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))
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))
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))
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))
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))
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))
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))
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))