[med-svn] [Git][med-team/constellations][upstream] New upstream version 0.1.12
Andreas Tille (@tille)
gitlab at salsa.debian.org
Tue Aug 22 19:27:26 BST 2023
Andreas Tille pushed to branch upstream at Debian Med / constellations
Commits:
b5559d69 by Andreas Tille at 2023-08-22T16:38:15+02:00
New upstream version 0.1.12
- - - - -
23 changed files:
- constellations/__init__.py
- constellations/definitions/cA.23.1+E484K.json
- constellations/definitions/cAV1.json
- constellations/definitions/cAY.4.2.json
- constellations/definitions/cB.1.1.318.json
- constellations/definitions/cB.1.1.529.json
- constellations/definitions/cB.1.525.json
- constellations/definitions/cB.1.617.1.json
- constellations/definitions/cB.1.617.3.json
- constellations/definitions/cBA.1.json
- constellations/definitions/cBA.2.json
- constellations/definitions/cBA.4.json
- constellations/definitions/cBA.5.json
- constellations/definitions/cC.37.json
- constellations/definitions/cP.2.json
- constellations/definitions/cP.3.json
- + constellations/definitions/cXBB-parent1.json
- + constellations/definitions/cXBB-parent2.json
- + constellations/definitions/cXBB.1.16.json
- + constellations/definitions/cXBB.1.5.json
- + constellations/definitions/cXBB.1.json
- + constellations/definitions/cXBB.json
- constellations/definitions/cXE.json
Changes:
=====================================
constellations/__init__.py
=====================================
@@ -1,3 +1,3 @@
_program = "constellations"
-__version__ = "v0.1.10"
+__version__ = "v0.1.12"
=====================================
constellations/definitions/cA.23.1+E484K.json
=====================================
@@ -9,14 +9,15 @@
"Pango_lineages": [
"A.23.1"
],
- "mrca_lineage": "A.23.1",
- "PHE_label": "VUI-21FEB-01",
+ "mrca_lineage": "A.23.1",
+ "PHE_label": "V-21FEB-01",
"representative_genome": ""
},
"tags": [
"A.23.1",
"VUI-21FEB-01",
- "VUI202102/01"
+ "VUI202102/01",
+ "V-21FEB-01"
],
"sites": [
"nsp3:L741F",
=====================================
constellations/definitions/cAV1.json
=====================================
@@ -9,11 +9,12 @@
"AV.1"
],
"mrca_lineage": "AV.1",
- "PHE_label": "VOC-20-DEC-01",
+ "PHE_label": "VOC-20DEC-01",
"representative_genome": ""
},
"tags": [
- "AV.1"
+ "AV.1",
+ "VOC-20DEC-01"
],
"sites": [
"s:D80G",
=====================================
constellations/definitions/cAY.4.2.json
=====================================
@@ -6,16 +6,17 @@
"type": "variant",
"variant": {
"Pango_lineages": [
- "AY.4.2"
+ "AY.4.2"
],
"mrca_lineage": "AY.4.2",
"lineage_name": "AY.4.2",
"parent_lineage": "AY.4",
- "PHE_label": "VUI-21OCT-01",
+ "PHE_label": "V-21OCT-01",
"representative_genome": ""
},
"tags": [
- "AY.4.2"
+ "AY.4.2",
+ "V-21OCT-01"
],
"sites": [
"nuc:T17040C",
=====================================
constellations/definitions/cB.1.1.318.json
=====================================
@@ -9,14 +9,15 @@
"Pango_lineages": [
"B.1.1.318"
],
- "mrca_lineage": "B.1.1.318",
- "PHE_label": "VUI-21FEB-04",
+ "mrca_lineage": "B.1.1.318",
+ "PHE_label": "V-21FEB-04",
"representative_genome": ""
},
"tags": [
"B.1.1.318",
"VUI-21FEB-04",
- "VUI202102/04"
+ "VUI202102/04",
+ "V-21FEB-04"
],
"sites": [
"nuc:C3961T",
=====================================
constellations/definitions/cB.1.1.529.json
=====================================
@@ -28,7 +28,6 @@
"spike:G339D",
"spike:S373P",
"spike:S375F",
- "spike:K417N",
"spike:N440K",
"spike:S477N",
"spike:T478K",
@@ -57,7 +56,7 @@
"rules": {
"default": {
"min_alt": 22,
- "max_ref": 2,
+ "max_ref": 3,
"spike:D614G": "not ref"
},
"Probable": {
=====================================
constellations/definitions/cB.1.525.json
=====================================
@@ -9,8 +9,8 @@
"Pango_lineages": [
"B.1.525"
],
