Merge pull request #28 from cov-lineages/dev

Dev
cov-lineages · Oct 19, 2021 · c942142 · c942142
2 parents cc5db67 + 1189ea9
commit c942142
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Showing 4 changed files with 105 additions and 23 deletions.
diff --git a/constellations/__init__.py b/constellations/__init__.py
@@ -1,3 +1,3 @@
 _program = "constellations"
-__version__ = "v0.0.16"
+__version__ = "v0.0.17"
 
diff --git a/constellations/definitions/cAY.4.2.json b/constellations/definitions/cAY.4.2.json
@@ -1,25 +1,40 @@
 {
-	"label": "Delta (AY.4.2-like)",
-	"description": "AY.4.2 lineage defining mutations",
-	"sources": [
+    "label": "Delta (AY.4.2-like)",
+    "description": "AY.4.2 lineage defining mutations",
+    "sources": [
+    ],
+    "type": "variant",
+    "variant": {
+	"Pango_lineages": [
+	    "AY.4.2"
 	],
-	"type": "variant",
-	"variant": {
-		"Pango_lineages": [
-			"AY.4.2"
-		],
-		"mrca_lineage": "AY.4.2",
-		"representative_genome": ""
-	},
-	"tags": [
-		"AY.4.2"
-	],
-	"sites": [
-		"s:Y145H",
-		"s:A222V"
-	],
-	"rules": {
-		"min_alt": 2,
-		"max_ref": 0
-	}
+	"mrca_lineage": "AY.4.2",
+        "lineage_name": "AY.4.2",
+        "parent_lineage": "AY.4",
+	"representative_genome": ""
+    },
+    "tags": [
+	"AY.4.2"
+    ],
+    "sites": [
+        "nuc:T17040C",
+        "spike:A222V",
+        "nuc:C25614T",
+        "spike:Y145H"
+    ],
+    "intermediate": [
+        "del:22029:6:0.961207",
+        "nuc:G210T:0.978338",
+        "nuc:C241T:0.978338",
+        "spike:T95I:0.978338",
+        "spike:G142D:0.978338",
+        "spike:D950N:0.978338"
+    ],
+    "rules": {
+        "min_alt": 3,
+        "max_ref": 1,
+        "spike:Y145H": "alt",
+        "spike:A222V": "not ref",
+        "nuc:T17040C": "alt"
+    }
 }
diff --git a/constellations/definitions/cAY.4.json b/constellations/definitions/cAY.4.json
@@ -0,0 +1,66 @@
+{
+    "label": "Delta (AY.4-like)",
+    "description": "AY.4 lineage defining mutations",
+    "sources": [
+    ],
+    "type": "variant",
+    "variant": {
+	"Pango_lineages": [
+	    "AY.4"
+	],
+	"mrca_lineage": "AY.4",
+        "lineage_name": "AY.4",
+        "parent_lineage": "B.1.617.2",
+	"representative_genome": ""
+    },
+    "tags": [
+	"AY.4"
+    ],
+    "sites": [
+        "del:28271:1",
+        "del:22029:6",
+        "del:28248:6",
+        "nuc:C241T",
+        "nuc:C3037T",
+        "orf1a:A1306S",
+        "orf1a:P2046L",
+        "orf1a:P2287S",
+        "orf1a:A2529V",
+        "nuc:C8986T",
+        "orf1a:V2930L",
+        "orf1a:T3255I",
+        "orf1a:T3646A",
+        "nuc:A11332G",
+        "orf1b:P314L",
+        "orf1b:G662S",
+        "orf1b:P1000L",
+        "orf1b:A1918V",
+        "spike:T19R",
+        "spike:L452R",
+        "spike:T478K",
+        "spike:D614G",
+        "spike:P681R",
+        "spike:D950N",
+        "orf3a:S26L",
+        "m:I82T",
+        "orf7a:V82A",
+        "orf7a:T120I",
+        "nuc:C27874T",
+        "n:D63G",
+        "n:R203M",
+        "n:G215C",
+        "n:D377Y",
+        "nuc:G29742T"
+    ],
+    "intermediate": [
+        "nuc:G210T:0.976009",
+        "nuc:T17040C:0.976009",
+        "spike:T95I:0.976009",
+        "spike:G142D:0.976009"
+    ],
+    "rules": {
+        "min_alt": 31,
+        "max_ref": 3,
+        "orf1a:A2529V": "alt"
+    }
+}
diff --git a/constellations/definitions/cB.1.617.2.json b/constellations/definitions/cB.1.617.2.json
@@ -12,6 +12,7 @@
             "AY.2"
         ],
 	    "mrca_lineage": "B.1.617.2",
+        "lineage_name": "B.1.617.2",
         "incompatible_lineage_calls": [
             "AY.1",
             "AY.2"
-Original file line number
+Diff line change
@@ Expand Up / @@ -12,6 +12,7 @@ @@
                 "AY.2"
             ],
     	    "mrca_lineage": "B.1.617.2",
+            "lineage_name": "B.1.617.2",
             "incompatible_lineage_calls": [
                 "AY.1",
                 "AY.2"
@@ Expand Down @@