Example #1
0
    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())
Example #2
0
    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())
Example #3
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    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())
Example #4
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    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())
Example #5
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    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())
Example #6
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    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())
Example #7
0
    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())