def testParseModel(self):
res_dir = os.path.join(self.results_dir, "baseml", "model")
for results_file in os.listdir(res_dir):
version = results_file.split('-')[1].split('.')[0]
model = results_file[5]
version_msg = "Improper parsing for model %s version %s" \
% (model, version.replace('_', '.'))
results_path = os.path.join(res_dir, results_file)
results = baseml.read(results_path)
# There are 6 top-levels: parameters, tree, lnL, version,
# tree length and lnL max
self.assertEqual(len(results), 6, version_msg)
self.assertTrue("parameters" in results, version_msg)
params = results["parameters"]
self.assertTrue("alpha" in params, version_msg)
self.assertTrue("rates" in params, version_msg)
self.assertTrue("parameter list" in params, version_msg)
self.assertTrue("rate frequencies" in params, version_msg)
if model in ["1", "3", "4", "5", "6"]:
self.assertTrue("kappa" in params, version_msg)
if model in ["7", "8"]:
self.assertTrue("base frequencies" in params, version_msg)
self.assertTrue("rate parameters" in params, version_msg)
self.assertTrue("Q matrix" in params, version_msg)
qmat = params["Q matrix"]
self.assertEqual(len(qmat), 2, version_msg)
self.assertTrue("matrix" in qmat)
matrix = qmat["matrix"]
self.assertEqual(len(matrix), 4, version_msg)
self.assertEqual(len(matrix[0]), 4, version_msg)
def testParseModel(self):
res_dir = os.path.join(self.results_dir, "baseml", "model")
for results_file in os.listdir(res_dir):
version = results_file.split('-')[1].split('.')[0]
model = results_file[5]
version_msg = "Improper parsing for model %s version %s" \
% (model, version.replace('_', '.'))
results_path = os.path.join(res_dir, results_file)
results = baseml.read(results_path)
# There are 6 top-levels: parameters, tree, lnL, version,
# tree length and lnL max
self.assertEqual(len(results), 6, version_msg)
self.assertTrue("parameters" in results, version_msg)
params = results["parameters"]
self.assertTrue("alpha" in params, version_msg)
self.assertTrue("rates" in params, version_msg)
self.assertTrue("parameter list" in params, version_msg)
self.assertTrue("rate frequencies" in params, version_msg)
if model in ["1", "3", "4", "5", "6"]:
self.assertTrue("kappa" in params, version_msg)
if model in ["7", "8"]:
self.assertTrue("base frequencies" in params, version_msg)
self.assertTrue("rate parameters" in params, version_msg)
self.assertTrue("Q matrix" in params, version_msg)
qmat = params["Q matrix"]
self.assertEqual(len(qmat), 2, version_msg)
self.assertTrue("matrix" in qmat)
matrix = qmat["matrix"]
self.assertEqual(len(matrix), 4, version_msg)
self.assertEqual(len(matrix[0]), 4, version_msg)
def testParseAllVersions(self):
folder = os.path.join("PAML","Results", "baseml", "versions")
for results_file in os.listdir(folder):
file_path = os.path.join(folder, results_file)
if os.path.isfile(file_path) and results_file[:6] == "baseml":
results = baseml.read(file_path)
self.assertEqual(len(results), 6)
self.assertEqual(len(results["parameters"]), 7)
def testParseAllVersions(self):
folder = os.path.join("PAML", "Results", "baseml", "versions")
for results_file in os.listdir(folder):
file_path = os.path.join(folder, results_file)
if os.path.isfile(file_path) and results_file[:6] == "baseml":
results = baseml.read(file_path)
self.assertEqual(len(results), 6)
self.assertEqual(len(results["parameters"]), 7)
def testParseSEs(self):
res_dir = os.path.join(self.results_dir, "baseml", "SE")
for results_file in os.listdir(res_dir):
version = results_file.split("-")[1].split(".")[0]
version_msg = f"Improper parsing for version {version.replace('_', '.')}"
results_path = os.path.join(res_dir, results_file)
results = baseml.read(results_path)
# There are 6 top-levels: parameters, tree, lnL, version,
# tree length and lnL max
self.assertEqual(len(results), 6, version_msg)
self.assertIn("parameters", results, version_msg)
params = results["parameters"]
self.assertIn("SEs", params, version_msg)
def testParseSEs(self):
res_dir = os.path.join(self.results_dir, "baseml", "SE")
for results_file in os.listdir(res_dir):
version = results_file.split('-')[1].split('.')[0]
version_msg = "Improper parsing for version %s" \
% version.replace('_', '.')
