def test_run_to_file(self):
op = ".kk_test"
if os.path.exists(op): shutil.rmtree(op)
args = base_args()
args.pvalue_column = "P"
args.or_column = "OR"
args.output_folder = op
M03_betas.run(args)
n = os.listdir(op)[0]
n = os.path.join(op,n)
r = pandas.read_table(n)
assert_beta_pb(self, r)
shutil.rmtree(op)
def test_run_to_file(self):
op = ".kk_test"
if os.path.exists(op): shutil.rmtree(op)
args = base_args()
args.pvalue_column = "P"
args.or_column = "OR"
args.output_folder = op
M03_betas.run(args)
n = os.listdir(op)[0]
n = os.path.join(op,n)
r = pandas.read_table(n)
assert_beta_pb(self, r)
shutil.rmtree(op)
def test_run_skip(self):
args = base_args("tests/_td/GWAS/scz2c")
args.pvalue_column = "P"
args.or_column = "OR"
args.skip_until_header = "\t".join(["HG19CHRC", "SNPID", "A1", "A2", "BP", "INFO", "OR", "SE", "P", "NGT", "BETA", "ZSCORE", "BETA_SIGN"])
r = M03_betas.run(args)
assert_beta_pb(self, r)
def test_run_split(self):
args = base_args("tests/_td/GWAS/scz2b")
args.gwas_file_pattern = ".*gz"
args.pvalue_column = "P"
args.or_column = "OR"
r = M03_betas.run(args)
assert_beta_pb(self, r)
def test_run_skip(self):
args = base_args("tests/_td/GWAS/scz2c")
args.pvalue_column = "P"
args.or_column = "OR"
args.skip_until_header = "\t".join(["HG19CHRC", "SNPID", "A1", "A2", "BP", "INFO", "OR", "SE", "P", "NGT", "BETA", "ZSCORE", "BETA_SIGN"])
r = M03_betas.run(args)
assert_beta_pb(self, r)
def test_run_split(self):
args = base_args("tests/_td/GWAS/scz2b")
args.gwas_file_pattern = ".*gz"
args.pvalue_column = "P"
args.or_column = "OR"
r = M03_betas.run(args)
assert_beta_pb(self, r)
def test_with_model(self):
args = base_args()
args.pvalue_column = "P"
args.or_column = "OR"
args.model_db_path = "tests/_td/dbs/test_3.db"
r = M03_betas.run(args)
assert_model_beta_pb(self, r)
def test_with_model(self):
args = base_args()
args.pvalue_column = "P"
args.or_column = "OR"
args.model_db_path = "tests/_td/dbs/test_3.db"
r = M03_betas.run(args)
assert_model_beta_pb(self, r)
def test_run_to_files(self):
op = ".kk_test"
if os.path.exists(op): shutil.rmtree(op)
args = base_args("tests/_td/GWAS/scz2b")
args.gwas_file_pattern = ".*gz"
args.pvalue_column = "P"
args.or_column = "OR"
args.output_folder = op
M03_betas.run(args)
r = pandas.DataFrame()
for n in sorted(os.listdir(op)):
n = os.path.join(op,n)
d = pandas.read_table(n)
r = pandas.concat([r,d])
assert_beta_pb(self, r)
shutil.rmtree(op)
def test_run_to_files(self):
op = ".kk_test"
if os.path.exists(op): shutil.rmtree(op)
args = base_args("tests/_td/GWAS/scz2b")
args.gwas_file_pattern = ".*gz"
args.pvalue_column = "P"
args.or_column = "OR"
args.output_folder = op
M03_betas.run(args)
r = pandas.DataFrame()
for n in sorted(os.listdir(op)):
n = os.path.join(op,n)
d = pandas.read_table(n)
r = pandas.concat([r,d])
assert_beta_pb(self, r)
shutil.rmtree(op)
def test_split_with_model(self):
args = base_args("tests/_td/GWAS/scz2b")
args.gwas_file_pattern = ".*gz"
args.pvalue_column = "P"
args.or_column = "OR"
args.model_db_path = "tests/_td/dbs/test_3.db"
r = M03_betas.run(args)
assert_model_beta_pb(self, r)
def test_fix_pvalue(self):
op = ".kk_test"
if os.path.exists(op): shutil.rmtree(op)
args = base_args("tests/_td/GWAS/scz2d")
args.gwas_file_pattern = ".*gz"
args.pvalue_column = "P"
args.or_column = "OR"
r = M03_betas.run(args)
assert_beta_pb_fix(self, r)
def test_fix_pvalue(self):
op = ".kk_test"
if os.path.exists(op): shutil.rmtree(op)
args = base_args("tests/_td/GWAS/scz2d")
args.gwas_file_pattern = ".*gz"
args.pvalue_column = "P"
args.or_column = "OR"
r = M03_betas.run(args)
assert_beta_pb_fix(self, r)
def test_split_with_model(self):
args = base_args("tests/_td/GWAS/scz2b")
args.gwas_file_pattern = ".*gz"
args.pvalue_column = "P"
args.or_column = "OR"
args.model_db_path = "tests/_td/dbs/test_3.db"
r = M03_betas.run(args)
assert_model_beta_pb(self, r)
def run(args):
if not args.overwrite and args.output_file and os.path.exists(args.output_file):
logging.info("%s already exists, move it or delete it if you want it done again", args.output_file)
return
if not args.model_db_path:
logging.info("Need to provide a model database file path")
return
args.output_folder = None
g = M03_betas.run(args)
M04_zscores.run(args, g)
def run(args):
if not args.overwrite and os.path.exists(args.output_file):
logging.info("%s already exists, move it or delete it if you want it done again", args.output_file)
