def setUpClass(cls):
name = "filtered_subread_summary.csv"
cls.filtered_subread_summary_csv = os.path.join(ROOT_DATA_DIR, _DATA_DIR_NAME, name)
log.info("Using {f}".format(f=cls.filtered_subread_summary_csv))
output_dir = tempfile.mkdtemp(suffix="filter_subread_")
t = tempfile.NamedTemporaryFile(delete=False, suffix=".json")
t.close()
cls.report_json = t.name
cls.report = to_report(cls.filtered_subread_summary_csv, output_dir)
cls.output_dir = output_dir
def test_basic(self):
name = "filtered_subread_summary_no_passed.csv"
filtered_subread_summary_csv = os.path.join(ROOT_DATA_DIR, _DATA_DIR_NAME, name)
log.info("Using {f}".format(f=filtered_subread_summary_csv))
output_dir = tempfile.mkdtemp(suffix="filter_subread_")
t = tempfile.NamedTemporaryFile(delete=False, suffix=".json")
t.close()
with self.assertRaises(NoSubreadsPassedFilter):
report = to_report(filtered_subread_summary_csv, output_dir)
log.info(report)
def setUpClass(cls):
name = "filtered_subread_summary.csv"
cls.filtered_subread_summary_csv = os.path.join(
ROOT_DATA_DIR, _DATA_DIR_NAME, name)
log.info("Using {f}".format(f=cls.filtered_subread_summary_csv))
output_dir = tempfile.mkdtemp(suffix="filter_subread_")
t = tempfile.NamedTemporaryFile(delete=False, suffix=".json")
t.close()
cls.report_json = t.name
cls.report = to_report(cls.filtered_subread_summary_csv, output_dir)
cls.output_dir = output_dir
def test_basic(self):
name = "filtered_subread_summary_no_passed.csv"
filtered_subread_summary_csv = os.path.join(ROOT_DATA_DIR,
_DATA_DIR_NAME, name)
log.info("Using {f}".format(f=filtered_subread_summary_csv))
output_dir = tempfile.mkdtemp(suffix="filter_subread_")
t = tempfile.NamedTemporaryFile(delete=False, suffix=".json")
t.close()
with self.assertRaises(NoSubreadsPassedFilter):
report = to_report(filtered_subread_summary_csv, output_dir)
log.info(report)
