def snapshot():
cutoff = 1
k = 28
r = Redis(**TEST_REDIS_ARGS)
r.flushdb()
host_path = os.path.join("data", "test", "unit_test_host.fa")
hosts_results_path = os.path.join("data", "snapshots", "hosts")
hosts = make_hosts(path=host_path, k=k)
print("hosts:")
print(hosts)
print("")
with open(hosts_results_path, "w+") as hosts_results_file:
hosts_results_file.writelines([f"{h}\n" for h in hosts])
alignment_path = os.path.join("data", "test", "unit_test_target.clu")
targets_results_path = os.path.join("data", "snapshots", "targets")
targets = make_targets(path=alignment_path, k=k)
print("targets:")
print(targets)
print("")
with open(targets_results_path, "w+") as targets_results_file:
targets_results_file.writelines([f"{t[0]}, {t[1]}\n" for t in targets])
good_targets = predict_side_effects(k=k, cutoff=cutoff)
good_targets_results_path = os.path.join("data", "snapshots",
"good_targets")
print("good_targets:")
print(good_targets)
print("")
with open(good_targets_results_path, "w+") as good_targets_results_file:
good_targets_results_file.writelines(
[f"{gt[0]}, {gt[1]}\n" for gt in good_targets])
def test_predict_side_effects():
k, cutoff = 28, 1
r = Redis(**TEST_REDIS_ARGS)
r.flushdb()
test_host_path = os.path.join("data", "test", "unit_test_host.fa")
make_hosts(path=test_host_path, k=k, redis_args=TEST_REDIS_ARGS)
test_alignment_path = os.path.join("data", "test", "unit_test_target.clu")
make_targets(path=test_alignment_path, id="nCoV", k=k, db=r)
good_targets_snapshot_path = os.path.join("data", "snapshots",
"good_targets")
with open(good_targets_snapshot_path, "r") as good_targets_snapshot_file:
good_targets_snapshot = list(csv.reader(good_targets_snapshot_file))
good_targets = predict_side_effects(k=k, cutoff=cutoff, db=r)
print("good_targets", good_targets)
print("good_targets_snapshot", good_targets_snapshot)
for good_target, snapshot in zip(good_targets, good_targets_snapshot):
assert good_target[0] == snapshot[0]
assert str(good_target[1]).strip(' ') == snapshot[1].strip(' ')
def test_predict_side_effects():
k, cutoff = 5, 1
r = Redis()
r.flushall()
test_host_path = os.path.join("data", "test", "unit_test_host.fa")
make_hosts(path=test_host_path, k=k)
test_alignment_path = os.path.join("data", "test", "unit_test_target.clu")
make_targets(path=test_alignment_path, id="nCoV", k=k)
good_targets_snapshot_path = os.path.join("data", "snapshots",
"good_targets")
with open(good_targets_snapshot_path, "r") as good_targets_snapshot_file:
good_targets_snapshot = list(csv.reader(good_targets_snapshot_file))
good_targets = predict_side_effects(k=k, cutoff=cutoff)
print("good_targets", good_targets)
print("good_targets_snapshot", good_targets_snapshot)
for good_target, snapshot in zip(good_targets, good_targets_snapshot):
assert good_target[0] == snapshot[0]
assert str(good_target[1]) == snapshot[1]
def test_make_hosts():
r, k = Redis(**TEST_REDIS_ARGS), 28
r.flushdb()
path = os.path.join("data", "test", "unit_test_host.fa")
hosts = make_hosts(path=path, k=k, redis_args=TEST_REDIS_ARGS)
hosts_snapshot_path = os.path.join("data", "snapshots", "hosts")
with open(hosts_snapshot_path, "r") as hosts_snapshot_file:
hosts_snapshot = hosts_snapshot_file.read().splitlines()
print("hosts", hosts)
print("hosts_snapshot", hosts_snapshot)
for host in hosts:
assert host in hosts_snapshot
def test_make_hosts():
r, k = Redis(), 5
r.flushall()
path = os.path.join("data", "test", "unit_test_host.fa")
hosts = make_hosts(path=path, k=k)
hosts_snapshot_path = os.path.join("data", "snapshots", "hosts")
with open(hosts_snapshot_path, "r") as hosts_snapshot_file:
hosts_snapshot = hosts_snapshot_file.read().splitlines()
print("hosts", hosts)
print("hosts_snapshot", hosts_snapshot)
for host in hosts:
assert host in hosts_snapshot