return
if not args.model_db_path:
logging.info("Need to provide a model database file path")
return
args.output_folder = None
g = M03_betas.run(args)
M04_zscores.run(args, g)
def test_split_with_model(self):
op = ".kk_test"
if os.path.exists(op): shutil.rmtree(op)
args = base_args("tests/_td/GWAS/scz2b")
args.gwas_file_pattern = ".*gz"
args.pvalue_column = "P"
args.or_column = "OR"
args.model_db_path = "tests/_td/dbs/test_3.db"
r = M03_betas.run(args)
assert_model_beta_pb(self, r)
def test_split_with_model(self):
op = ".kk_test"
if os.path.exists(op): shutil.rmtree(op)
args = base_args("tests/_td/GWAS/scz2b")
args.gwas_file_pattern = ".*gz"
args.pvalue_column = "P"
args.or_column = "OR"
args.model_db_path = "tests/_td/dbs/test_3.db"
r = M03_betas.run(args)
assert_model_beta_pb(self, r)
def testWrongArguments(self, patch_validate_basic, patch_validate_strict):
args = DummyArgs()
with self.assertRaises(Exception) as c: M03_betas.run(args)
args.gwas_folder = "tests/_td/GWAS/scz2"
patch_validate_basic.side_effect = RuntimeError("k")
with self.assertRaises(RuntimeError) as c: M03_betas.run(args)
patch_validate_basic.side_effect = None
patch_validate_strict.side_effect = RuntimeError()
with self.assertRaises(RuntimeError) as c: M03_betas.run(args)
def testWrongArguments(self, patch_validate_basic, patch_validate_strict):
args = DummyArgs()
with self.assertRaises(Exception) as c: M03_betas.run(args)
args.gwas_folder = "tests/_td/GWAS/scz2"
patch_validate_basic.side_effect = RuntimeError("k")
with self.assertRaises(RuntimeError) as c: M03_betas.run(args)
patch_validate_basic.side_effect = None
patch_validate_strict.side_effect = RuntimeError()
with self.assertRaises(RuntimeError) as c: M03_betas.run(args)
def run_folder_or_file(self, folder, file):
args = base_args(folder, file)
args.pvalue_column = "P"
args.or_column = "OR"
r = M03_betas.run(args)
assert_beta_pb(self, r)
args = base_args(folder, file)
args.pvalue_column = "P"
args.beta_column = "BETA"
r = M03_betas.run(args)
assert_beta_pb(self, r)
args = base_args(folder, file)
args.pvalue_column = "P"
args.beta_sign_column = "BETA_SIGN"
r = M03_betas.run(args)
assert_beta_p(self, r)
args = base_args(folder, file)
args.beta_column = "BETA"
args.se_column = "SE"
r = M03_betas.run(args)
assert_beta_bse(self, r)
args = base_args(folder, file)
args.beta_column = "BETA"
args.se_column = "SE"
r = M03_betas.run(args)
assert_beta_bse(self, r)
args = base_args(folder, file)
args.or_column = "OR"
args.se_column = "SE"
r = M03_betas.run(args)
assert_beta_bse(self, r)
#Should fail
args = base_args(folder, file)
args.or_column = "BETA"
args.se_column = "SE"
with self.assertRaises(Exception):
M03_betas.run(args)
def run_folder_or_file(self, folder, file):
args = base_args(folder, file)
args.pvalue_column = "P"
args.or_column = "OR"
r = M03_betas.run(args)
assert_beta_pb(self, r)
args = base_args(folder, file)
args.pvalue_column = "P"
args.beta_column = "BETA"
r = M03_betas.run(args)
assert_beta_pb(self, r)
args = base_args(folder, file)
args.pvalue_column = "P"
args.beta_sign_column = "BETA_SIGN"
r = M03_betas.run(args)
assert_beta_p(self, r)
args = base_args(folder, file)
args.beta_column = "BETA"
args.se_column = "SE"
r = M03_betas.run(args)
assert_beta_bse(self, r)
args = base_args(folder, file)
args.beta_column = "BETA"
args.se_column = "SE"
r = M03_betas.run(args)
assert_beta_bse(self, r)
args = base_args(folder, file)
args.or_column = "OR"
args.se_column = "SE"
r = M03_betas.run(args)
assert_beta_bse(self, r)
#Should fail
args = base_args(folder, file)
args.or_column = "BETA"
args.se_column = "SE"
with self.assertRaises(Exception): M03_betas.run(args)
def buildBetas(self):
logging.info("Processing betas!")
self.args.output_folder = args.beta_folder
M03_betas.run(self.args)
def test_fail_incompatible_arguments(self):
args = base_args("tests/_td/GWAS/scz2", "tests/_td/GWAS/scz2/scz2.gwas.results.txt.gz")
with self.assertRaises(Exceptions.InvalidArguments) as c: M03_betas.run(args)
def test_fail_incompatible_arguments(self):
args = base_args("tests/_td/GWAS/scz2",
"tests/_td/GWAS/scz2/scz2.gwas.results.txt.gz")
with self.assertRaises(Exceptions.InvalidArguments) as c:
M03_betas.run(args)
def buildBetas(self):
logging.info("Processing betas!")
self.args.output_folder = args.beta_folder
M03_betas.run(self.args)