Merge pull request #36 from cov-lineages/add_b.1.1.529

Add B.1.1.529 constellation

constellations/__init__.py

@@ -1,3 +1,3 @@
 _program = "constellations"
-__version__ = "v0.0.21"
+__version__ = "v0.0.22"
 

constellations/definitions/cB.1.1.529.json

@@ -0,0 +1,78 @@
+{
+    "label": "B.1.1.529-like",
+    "description": "B.1.1.529 lineage defining mutations",
+    "sources": [
+    ],
+    "type": "variant",
+    "variant": {
+        "Pango_lineages": [
+            "B.1.1.529"
+        ],
+	"mrca_lineage": "B.1.1.529",
+        "representative_genome": ""
+    },
+    "tags": [
+        "B.1.1.529"
+    ],
+    "sites": [
+        "del:6513:3",
+        "del:11283:9",
+        "nuc:C241T",
+        "orf1a:K856R",
+        "nuc:C3037T",
+        "nuc:T5386G",
+        "orf1a:A2710T",
+        "orf1a:T3255I",
+        "orf1a:P3395H",
+        "orf1a:I3758V",
+        "nuc:T13195C",
+        "orf1b:P314L",
+        "nuc:C15240T",
+        "orf1b:I1566V",
+        "spike:A67V",
+        "spike:T95I",
+        "spike:G339D",
+        "spike:S371L",
+        "spike:S373P",
+        "spike:K417N",
+        "spike:N440K",
+        "spike:G446S",
+        "spike:S477N",
+        "spike:T478K",
+        "spike:E484A",
+        "spike:Q493R",
+        "spike:G496S",
+        "spike:Q498R",
+        "spike:N501Y",
+        "spike:T547K",
+        "spike:D614G",
+        "spike:H655Y",
+        "spike:N679K",
+        "spike:P681H",
+        "spike:N764K",
+        "spike:D796Y",
+        "spike:N856K",
+        "spike:Q954H",
+        "spike:N969K",
+        "nuc:C25000T",
+        "e:T9I",
+        "m:D3G",
+        "m:Q19E",
+        "m:A63T",
+        "nuc:A27259C",
+        "nuc:C27807T",
+        "n:RG203KR"
+    ],
+    "note": "We have included spike mutations S477N T478K E484A Q493R G496S Q498R N501Y, but these drop out in some early sequences. Additional rules have been added to compensate.",
+    "rules": {
+        "min_alt": 32,
+        "max_ref": 3,
+        "spike:S477N": "not ref",
+        "spike:T478K": "not ref",
+        "spike:E484A": "not ref",
+        "spike:Q493R": "not ref",
+        "spike:G496S": "not ref",
+        "spike:Q498R": "not ref",
+        "spike:N501Y": "not ref"
+    }
+}