def test_NA10860_debug(monkeypatch, solver):
file = script_path("aldy.tests.resources/NA10860.bam")
with tmpfile(suffix=".tar.gz") as tmp:
with tmpfile(mode="w") as out, tmpfile(mode="w") as out_log:
out.close()
out_log.close()
assert_file(
monkeypatch,
file,
solver,
EXPECTED_NA10860 + "Preparing debug archive...",
{"--debug": tmp.name[:-7], "--log": out_log.name, "--output": out.name},
)
with open(script_path("aldy.tests.resources/NA10860.out.expected")) as f:
expected = f.read()
with open(out.name) as f:
produced = f.read()
assert produced == expected
# Check logs
with open(out_log.name) as f:
log = f.read()
s = " rs1058172 42523528.C>T 3267G>A "
s += "(cov= 21, cn= 0.9; impact=R365H)\n"
s = "[major] status= optimal; opt= 1.48; solution= 1x*4.021, 1x*4J, 1x*61\n"
assert s in log
out = subprocess.check_output(f"tar tzf {tmp.name}", shell=True).decode("utf-8")
out = "\n".join(sorted(out.strip().split("\n")))
assert out == EXPECTED_NA10860_DEBUG_TAR.strip()
def test_NA10860_debug(monkeypatch, solver):
file = script_path("aldy.tests.resources/NA10860.bam")
with tmpfile(suffix=".tar.gz") as tmp:
with tmpfile(mode="w") as out, tmpfile(mode="w") as out_log:
out.close()
out_log.close()
assert_file(
monkeypatch,
file,
solver,
EXPECTED_NA10860 + "Preparing debug archive...",
{
"--debug": tmp.name[:-7],
"--log": out_log.name,
"--output": out.name
},
)
with open(script_path(
"aldy.tests.resources/NA10860.out.expected")) as f:
expected = f.read()
with open(out.name) as f:
produced = f.read()
assert produced == expected
# Check logs
with open(out_log.name) as f:
log = f.read()
s = "Major solver: MajorSol[1.33; sol=(1x*4, 1x*4.f, 1x*61); "
s += "cn=CNSol[6.73; sol=(2x*1,1x*61); "
s += "cn=3333333333333322222_2|333333333333334444444]"
assert s in log
out = subprocess.check_output(f"tar tzf {tmp.name}",
shell=True).decode("utf-8")
out = "\n".join(sorted(out.strip().split("\n")))
assert out == EXPECTED_NA10860_DEBUG_TAR.strip()
def test_NA10860_vcf_out(monkeypatch, solver):
file = script_path("aldy.tests.resources/NA10860.bam")
with tmpfile(suffix=".vcf", mode="w") as out:
out.close()
assert_file(monkeypatch, file, solver, EXPECTED_NA10860, {"--output": out.name})
with open(script_path("aldy.tests.resources/NA10860.vcf.expected")) as f:
expected = f.read()
with open(out.name) as f:
produced = f.read()
assert produced == expected.replace("aldy-v3.1", f"aldy-v{__version__}")
def test_NA07000_phase(monkeypatch, solver):
file = script_path("aldy.tests.resources/NA07000_SLCO1B1.vcf.gz")
assert_file(
monkeypatch,
file,
solver,
EXPECTED_NA07000_PHASE,
{
"--max-minor-solutions": "1",
"--gene": "SLCO1B1",
"--phase": script_path("aldy.tests.resources/NA07000_SLCO1B1.phase"),
},
warn=True,
)
def test_profile(monkeypatch, capsys):
lines = []
def log_info(*args):
s = str.format(*args)
lines.append(s)
monkeypatch.setattr(log, "info", log_info)
main(["profile", script_path("aldy.tests.resources/NA10860.bam")])
lines = escape_ansi("\n".join(lines)).strip()
assert lines == EXPECTED_PROFILE.strip()
captured = capsys.readouterr()
with open(script_path("aldy.tests.resources/NA10860.profile")) as f:
expected = f.read()
assert captured.out == expected
def test_fix_insertions(monkeypatch, solver):
file = script_path("aldy.tests.resources/INS.dump")
assert_file(
monkeypatch,
file,
solver,
EXPECTED_INS,
{"--profile": "pgrnseq-v3", "--max-minor-solutions": "1"},
)
def test_hard_fusion(monkeypatch, solver):
file = script_path("aldy.tests.resources/HARD.dump")
assert_file(
monkeypatch,
file,
solver,
EXPECTED_HARD_FUSION,
{"--profile": "pgrnseq-v1", "--fusion-penalty": "5"},
)
def assert_show(monkeypatch, expected, params=None):
lines = []
def log_info(*args):
s = str.format(*args)
lines.append(s)
monkeypatch.setattr(log, "info", log_info)
args = ["show", "--gene", script_path("aldy.tests.resources/toy.yml")]
main(args + (params or []))
expected = expected.strip()
lines = escape_ansi("\n".join(lines)).strip()
assert lines == expected
def assert_show(monkeypatch,
expected,
query=None,
gene="aldy.tests.resources/toy.yml"):
lines = []
def log_info(*args):
s = str.format(*args)
lines.append(s)
monkeypatch.setattr(log, "info", log_info)
args = ["q", script_path(gene)]
if query:
args[1] += "*" + query
main(args)
expected = expected.strip()
lines = escape_ansi("\n".join(lines)).strip()
assert lines == expected
def read_data(path):
with open(script_path(path)) as f:
data = f.read()
data = ast.literal_eval(data)
return data
def real_gene():
return Gene(script_path("aldy.resources.genes/cyp2d6.yml"))
def toy_gene():
return Gene(script_path("aldy.tests.resources/toy.yml"))
def test_NA10860_hg38(monkeypatch, solver):
file = script_path("aldy.tests.resources/NA10860_hg38.bam")
assert_file(
monkeypatch, file, solver, EXPECTED_NA10860.replace("NA10860", "NA10860_hg38")
)
def test_NA10860(monkeypatch, solver):
file = script_path("aldy.tests.resources/NA10860.bam")
assert_file(monkeypatch, file, solver, EXPECTED_NA10860)
def test_NA10860_gap(monkeypatch, solver):
file = script_path("aldy.tests.resources/NA10860.bam")
assert_file(monkeypatch, file, solver, EXPECTED_NA10860_GAP, {"--gap": "0.1"})
def test_NA10860_cn(monkeypatch, solver):
file = script_path("aldy.tests.resources/NA10860.bam")
assert_file(monkeypatch, file, solver, EXPECTED_NA10860_CN, {"--cn": "1,1"})
def test_hard(monkeypatch, solver):
file = script_path("aldy.tests.resources/HARD.dump")
assert_file(monkeypatch, file, solver, EXPECTED_HARD, {"--profile": "pgrnseq-v1"})