def test_basic(self):
"""Basic smoke test"""
output_dir = tempfile.mkdtemp()
report = to_report(self.ccs_set, output_dir)
validate_report_complete(self, report)
d = report.to_dict()
self.assertIsNotNone(d)
def test_ccs_mulitple_movies_single_bam(self):
"""
Check that the report doesn't crash when a single BAM file contains
reads from multiple movies
"""
ds = ConsensusReadSet(self.CCS_BAM)
r = to_report(ds, tempfile.mkdtemp())
def test_ccs_barcodes_table_asymmetric(self):
CCS_DS = op.join(ROOT_DATA_DIR, "ccs", "asym_barcodes",
"ccs.consensusreadset.xml")
ds = ConsensusReadSet(CCS_DS)
r = to_report(ds, tempfile.mkdtemp())
self.assertEqual(r.tables[1].columns[0].values,
['F5, R5', 'F8, R8', 'F20, R20', 'F29, R29', 'F30, R30'])
def test_basic(self):
"""Basic smoke test"""
output_dir = tempfile.mkdtemp()
report = to_report(self.ccs_set, output_dir)
validate_report_complete(self, report)
d = report.to_dict()
self.assertIsNotNone(d)
def test_ccs_barcodes_table_asymmetric(self):
CCS_DS = op.join(ROOT_DATA_DIR, "ccs", "asym_barcodes",
"ccs.consensusreadset.xml")
ds = ConsensusReadSet(CCS_DS)
r = to_report(ds, tempfile.mkdtemp())
self.assertEqual(r.tables[1].columns[0].values,
['F5--R5', 'F8--R8', 'F20--R20', 'F29--R29', 'F30--R30'])
def test_ccs_mulitple_movies_single_bam(self):
"""
Check that the report doesn't crash when a single BAM file contains
reads from multiple movies
"""
ds = ConsensusReadSet(self.CCS_BAM)
r = to_report(ds, tempfile.mkdtemp())
def test_ccs_barcodes_table(self):
ds = ConsensusReadSet(self.CCS_DS)
r = to_report(ds, tempfile.mkdtemp())
self.assertEqual([c.values for c in r.tables[1].columns[0:4]],
[["lbc1", "lbc3"], [1,1], [1958,1954], [1958,1954]])
self.assertAlmostEqual(r.tables[1].columns[4].values[0], 0.9724,
places=4)
self.assertAlmostEqual(r.tables[1].columns[4].values[1], 0.9926,
places=4)
def test_ccs_barcodes_table(self):
CCS_DS = pbtestdata.get_file("ccs-barcoded")
ds = ConsensusReadSet(CCS_DS)
r = to_report(ds, tempfile.mkdtemp())
self.assertEqual([c.values for c in r.tables[1].columns[0:4]],
[["lbc1--lbc1", "lbc3--lbc3"], [1, 1], [1958, 1954], [1958, 1954]])
self.assertAlmostEqual(r.tables[1].columns[4].values[0], 0.9724,
places=4)
self.assertAlmostEqual(r.tables[1].columns[4].values[1], 0.9926,
places=4)
def setUpClass(cls):
cls.output_dir = tempfile.mkdtemp()
cls.ccs_set = ConsensusReadSet(cls.XML_FILE)
cls.report = to_report(cls.ccs_set, cls.output_dir)
def setUpClass(cls):
cls.setUpData()
output_dir = tempfile.mkdtemp()
cls.ccs_set = ConsensusReadSet(cls.xml_file_name)
cls.report = to_report(cls.ccs_set, output_dir)
cls.output_dir = output_dir
def setUpClass(cls):
cls.output_dir = tempfile.mkdtemp()
cls.ccs_set = ConsensusReadSet(cls.XML_FILE)
cls.report = to_report(cls.ccs_set, cls.output_dir)
