def test_execute_pham_review_1(self):
"""Verify execute_pham_review() creates new directory as expected.
"""
pham_review.execute_pham_review(self.alchemist,
folder_path=self.test_dir,
folder_name=self.review_test_dir.name)
self.assertTrue(self.review_test_dir.is_dir())
def test_execute_pham_review_5(self):
"""Verify execute_pham_review() review parameter functions as expected.
"""
pham_review.execute_pham_review(self.alchemist,
folder_path=self.test_dir,
folder_name=self.review_test_dir.name,
no_review=True)
self.assertTrue(self.review_test_dir.is_dir())
def test_execute_pham_review_4(self):
"""Verify execute_pham_review() sort parameter functions as expected.
"""
pham_review.execute_pham_review(self.alchemist,
folder_path=self.test_dir,
folder_name=self.review_test_dir.name,
sort=["gene.Name"])
self.assertTrue(self.review_test_dir.is_dir())
def test_execute_pham_review_2(self):
"""Verify execute_pham_review() filter parameter functions as expected.
"""
pham_review.execute_pham_review(self.alchemist,
folder_path=self.test_dir,
folder_name=self.review_test_dir.name,
filters=("phage.Cluster='A' "
"AND phage.Subcluster='A2'"))
self.assertTrue(self.review_test_dir.is_dir())
def test_execute_pham_review_3(self):
"""Verify execute_pham_review() group parameter functions as expected.
"""
pham_review.execute_pham_review(self.alchemist,
folder_path=self.test_dir,
folder_name=self.review_test_dir.name,
groups=["phage.Cluster"])
self.assertTrue(self.review_test_dir.is_dir())
clusterA_dir = self.review_test_dir.joinpath("A")
self.assertTrue(clusterA_dir.is_dir())
def test_execute_pham_review_8(self):
"""Verify execute_pham_review() psr_reports parameter functions as expected.
"""
pham_review.execute_pham_review(self.alchemist,
folder_path=self.test_dir,
folder_name=self.review_test_dir.name,
psr_reports=True)
self.assertTrue(self.review_test_dir.is_dir())
pham_report_dir = self.review_test_dir.joinpath("PhamReports")
self.assertTrue(pham_report_dir.is_dir())
def test_execute_pham_review_7(self):
"""Verify execute_pham_review() s_report parameter functions as expected.
"""
pham_review.execute_pham_review(self.alchemist,
folder_path=self.test_dir,
folder_name=self.review_test_dir.name,
s_report=True)
self.assertTrue(self.review_test_dir.is_dir())
summary_report_file = self.review_test_dir.joinpath(
"SummaryReport.txt")
self.assertTrue(summary_report_file.is_file())