Python checkFolderEquality Examples

Example #1

File: test_circleseq_std.py Project: simwiki/circleseq

    def testFullPipeline(self):
        c = circleseq.CircleSeq()
        c.parseManifest(TEST_MANIFEST_PATH)

        # Align and test the alignment output
        c.alignReads()
        self.assertTrue(
            utils.checkFolderEquality(
                os.path.join(c.analysis_folder, "aligned"),
                CORRECT_ALIGNED_OUTPUT))

        # Find cleavage sites
        c.findCleavageSites()
        self.assertTrue(
            utils.checkFolderEquality(
                os.path.join(c.analysis_folder, 'identified'),
                CORRECT_IDENTIFIED_OUTPUT))

        # Visualize filtered sites
        c.visualize()
        self.assertTrue(
            utils.checkFolderEquality(
                os.path.join(c.analysis_folder, 'visualization'),
                CORRECT_VISUALIZATION_OUTPUT))

        # Look for genomic variants
        c.callVariants()
        self.assertTrue(
            utils.checkFolderEquality(
                os.path.join(c.analysis_folder, 'variants'),
                CORRECT_VARIANTS_OUTPUT))

Example #2

File: test_umitag.py Project: bh0085/multi-umi

    def testUMITagTestCase(self):
        # Run the umitag module on the test data
        umitag.umitag(TEST_DATA_FILES['read1'], TEST_DATA_FILES['read2'],
                      TEST_DATA_FILES['index1'], TEST_DATA_FILES['index2'],
                      TEST_DATA_FILES['read1_out'],
                      TEST_DATA_FILES['read2_out'], TEST_OUTPUT_PATH)

        self.assertTrue(
            utils.checkFolderEquality(TEST_OUTPUT_PATH,
                                      CORRECT_UMITAGGED_OUTPUT_FOLDER))

Example #3

File: test_demultiplex.py Project: alliemacleay/umi

    def testDemultiplexTestCase(self):
        # Run the demultiplex module on the test data
        demultiplex.demultiplex(TEST_DATA_FILES['read1'],
                                TEST_DATA_FILES['read2'],
                                TEST_DATA_FILES['index1'],
                                TEST_DATA_FILES['index2'],
                                TEST_SAMPLE_BARCODES,
                                TEST_OUTPUT_PATH,
                                min_reads=TEST_MIN_READS)

        self.assertTrue(utils.checkFolderEquality(TEST_OUTPUT_PATH, CORRECT_DEMULTIPLEX_OUTPUT_FOLDER))

Example #4

File: test_umitag.py Project: alliemacleay/umi

    def testUMITagTestCase(self):
        # Run the umitag module on the test data
        umitag.umitag(TEST_DATA_FILES['read1'],
                                TEST_DATA_FILES['read2'],
                                TEST_DATA_FILES['index1'],
                                TEST_DATA_FILES['index2'],
                                TEST_DATA_FILES['read1_out'],
                                TEST_DATA_FILES['read2_out'],
                                TEST_OUTPUT_PATH)

        self.assertTrue(utils.checkFolderEquality(TEST_OUTPUT_PATH, CORRECT_UMITAGGED_OUTPUT_FOLDER))

Example #5

File: test_guideseq.py Project: aryeelab/guideseq

    def testFullPipeline(self):
        g = guideseq.GuideSeq()
        g.parseManifest(TEST_MANIFEST_PATH)

        # Demultiplex and test the demultiplex output
        g.demultiplex()
        self.assertTrue(utils.checkFolderEquality(os.path.join(TEST_OUTPUT_PATH, 'demultiplexed'), CORRECT_DEMULTIPLEXED_OUTPUT))

        # UMITag and test the umitagging output
        g.umitag()
        self.assertTrue(utils.checkFolderEquality(os.path.join(TEST_OUTPUT_PATH, 'umitagged'), CORRECT_UMITAGGED_OUTPUT))