results_path = os.path.join(res_dir, results_file)
results = baseml.read(results_path)
# There are 6 top-levels: parameters, tree, lnL, version,
# tree length and lnL max
self.assertEqual(len(results), 6, version_msg)
self.assertTrue("parameters" in results, version_msg)
params = results["parameters"]
self.assertTrue("SEs" in params, version_msg)
def testParseNhomo(self):
res_dir = os.path.join(self.results_dir, "baseml", "nhomo")
for results_file in os.listdir(res_dir):
version = results_file.split('-')[1].split('.')[0]
n = results_file[5]
version_msg = "Improper parsing for nhomo %s version %s" \
% (n, version.replace('_', '.'))
results_path = os.path.join(res_dir, results_file)
results = baseml.read(results_path)
# There are 6 top-levels: parameters, tree, lnL, version,
# tree length and lnL max
self.assertEqual(len(results), 6, version_msg)
self.assertTrue("parameters" in results, version_msg)
params = results["parameters"]
if n == "1":
self.assertTrue("base frequencies" in params, version_msg)
else:
self.assertTrue("nodes" in params)
nodes = params["nodes"]
self.assertEqual(len(nodes), 8, version_msg)
self.assertEqual(len(nodes[1]), 2, version_msg)
def testParseNhomo(self):
res_dir = os.path.join(self.results_dir, "baseml", "nhomo")
for results_file in os.listdir(res_dir):
version = results_file.split('-')[1].split('.')[0]
n = results_file[5]
version_msg = "Improper parsing for nhomo %s version %s" \
% (n, version.replace('_', '.'))
results_path = os.path.join(res_dir, results_file)
results = baseml.read(results_path)
# There are 6 top-levels: parameters, tree, lnL, version,
# tree length and lnL max
self.assertEqual(len(results), 6, version_msg)
self.assertTrue("parameters" in results, version_msg)
params = results["parameters"]
if n == "1":
self.assertTrue("base frequencies" in params, version_msg)
else:
self.assertTrue("nodes" in params)
nodes = params["nodes"]
self.assertEqual(len(nodes), 8, version_msg)
self.assertEqual(len(nodes[1]), 2, version_msg)
def testParseAlpha1Rho1(self):
# Test the auto-discrete gamma model
# Cannot test for baseml 4.3-4.5 due to bug in the program which
# prevents this analysis from completing
res_dir = os.path.join(self.results_dir, "baseml", "alpha1rho1")
for results_file in os.listdir(res_dir):
version = results_file.split('-')[1].split('.')[0]
model = results_file[5]
version_msg = "Improper parsing for model %s version %s" \
% (model, version.replace('_', '.'))
results_path = os.path.join(res_dir, results_file)
results = baseml.read(results_path)
# There are 6 top-levels: parameters, tree, lnL, version,
# tree length and lnL max
self.assertEqual(len(results), 6, version_msg)
self.assertTrue("parameters" in results, version_msg)
params = results["parameters"]
self.assertTrue("rho" in params, version_msg)
self.assertTrue("transition probs." in params, version_msg)
trans_p = params["transition probs."]
self.assertEqual(len(trans_p), 5, version_msg)
self.assertEqual(len(trans_p[0]), 5, version_msg)
def testParseAlpha1Rho1(self):
# Test the auto-discrete gamma model
# Cannot test for baseml 4.3-4.5 due to bug in the program which
# prevents this analysis from completing
res_dir = os.path.join(self.results_dir, "baseml", "alpha1rho1")
for results_file in os.listdir(res_dir):
version = results_file.split('-')[1].split('.')[0]
model = results_file[5]
version_msg = "Improper parsing for model %s version %s" \
% (model, version.replace('_', '.'))
results_path = os.path.join(res_dir, results_file)
results = baseml.read(results_path)
# There are 6 top-levels: parameters, tree, lnL, version,
# tree length and lnL max
self.assertEqual(len(results), 6, version_msg)
self.assertTrue("parameters" in results, version_msg)
params = results["parameters"]
self.assertTrue("rho" in params, version_msg)
self.assertTrue("transition probs." in params, version_msg)
trans_p = params["transition probs."]
self.assertEqual(len(trans_p), 5, version_msg)
self.assertEqual(len(trans_p[0]), 5, version_msg)
def testParseSEs(self):
SE_results_file = os.path.join("PAML", "Results", "baseml",
"baseml_SE.out")
SE_results = baseml.read(SE_results_file)
SE_parameters = SE_results.get("parameters")
self.assertNotEqual(SE_parameters.get("SEs"), None)
def testParseSEs(self):
SE_results_file = os.path.join("PAML", "Results", "baseml",
"baseml_SE.out")
SE_results = baseml.read(SE_results_file)
SE_parameters = SE_results.get("parameters")
self.assertNotEqual(SE_parameters.get("SEs"), None)
