.calc_min_hamming(rev_comp, library, max_hamming_dist)
# TODO: don't try hamming correction if it's another group's
if allele is None:
n_unmatched += 1
else:
redis_db.set(dict_prefix + rev_comp, allele)
#read_to_allele[rev_comp] = allele
#try:
# read_to_allele[rev_comp] = library[rev_comp]
#except KeyError:
# n_unmatched += 1
i += 1
if i % 100000 == 0:
print("Ran " + str(i))
print("There were %i unmatched reads." % n_unmatched)
def guess_alleles(fastq_records, library, redis_db, max_hamming_dist=2):
n_unmatched = 0
i = 0
for read in fastq_records:
rev_comp = read.get_barcode_rev_comp()
got = redis_db.get(dict_prefix + rev_comp)
#if read not in read_to_allele:
if got is None:
allele, hamming_dist = hamming.calc_min_hamming(
rev_comp, library, max_hamming_dist)
# TODO: don't try hamming correction if it's another group's
if allele is None:
n_unmatched += 1
else:
redis_db.set(dict_prefix + rev_comp, allele)
#read_to_allele[rev_comp] = allele
#try:
# read_to_allele[rev_comp] = library[rev_comp]
#except KeyError:
# n_unmatched += 1
i += 1
if i % 100000 == 0:
print("Ran " + str(i))
print("There were %i unmatched reads." % n_unmatched)
import hamming
import pickle
with open('../../allele_dic_with_WT.pkl', 'rb') as f:
library = pickle.load(f)
test_strings = [chr(x) * 18 for x in range(ord('A'), ord('Z'))]
for s in range(1, 4000):
found, dist = hamming.calc_min_hamming('A' * 18, library)
import hamming
import pickle
with open('../../allele_dic_with_WT.pkl', 'rb') as f:
library = pickle.load(f)
test_strings = [chr(x) * 18 for x in range(ord('A'), ord('Z'))]
for s in range(1, 4000):
found, dist = hamming.calc_min_hamming('A' * 18, library)
import hamming
library = ['AABB', 'EEFF', 'ZYZY']
found, dist = hamming.calc_min_hamming('AAAA', library)
assert found == 'AABB'
assert dist == 2
found, dist = hamming.calc_min_hamming('QQQY', library)
assert found == None
assert dist == 4
found, dist = hamming.calc_min_hamming('EEFF', library)
assert found == 'EEFF'
assert dist == 0
found, dist = hamming.calc_min_hamming('AABC', library)
assert found == 'AABB'
assert dist == 1
