def test_partial_settings(valid_partial_settings):
parsed = parse_settings(valid_partial_settings)
assert parsed == {
"primer_min_gc": 20,
"primer_internal_min_gc": 20,
"primer_opt_gc_percent": 50,
"primer_internal_opt_gc_percent": 50,
"primer_max_gc": 80,
"primer_internal_max_gc": 80,
"primer_wt_gc_percent_lt": 0,
"primer_internal_wt_gc_percent_lt": 0,
"primer_wt_gc_percent_gt": 0,
"primer_internal_wt_gc_percent_gt": 0,
"primer_gc_clamp": 1,
"primer_max_end_gc": 0,
"primer_opt_size": 21,
"primer_min_size": 19,
"primer_max_size": 29,
"primer_max_ns_accepted": 1,
"primer_product_size_range": "300-500",
"primer_product_opt_size": 400,
"primer_pair_wt_product_size_gt": 0.12,
"primer_pair_wt_product_size_lt": 0.12,
"primer_min_tm": 55,
"primer_max_tm": 75,
"primer_num_return": 100,
"primer_opt_tm": 60,
"primer_pair_max_diff_tm": 100,
"primer_max_hairpin_th": 47
}
def test_none_settings():
parsed = parse_settings()
assert parsed == {
"primer_min_gc": 20,
"primer_internal_min_gc": 20,
"primer_opt_gc_percent": 50,
"primer_internal_opt_gc_percent": 50,
"primer_max_gc": 80,
"primer_internal_max_gc": 80,
"primer_wt_gc_percent_lt": 0,
"primer_internal_wt_gc_percent_lt": 0,
"primer_wt_gc_percent_gt": 0,
"primer_internal_wt_gc_percent_gt": 0,
"primer_gc_clamp": 0,
"primer_max_end_gc": 5,
"primer_opt_size": 25,
"primer_min_size": 20,
"primer_max_size": 30,
"primer_max_ns_accepted": 0,
"primer_product_size_range": "200-450",
"primer_product_opt_size": 325,
"primer_pair_wt_product_size_gt": 0.1,
"primer_pair_wt_product_size_lt": 0.1,
"primer_min_tm": 58,
"primer_max_tm": 62,
"primer_num_return": 200,
"primer_opt_tm": 60,
"primer_pair_max_diff_tm": 100,
"primer_max_hairpin_th": 47
}
def test_primer3_configuration(settings_json, conf):
parsed_settings = parse_settings(settings_json)
generated_conf = create_primer3_config(parsed_settings, "ACTG", "50-60",
"50-60")
with conf.open("r") as chandle:
expected_conf = chandle.read().strip()
assert generated_conf == expected_conf
def test_primer3_conf_with_params(conf_params):
some_path = Path("/some/path/to/params")
generated_conf = create_primer3_config(parse_settings(),
"ACTG",
"50-60",
"50-60",
thermodynamic_params=some_path)
with conf_params.open("r") as chandle:
expected_conf = chandle.read().strip()
assert generated_conf == expected_conf
def test_primer3_run_non_failing(settings_json, ignored, rCRS):
settings_dict = parse_settings(settings_json)
# assumes primer3_core is on the PATH
primer3_exe = which("primer3_core")
p = Primer3(primer3_exe, rCRS, "3200,300", "3300,50", settings_dict)
p.run()