Commit ec1b3935 authored by Sander Bollen's avatar Sander Bollen
Browse files

add test for thermodynamic params

parent c3006d80
SEQUENCE_ID=prinia_template
SEQUENCE_TEMPLATE=ACTG
SEQUENCE_TARGET=50-60
SEQUENCE_EXCLUDED_REGION=50-60
PRIMER_TASK=pick_detection_primers
PRIMER_PICK_LEFT_PRIMER=1
PRIMER_PICK_INTERNAL_OLIGO=0
PRIMER_PICK_RIGHT_PRIMER=1
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
P3_FILE_FLAG=1
SEQUENCE_INTERNAL_EXCLUDED_REGION=37,21
PRIMER_EXPLAIN_FLAG=1
PRIMER_MIN_TM=58
PRIMER_OPT_TM=60
PRIMER_MAX_TM=62
PRIMER_PAIR_MAX_DIFF_TM=100
PRIMER_MAX_HAIRPIN_TH=47
PRIMER_NUM_RETURN=200
PRIMER_THERMODYNAMIC_PARAMETERS_PATH=/some/path/to/params
=
\ No newline at end of file
......@@ -146,6 +146,24 @@ def test_primer3_configuration(settings_json, conf):
assert generated_conf == expected_conf
@pytest.fixture
def conf_params():
return (data_dir /
Path("primer3_conf_default_with_thermodynamic_params.txt"))
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
@pytest.fixture
def rCRS():
rCRS_path = data_dir / Path("rCRS.fa")
......
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