def test_generate_parameters_string_error(self):
parameters = {
"min_seq_len": 200, "max_seq_len": 1000, "trim_seq_length": False,
"min_qual_score": 25, "max_ambig": 6, "max_homopolymer": 6,
"max_primer_mismatch": 0, "barcode_type": "golay_12",
"max_barcode_errors": 1.5, "disable_bc_correction": False,
"qual_score_window": 0, "disable_primers": False,
"reverse_primers": "whops", "reverse_primer_mismatches": 0,
"truncate_ambi_bases": False, "input_data": 1}
with self.assertRaises(ValueError):
generate_parameters_string(parameters)
def test_generate_parameters_string(self):
parameters = {
"min_seq_len": 200,
"max_seq_len": 1000,
"trim_seq_length": False,
"min_qual_score": 25,
"max_ambig": 6,
"max_homopolymer": 6,
"max_primer_mismatch": 0,
"barcode_type": "golay_12",
"max_barcode_errors": 1.5,
"disable_bc_correction": False,
"qual_score_window": 0,
"disable_primers": False,
"reverse_primers": "disable",
"reverse_primer_mismatches": 0,
"truncate_ambi_bases": False,
"input_data": 1
}
obs = generate_parameters_string(parameters)
exp = ("--min_seq_len 200 --max_seq_len 1000 --min_qual_score 25 "
"--max_ambig 6 --max_homopolymer 6 --max_primer_mismatch 0 "
"--barcode_type golay_12 --max_barcode_errors 1.5 "
"--qual_score_window 0 --reverse_primer_mismatches 0 "
"--reverse_primers disable")
self.assertEqual(obs, exp)
def test_generate_parameters_string_error(self):
parameters = {
"min_seq_len": 200,
"max_seq_len": 1000,
"trim_seq_length": False,
"min_qual_score": 25,
"max_ambig": 6,
"max_homopolymer": 6,
"max_primer_mismatch": 0,
"barcode_type": "golay_12",
"max_barcode_errors": 1.5,
"disable_bc_correction": False,
"qual_score_window": 0,
"disable_primers": False,
"reverse_primers": "whops",
"reverse_primer_mismatches": 0,
"truncate_ambi_bases": False,
"input_data": 1
}
with self.assertRaises(ValueError):
generate_parameters_string(parameters)
def test_generate_parameters_string(self):
parameters = {
"min_seq_len": 200, "max_seq_len": 1000, "trim_seq_length": False,
"min_qual_score": 25, "max_ambig": 6, "max_homopolymer": 6,
"max_primer_mismatch": 0, "barcode_type": "golay_12",
"max_barcode_errors": 1.5, "disable_bc_correction": False,
"qual_score_window": 0, "disable_primers": False,
"reverse_primers": "disable", "reverse_primer_mismatches": 0,
"truncate_ambi_bases": False, "input_data": 1}
obs = generate_parameters_string(parameters)
exp = ("--min_seq_len 200 --max_seq_len 1000 --min_qual_score 25 "
"--max_ambig 6 --max_homopolymer 6 --max_primer_mismatch 0 "
"--barcode_type golay_12 --max_barcode_errors 1.5 "
"--qual_score_window 0 --reverse_primer_mismatches 0 "
"--reverse_primers disable")
self.assertEqual(obs, exp)