def test_load_opensnp_datadump_file(self):
# temporarily set resources dir to tests
r = Resources()
r._resources_dir = "tests/resources"
# write test openSNP datadump zip
with atomic_write("tests/resources/opensnp_datadump.current.zip",
mode="wb",
overwrite=True) as f:
with zipfile.ZipFile(f, "w") as f_zip:
f_zip.write("tests/input/generic.csv", arcname="generic1.csv")
f_zip.write("tests/input/generic.csv", arcname="generic2.csv")
snps1 = SNPs(r.load_opensnp_datadump_file("generic1.csv"))
snps2 = SNPs(r.load_opensnp_datadump_file("generic2.csv"))
pd.testing.assert_frame_equal(snps1.snps, self.generic_snps())
pd.testing.assert_frame_equal(snps2.snps, self.generic_snps())
r._resources_dir = "resources"
def _setup_gsa_test(resources_dir):
# reset resource if already loaded
r = Resources()
r._resources_dir = resources_dir
r._gsa_resources = {}
gzip_file(
"tests/resources/gsa_rsid_map.txt",
os.path.join(resources_dir, "gsa_rsid_map.txt.gz"),
)
gzip_file(
"tests/resources/gsa_chrpos_map.txt",
os.path.join(resources_dir, "gsa_chrpos_map.txt.gz"),
)
def _setup_gsa_test(resources_dir):
# reset resource if already loaded
r = Resources()
r._resources_dir = resources_dir
r._init_resource_attributes()
gzip_file(
"tests/resources/gsa_rsid_map.txt",
os.path.join(resources_dir, "gsa_rsid_map.txt.gz"),
)
gzip_file(
"tests/resources/gsa_chrpos_map.txt",
os.path.join(resources_dir, "gsa_chrpos_map.txt.gz"),
)
gzip_file(
"tests/resources/dbsnp_151_37_reverse.txt",
os.path.join(resources_dir, "dbsnp_151_37_reverse.txt.gz"),
)
def _teardown_gsa_test():
r = Resources()
r._resources_dir = "resources"
r._gsa_resources = {}
def _teardown_gsa_test():
r = Resources()
r._resources_dir = "resources"
r._init_resource_attributes()
