Commit 79eb5c59 authored by Sander Bollen's avatar Sander Bollen
Browse files

add a few more primer3 settings

parent c77faac1
......@@ -29,6 +29,9 @@ P3_FILE_FLAG=1
SEQUENCE_INTERNAL_EXCLUDED_REGION=37,21
PRIMER_EXPLAIN_FLAG=1
PRIMER_MIN_TM={{ settings.primer_min_tm }}
PRIMER_OPT_TM={{ settings.primer_opt_tm }}
PRIMER_MAX_TM={{ settings.primer_max_tm }}
PRIMER_PAIR_MAX_DIFF_TM={{ settings.primer_pair_max_diff_tm }}
PRIMER_MAX_HAIRPIN_TH={{ settings.primer_max_hairpin_th }}
PRIMER_NUM_RETURN={{ settings.primer_num_return }}
=
\ No newline at end of file
......@@ -127,11 +127,26 @@
"type": "number",
"default": 58
},
"primer_opt_tm": {
"description": "Optimum melting temperature of primer in degrees Celcius",
"type": "number",
"default": 60
},
"primer_max_tm": {
"description": "Maximum melting temperature in degrees Celsius",
"type": "number",
"default": 62
},
"primer_pair_max_diff_tm": {
"description": "Maximum acceptable difference in melting temperature between primers",
"type": "number",
"default": 100,
"minimum": 0
},
"primer_max_hairpin_th": {
"type": "number",
"default": 47
},
"primer_num_return": {
"description": "Number of returned primers. Increase to increase search space",
"type": "integer",
......
......@@ -29,6 +29,9 @@ 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
=
\ No newline at end of file
......@@ -29,6 +29,9 @@ P3_FILE_FLAG=1
SEQUENCE_INTERNAL_EXCLUDED_REGION=37,21
PRIMER_EXPLAIN_FLAG=1
PRIMER_MIN_TM=55
PRIMER_OPT_TM=60
PRIMER_MAX_TM=75
PRIMER_PAIR_MAX_DIFF_TM=100
PRIMER_MAX_HAIRPIN_TH=47
PRIMER_NUM_RETURN=100
=
\ No newline at end of file
......@@ -29,6 +29,9 @@ P3_FILE_FLAG=1
SEQUENCE_INTERNAL_EXCLUDED_REGION=37,21
PRIMER_EXPLAIN_FLAG=1
PRIMER_MIN_TM=55
PRIMER_OPT_TM=60
PRIMER_MAX_TM=75
PRIMER_PAIR_MAX_DIFF_TM=100
PRIMER_MAX_HAIRPIN_TH=47
PRIMER_NUM_RETURN=100
=
\ No newline at end of file
{
"primer_min_size": 18,
"primer_max_size": 25,
"primer_min_tm": 57,
"primer_opt_tm": 60,
"primer_pair_max_diff_tm": 2,
"primer_max_hairpin_th": 47
}
\ No newline at end of file
......@@ -49,7 +49,10 @@ def test_none_settings():
"primer_pair_wt_product_size_lt": 0.1,
"primer_min_tm": 58,
"primer_max_tm": 62,
"primer_num_return": 200
"primer_num_return": 200,
"primer_opt_tm": 60,
"primer_pair_max_diff_tm": 100,
"primer_max_hairpin_th": 47
}
......@@ -77,7 +80,10 @@ def test_complete_settings(valid_settings):
"primer_pair_wt_product_size_lt": 0.12,
"primer_min_tm": 55,
"primer_max_tm": 75,
"primer_num_return": 100
"primer_num_return": 100,
"primer_opt_tm": 60,
"primer_pair_max_diff_tm": 100,
"primer_max_hairpin_th": 47
}
......@@ -106,7 +112,10 @@ def test_partial_settings(valid_partial_settings):
"primer_pair_wt_product_size_lt": 0.12,
"primer_min_tm": 55,
"primer_max_tm": 75,
"primer_num_return": 100
"primer_num_return": 100,
"primer_opt_tm": 60,
"primer_pair_max_diff_tm": 100,
"primer_max_hairpin_th": 47
}
......
......@@ -26,6 +26,7 @@ data_dir = Path(__file__).parent / Path("data")
setting_jsons_data = [
(data_dir / Path("valid_settings.json"), True),
(data_dir / Path("valid_partial_settings.json"), True),
(data_dir / Path("valid_partial_settings2.json"), True),
(data_dir / Path("settings_wrong_types.json"), False),
(data_dir / Path("settings_invalid_values.json"), False)
]
......
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