def test_filter_csv_error(self):
expected_str = "Unrecognized filter type 'flagged_cons_fnames'"
args = [
"subset_csv.py", f"{self.dummy_dir}/dummy_table.csv",
"flagged_cons_fnames"
]
real_str, real_code = filter_csv(args)
self.assertEqual(expected_str, real_str)
self.assertEqual(1, real_code)
def test_filter_csv_not_na_cons_fnames_w_dir(self):
expected_str = "dummy_dir/040idSEARCH-5367-SAN_L001_L002_L003_L004.trimmed.sorted.pileup.consensus.fa dummy_dir/041idSEARCH-5368-SAN_L001_L002_L003_L004.trimmed.sorted.pileup.consensus.fa dummy_dir/042idSEARCH-5369-SAN_L001_L002_L003_L004.trimmed.sorted.pileup.consensus.fa dummy_dir/043idSEARCH-5370-SAN_L001_L002_L003_L004.trimmed.sorted.pileup.consensus.fa dummy_dir/044idSEARCH-5371-SAN_L001_L002_L003_L004.trimmed.sorted.pileup.consensus.fa dummy_dir/045idSEARCH-5371-SAN_L001_L002_L003_L004.trimmed.sorted.pileup.consensus.fa" #noqa 501
args = [
"subset_csv.py", f"{self.dummy_dir}/dummy_table.csv",
"not_na_cons_fnames", "dummy_dir"
]
real_str, real_code = filter_csv(args)
self.assertEqual(expected_str, real_str)
self.assertEqual(0, real_code)
def test_filter_csv_indel_flagged_cons_fnames(self):
expected_str = "043idSEARCH-5370-SAN_L001_L002_L003_L004.trimmed.sorted.pileup.consensus.fa 045idSEARCH-5371-SAN_L001_L002_L003_L004.trimmed.sorted.pileup.consensus.fa" #noqa 501
args = [
"subset_csv.py", f"{self.dummy_dir}/dummy_table.csv",
"indel_flagged_cons_fnames"
]
real_str, real_code = filter_csv(args)
self.assertEqual(expected_str, real_str)
self.assertEqual(0, real_code)
def test_filter_csv_filter_lines(self):
output_fp = f"{self.test_temp_dir}/temp_test_filter_lines.csv"
expected_fp = f"{self.dummy_dir}/dummy_filtered_lines.csv"
args = [
"subset_csv.py", f"{self.dummy_dir}/dummy_table.csv",
"filtered_lines", "seq_run",
"210109_A00953_0209_BHYHCVDRXX,PDH_79-233476243", output_fp
]
try:
real_str, real_code = filter_csv(args)
self.assertEqual("", real_str)
self.assertEqual(0, real_code)
self.assertTrue(os.path.isfile(output_fp))
self.assertTrue(filecmp.cmp(output_fp, expected_fp))
finally:
try:
os.remove(output_fp)
except OSError:
pass