config.py

config.py

@@ -0,0 +1,66 @@
+PEVE_VERSION = "1.1.0"
+THRESHOLD_VERSION = "2024-01"
+
+MODELS = {
+    "splice":  "nileshhanotia/mutation-predictor-splice",
+    "context": "nileshhanotia/mutation-predictor-v4",
+    "protein": "nileshhanotia/mutation-pathogenicity-predictor",
+}
+
+SPLICE_PROB_HIGH        = 0.90
+SPLICE_PROB_MODERATE    = 0.80
+SPLICE_PROB_WEAK        = 0.60
+SPLICE_SIGNAL_MIN       = 0.65
+SPLICE_DOMINANT_MIN     = SPLICE_PROB_HIGH
+
+ACTIVATION_NORM_HIGH     = 0.80
+ACTIVATION_NORM_MODERATE = 0.70
+ACTIVATION_NORM_WEAK     = 0.60
+CONTEXT_ACTIVE_MIN       = ACTIVATION_NORM_MODERATE
+
+SEQUENCE_WINDOW         = 401
+WINDOW_BP               = 401
+WINDOW_HALF             = WINDOW_BP // 2
+PEAK_OFF_CENTER_FRAC    = 0.10
+
+BIOCHEMICAL_RISK_ACTIVE  = 0.60
+AF_RARITY_THRESHOLD      = 0.001
+AF_HIGH_CONFLICT         = 0.010
+BOUNDARY_TOLERANCE       = 0.05
+
+VEP_CONSEQUENCE_MAP = {
+    "missense_variant":             "substitution_missense",
+    "synonymous_variant":           "substitution_synonymous",
+    "stop_gained":                  "stop_gained",
+    "stop_lost":                    "stop_gained",
+    "start_lost":                   "start_lost",
+    "frameshift_variant":           "frameshift",
+    "inframe_insertion":            "in_frame_indel",
+    "inframe_deletion":             "in_frame_indel",
+    "splice_donor_variant":         "canonical_splice",
+    "splice_acceptor_variant":      "canonical_splice",
+    "splice_region_variant":        "canonical_splice",
+    "intron_variant":               "deep_intronic",
+    "5_prime_utr_variant":          "utr_regulatory",
+    "3_prime_utr_variant":          "utr_regulatory",
+    "upstream_gene_variant":        "utr_regulatory",
+    "downstream_gene_variant":      "utr_regulatory",
+    "regulatory_region_variant":    "utr_regulatory",
+}
+
+L3_SUBSTITUTION_INVALID = {
+    "frameshift", "stop_gained", "start_lost", "canonical_splice",
+    "in_frame_indel", "deep_intronic", "utr_regulatory",
+}
+
+GNOMAD_VERSION = "4.0"
+AF_POPULATIONS = ["afr", "amr", "asj", "eas", "fin", "mid", "nfe", "sas"]
+
+BAND_COLORS = {
+    "High":         "#d73027",
+    "Moderate":     "#fc8d59",
+    "Weak":         "#fee090",
+    "Inactive":     "#abd9e9",
+    "Active":       "#4575b4",
+    "Insufficient": "#aaaaaa",
+}