        # Consolidate and test the consolidation output
        g.consolidate()
        self.assertTrue(utils.checkFolderEquality(os.path.join(TEST_OUTPUT_PATH, 'consolidated'), CORRECT_CONSOLDIATED_OUTPUT))

        # Align and test the alignment output
        g.alignReads()
        self.assertTrue(utils.checkFolderEquality(os.path.join(TEST_OUTPUT_PATH, 'aligned'), CORRECT_ALIGNED_OUTPUT))

        # Identify offtargets and test the output
        g.identifyOfftargetSites()
        self.assertTrue(utils.checkFolderEquality(os.path.join(TEST_OUTPUT_PATH, 'identified'), CORRECT_IDENTIFIED_OUTPUT))

        # Filter background sites and test if correct
        g.filterBackgroundSites()
        self.assertTrue(utils.checkFolderEquality(os.path.join(TEST_OUTPUT_PATH, 'filtered'), CORRECT_FILTERED_OUTPUT))

Example #6

File: test_consolidate.py Project: alliemacleay/umi

    def testConsolidateTestCase(self):
        # Run the consolidation module on the test data
        consolidate.consolidate(TEST_DATA_FILES['read1'],
                                TEST_DATA_FILES['read1_out'],
                                TEST_MIN_QUAL,
                                TEST_MIN_FREQ)

        consolidate.consolidate(TEST_DATA_FILES['read2'],
                                TEST_DATA_FILES['read2_out'],
                                TEST_MIN_QUAL,
                                TEST_MIN_FREQ)

        self.assertTrue(utils.checkFolderEquality(TEST_OUTPUT_PATH, CORRECT_UMITAGGED_OUTPUT_FOLDER))

Example #7

    def testConsolidateTestCase(self):
        # Run the consolidation module on the test data
        consolidate.consolidate(TEST_DATA_FILES['read1'],
                                TEST_DATA_FILES['read1_out'], TEST_MIN_QUAL,
                                TEST_MIN_FREQ)

        consolidate.consolidate(TEST_DATA_FILES['read2'],
                                TEST_DATA_FILES['read2_out'], TEST_MIN_QUAL,
                                TEST_MIN_FREQ)

        self.assertTrue(
            utils.checkFolderEquality(TEST_OUTPUT_PATH,
                                      CORRECT_UMITAGGED_OUTPUT_FOLDER))

Example #8

    def testFullPipeline(self):
        g = guideseq.GuideSeq()
        g.parseManifest(TEST_MANIFEST_PATH)

        # Demultiplex and test the demultiplex output
        g.demultiplex()
        self.assertTrue(
            utils.checkFolderEquality(
                os.path.join(TEST_OUTPUT_PATH, 'demultiplexed'),
                CORRECT_DEMULTIPLEXED_OUTPUT))

        # UMITag and test the umitagging output
        g.umitag()
        self.assertTrue(
            utils.checkFolderEquality(
                os.path.join(TEST_OUTPUT_PATH, 'umitagged'),
                CORRECT_UMITAGGED_OUTPUT))

        # Consolidate and test the consolidation output
        g.consolidate()
        self.assertTrue(
            utils.checkFolderEquality(
                os.path.join(TEST_OUTPUT_PATH, 'consolidated'),
                CORRECT_CONSOLDIATED_OUTPUT))

        # Align and test the alignment output
        g.alignReads()
        self.assertTrue(
            utils.checkFolderEquality(
                os.path.join(TEST_OUTPUT_PATH, 'aligned'),
                CORRECT_ALIGNED_OUTPUT))

        # Identify offtargets and test the output
        g.identifyOfftargetSites()
        self.assertTrue(
            utils.checkFolderEquality(
                os.path.join(TEST_OUTPUT_PATH, 'identified'),
                CORRECT_IDENTIFIED_OUTPUT))

        # Filter background sites and test if correct
        g.filterBackgroundSites()
        self.assertTrue(
            utils.checkFolderEquality(
                os.path.join(TEST_OUTPUT_PATH, 'filtered'),
                CORRECT_FILTERED_OUTPUT))