def test_estimate_functions_1():
res = functions.estimate_optimal_with_N_and_M(99, 1024)
assert res[0] == 7, res[0]
assert res[1] == 146, res[1]
assert res[2] == 1022, res[2]
assert abs(.008 - res[3]) < .001, res[3]
res = functions.estimate_optimal_with_N_and_f(99, 0.00701925498897)
assert res[0] == 7, res[0]
assert res[1] == 145, res[1]
assert res[2] == 1015, res[2]
assert abs(.008 - res[3]) < .002, res[3]
res = functions.estimate_optimal_with_N_and_M(1024, 2)
assert res[0] == 1, res[0]
assert res[1] == 2, res[1]
assert res[2] == 2, res[2]
assert res[3] == 1.0, res[3]
# using a crazy high FP rate just for coverage
res = functions.estimate_optimal_with_N_and_f(1024, 0.7)
assert res[0] == 1, res[0]
assert res[1] == 850, res[1]
assert res[2] == 850, res[2]
assert abs(.7 - res[3]) < 0.0022, abs(.7 - res[3])
def main():
info('estimate_optimal_hash.py', ['counting'])
args = get_parser().parse_args()
N = args.N
if args.M:
M = args.M
result = estimate_optimal_with_N_and_M(N,M)
print("number of estimated distinct k-mers: ", N, file=sys.stderr)
print("size of memory available to use: ", M, file=sys.stderr)
print("optimal number of hash tables: ", result.num_htables,
file=sys.stderr)
print("optimal size of hash tables: ", result.htable_size,
file=sys.stderr)
print("estimated false positive rate: ", result.fp_rate,
file=sys.stderr)
print("estimated usage of memory: ", result.mem_use,
file=sys.stderr)
elif args.f:
f = args.f
result = estimate_optimal_with_N_and_f(N,f)
print("number of estimated distinct k-mers: ", N, file=sys.stderr)
print("desired maximum false positive rate: ", f, file=sys.stderr)
print("optimal number of hash tables: ", result.num_htables,
file=sys.stderr)
print("optimal size of hash tables: ", result.htable_size,
file=sys.stderr)
print("estimated false positive rate: ", result.fp_rate,
file=sys.stderr)
print("estimated usage of memory: ", result.mem_use,
file=sys.stderr)
else:
get_parser().error('No action requested, add -M (size of memory available to use) or -f (desired maximum false posotive rate)')
def test_estimate_functions_namedtup():
res = functions.estimate_optimal_with_N_and_M(99, 1024)
assert res.num_htables == 7, res[0]
assert res.htable_size == 146, res[1]
assert res.mem_use == 1022, res[2]
assert abs(.008 - res.fp_rate) < .001, res[3]
res = functions.estimate_optimal_with_N_and_f(99, 0.00701925498897)
assert res.num_htables == 7, res[0]
assert res.htable_size == 145, res[1]
assert res.mem_use == 1015, res[2]
assert abs(.008 - res.fp_rate) < .002, res[3]
def main():
info('estimate_optimal_hash.py', ['counting'])
args = get_parser().parse_args()
N = args.N
if args.M:
M = args.M
result = estimate_optimal_with_N_and_M(N, M)
print("number of estimated distinct k-mers: ", N, file=sys.stderr)
print("size of memory available to use: ", M, file=sys.stderr)
print("optimal number of hash tables: ",
result.num_htables,
file=sys.stderr)
print("optimal size of hash tables: ",
result.htable_size,
file=sys.stderr)
print("estimated false positive rate: ",
result.fp_rate,
file=sys.stderr)
print("estimated usage of memory: ",
result.mem_use,
file=sys.stderr)
elif args.f:
f = args.f
result = estimate_optimal_with_N_and_f(N, f)
print("number of estimated distinct k-mers: ", N, file=sys.stderr)
print("desired maximum false positive rate: ", f, file=sys.stderr)
print("optimal number of hash tables: ",
result.num_htables,
file=sys.stderr)
print("optimal size of hash tables: ",
result.htable_size,
file=sys.stderr)
print("estimated false positive rate: ",
result.fp_rate,
file=sys.stderr)
print("estimated usage of memory: ",
result.mem_use,
file=sys.stderr)
else:
get_parser().error(
'No action requested, add -M (size of memory available to use) or -f (desired maximum false posotive rate)'
)
