def test_duplicate_subreads(self):
"""Test that report doesn't crash on duplicate subreads"""
output_dir = tempfile.mkdtemp(suffix="_mapping_stats")
with warnings.catch_warnings(record=True) as w:
report = to_report(self.bam_file, output_dir)
shutil.rmtree(output_dir)
self.assertTrue(w >= 4)
def test_duplicate_subreads(self):
"""Test that report doesn't crash on duplicate subreads"""
output_dir = tempfile.mkdtemp(suffix="_mapping_stats")
with warnings.catch_warnings(record=True) as w:
report = to_report(self.bam_file, output_dir)
shutil.rmtree(output_dir)
self.assertTrue(w >= 4)
def setUpClass(cls):
cls.output_dir = tempfile.mkdtemp(suffix="_mapping_stats")
t = tempfile.NamedTemporaryFile(
delete=False, suffix="mapping_report.json")
t.close()
cls.report_json = t.name
cls.report = to_report(cls._get_input_file(), cls.output_dir)
cls.report.write_json(cls.report_json)
assert isinstance(cls.report, Report)
log.info(pprint.pformat(cls.report.to_dict()))
for table in cls.report.tables:
log.info(str(table))
def setUpClass(cls):
cls.output_dir = tempfile.mkdtemp(suffix="_mapping_stats")
t = tempfile.NamedTemporaryFile(delete=False,
suffix="mapping_report.json")
t.close()
cls.report_json = t.name
cls.report = to_report(cls._get_input_file(), cls.output_dir)
cls.report.write_json(cls.report_json)
assert isinstance(cls.report, Report)
log.info(pprint.pformat(cls.report.to_dict()))
for table in cls.report.tables:
log.info(str(table))
def setUpClass(cls):
_to_p = lambda x: os.path.join(_GMAP_DATA_DIR, x)
cls.output_dir = tempfile.mkdtemp(suffix="_mapping_stats")
cls.input_fofn = _to_p('input.fofn')
cls.aligned_reads_cmph5 = _to_p('aligned_reads.cmp.h5')
t = tempfile.NamedTemporaryFile(
delete=False, suffix="mapping_report.json")
t.close()
cls.report_json = t.name
cls.report = to_report(cls.aligned_reads_cmph5, cls.output_dir)
if isinstance(cls.report, Report):
log.info(pprint.pformat(cls.report.to_dict()))
for table in cls.report.tables:
log.info(str(table))
def setUpClass(cls):
_to_p = lambda x: op.join(_GMAP_DATA_DIR, x)
cls.output_dir = tempfile.mkdtemp(suffix="_mapping_stats")
cls.input_fofn = _to_p('input.fofn')
cls.aligned_reads_cmph5 = _to_p('aligned_reads.cmp.h5')
t = tempfile.NamedTemporaryFile(delete=False,
suffix="mapping_report.json")
t.close()
cls.report_json = t.name
cls.report = to_report(cls.aligned_reads_cmph5, cls.output_dir)
if isinstance(cls.report, Report):
log.info(pprint.pformat(cls.report.to_dict()))
for table in cls.report.tables:
log.info(str(table))
