def f():
s = SNPs("tests/input/generic.csv")
self.assertTrue(s.is_valid())
class TestSnps(BaseSNPsTestCase):
def setUp(self):
self.snps_GRCh38 = SNPs("tests/input/GRCh38.csv")
self.snps = SNPs("tests/input/chromosomes.csv")
self.snps_only_detect_source = SNPs("tests/input/chromosomes.csv",
only_detect_source=True)
self.snps_none = SNPs(None)
with open("tests/input/chromosomes.csv", "r") as f:
self.snps_buffer = SNPs(f.read().encode("utf-8"))
with atomic_write("tests/input/chromosomes.csv.zip",
mode="wb",
overwrite=True) as f:
with zipfile.ZipFile(f, "w") as f_zip:
f_zip.write("tests/input/chromosomes.csv",
arcname="chromosomes.csv")
with open("tests/input/chromosomes.csv.zip", "rb") as f:
data = f.read()
self.snps_buffer_zip = SNPs(data)
os.remove("tests/input/chromosomes.csv.zip")
with open("tests/input/chromosomes.csv", "rb") as f_in:
with atomic_write("tests/input/chromosomes.csv.gz",
mode="wb",
overwrite=True) as f_out:
with gzip.open(f_out, "wb") as f_gzip:
shutil.copyfileobj(f_in, f_gzip)
with open("tests/input/chromosomes.csv.gz", "rb") as f:
data = f.read()
self.snps_buffer_gz = SNPs(data)
os.remove("tests/input/chromosomes.csv.gz")
def snps_discrepant_pos(self):
return self.create_snp_df(rsid=["rs3094315"],
chrom=["1"],
pos=[1],
genotype=["AA"])
def test_assembly(self):
assert self.snps_GRCh38.assembly == "GRCh38"
def test_assembly_no_snps(self):
assert self.snps_none.assembly == ""
def test_snp_buffer_zip(self):
assert self.snps_buffer_zip.snp_count == 6
def test_snp_buffer_gz(self):
assert self.snps_buffer_gz.snp_count == 6
def test_snp_buffer(self):
assert self.snps_buffer.snp_count == 6
def test_snp_count(self):
assert self.snps.snp_count == 6
def test_snp_count_no_snps(self):
assert self.snps_none.snp_count == 0
def test_chromosomes(self):
assert self.snps.chromosomes == ["1", "2", "3", "5", "PAR", "MT"]
def test_chromosomes_no_snps(self):
assert self.snps_none.chromosomes == []
def test_chromosomes_summary(self):
assert self.snps.chromosomes_summary == "1-3, 5, PAR, MT"
def test_chromosomes_summary_no_snps(self):
assert self.snps_none.chromosomes_summary == ""
def test_build_no_snps(self):
assert not self.snps_none.build
def test_build_detected_no_snps(self):
assert not self.snps_none.build_detected
def test_build_detected_PAR_snps(self):
if (not os.getenv("DOWNLOADS_ENABLED")
or os.getenv("DOWNLOADS_ENABLED") == "true"):
snps = SNPs("tests/input/GRCh37_PAR.csv")
assert snps.build == 37
assert snps.build_detected
def test_sex_no_snps(self):
assert self.snps_none.sex == ""
def test_sex_Male_Y_chrom(self):
s = self.simulate_snps(chrom="Y",
pos_start=1,
pos_max=59373566,
pos_step=10000)
file = s.save_snps()
snps = SNPs(file)
assert snps.sex == "Male"
def test_get_summary(self):
assert self.snps_GRCh38.get_summary() == {
"source": "generic",
"assembly": "GRCh38",
"build": 38,
"build_detected": True,
"snp_count": 4,
"chromosomes": "1, 3",
"sex": "",
}
def test_get_summary_no_snps(self):
assert not self.snps_none.get_summary()
def test_is_valid_True(self):
assert self.snps_GRCh38.is_valid()
def test_is_valid_False(self):
assert not self.snps_none.is_valid()
def test__read_raw_data(self):
assert self.snps_none.snps.empty
assert self.snps_none.source == ""
def test__lookup_build_with_snp_pos_None(self):
snps = SNPs()
snps._snps = self.snps_discrepant_pos()
assert not snps.detect_build()
def test_get_assembly_None(self):
snps = SNPs()
assert snps.get_assembly() is ""
def test_save_snps_source(self):
assert (os.path.relpath(
self.snps_GRCh38.save_snps()) == "output/generic_GRCh38.csv")
snps = SNPs("output/generic_GRCh38.csv")
pd.testing.assert_frame_equal(snps.snps, self.snps_GRCh38.snps)
def test_save_snps_buffer(self):
out = io.StringIO()
self.snps.save_snps(out)
assert out.read().startswith("# Generated by snps")
def test_snps_only_detect_source(self):
assert self.snps_only_detect_source.source == "generic"
def test_duplicate_rsids(self):
snps = SNPs("tests/input/duplicate_rsids.csv")
result = self.create_snp_df(rsid=["rs1"],
chrom=["1"],
pos=[101],
genotype=["AA"])
duplicate_snps = self.create_snp_df(rsid=["rs1", "rs1"],
chrom=["1", "1"],
pos=[102, 103],
genotype=["CC", "GG"])
pd.testing.assert_frame_equal(snps.snps, result)
pd.testing.assert_frame_equal(snps.duplicate_snps, duplicate_snps)
def test_deduplicate_false(self):
snps = SNPs("tests/input/duplicate_rsids.csv", deduplicate=False)
result = self.create_snp_df(
rsid=["rs1", "rs1", "rs1"],
chrom=["1", "1", "1"],
pos=[101, 102, 103],
genotype=["AA", "CC", "GG"],
)
pd.testing.assert_frame_equal(snps.snps, result)