- "mrca_lineage": "B.1.525",
- "PHE_label": "VUI-21FEB-03",
+ "mrca_lineage": "B.1.525",
+ "PHE_label": "V-21FEB-03",
"WHO_label": "Eta",
"representative_genome": ""
},
@@ -20,7 +20,8 @@
"VUI202102/03",
"Eta",
"G/484K.V3",
- "20A"
+ "20A",
+ "V-21FEB-03"
],
"sites": [
"nuc:C1498T",
=====================================
constellations/definitions/cB.1.617.1.json
=====================================
@@ -10,13 +10,14 @@
"Pango_lineages": [
"B.1.617.1"
],
- "mrca_lineage": "B.1.617.1",
- "PHE_label": "VUI-21APR-01",
+ "mrca_lineage": "B.1.617.1",
+ "PHE_label": "V-21APR-01",
"representative_genome": ""
},
"tags": [
"B.1.617.1",
- "VUI-21APR-01"
+ "VUI-21APR-01",
+ "V-21APR-01"
],
"sites": [
"nuc:C3457T",
=====================================
constellations/definitions/cB.1.617.3.json
=====================================
@@ -10,12 +10,13 @@
"B.1.617.3"
],
"mrca_lineage": "B.1.617.3",
- "PHE_label": "VUI-21APR-03",
+ "PHE_label": "V-21APR-03",
"representative_genome": ""
},
"tags": [
"B.1.617.3",
- "VUI-21APR-03"
+ "VUI-21APR-03",
+ "V-21APR-03"
],
"sites": [
"nuc:C835T",
=====================================
constellations/definitions/cBA.1.json
=====================================
@@ -9,13 +9,15 @@
"BA.1"
],
"WHO_label": "Omicron",
- "mrca_lineage": "BA.1",
+ "mrca_lineage": "BA.1",
"lineage_name": "BA.1",
"parent_lineage": "B.1.1.529",
+ "PHE_label": "VOC-21NOV-01",
"representative_genome": ""
},
"tags": [
- "BA.1"
+ "BA.1",
+ "VOC-21NOV-01"
],
"sites": [
"orf1ab:K856R",
=====================================
constellations/definitions/cBA.2.json
=====================================
@@ -9,17 +9,19 @@
"BA.2"
],
"WHO_label": "Omicron",
- "mrca_lineage": "BA.2",
+ "mrca_lineage": "BA.2",
"lineage_name": "BA.2",
"parent_lineage": "B.1.1.529",
+ "PHE_label": "VOC-22JAN-01",
"representative_genome": ""
},
"tags": [
- "BA.2"
+ "BA.2",
+ "VOC-22JAN-01"
],
"sites": [
"orf1ab:S135R",
- "orf1ab:T842I",
+ "orf1ab:T842I",
"orf1ab:G1307S",
"nuc:C4321T",
"orf1ab:L3027F",
@@ -36,15 +38,14 @@
"nuc:A20055G",
"spike:T19I",
"del:21633:9",
- "nuc:T22200G",
+ "spike:V213G",
"spike:S371F",
"spike:T376A",
"spike:D405N",
- "spike:R408S",
"spike:Q493R",
+ "orf3a:T223I",
"nuc:C25000T",
"nuc:C25584T",
- "nuc:C26060T",
"nuc:C26858T",
"orf6:D61L",
"n:RG203KR",
@@ -53,11 +54,8 @@
"note": "Unique mutations for sublineage",
"rules": {
"default": {
- "min_alt": 27,
- "max_ref": 3,
- "spike:Q493":"alt",
- "n:P151":"ref",
- "nuc:G27788":"ref"
+ "min_alt": 23,
+ "max_ref": 4
}
}
}
=====================================
constellations/definitions/cBA.4.json
=====================================
@@ -12,10 +12,12 @@
"mrca_lineage": "BA.4",
"lineage_name": "BA.4",
"parent_lineage": "B.1.1.529",
+ "PHE_label": "V-22APR-03",
"representative_genome": ""
},
"tags": [
- "BA.4"
+ "BA.4",
+ "V-22APR-03"
],
"sites": [
"orf1ab:S135R",
=====================================
constellations/definitions/cBA.5.json
=====================================
@@ -9,13 +9,15 @@
"BA.5"
],
"WHO_label": "Omicron",
- "mrca_lineage": "BA.5",
+ "mrca_lineage": "BA.5",
"lineage_name": "BA.5",
"parent_lineage": "B.1.1.529",
+ "PHE_label": "V-22APR-04",
"representative_genome": ""
},
"tags": [
- "BA.5"
+ "BA.5",
+ "V-22APR-04"
],
"sites": [
"orf1ab:S135R",
@@ -50,8 +52,8 @@
"note": "Unique mutations for sublineage",
"rules": {
"default": {
- "min_alt": 27,
- "max_ref": 5,
+ "min_alt": 25,
+ "max_ref": 4,
"s:Q493":"ref",
"nuc:C26858":"ref",
"nuc:G27788":"ref",
=====================================
constellations/definitions/cC.37.json
=====================================
@@ -10,11 +10,13 @@
],
"mrca_lineage": "C.37",
"WHO_label": "Lambda",
+ "PHE_label": "V-21JUN-01",
"representative_genome": ""
},
"tags": [
"Lambda",
- "C.37"
+ "C.37",
+ "V-21JUN-01"
],
"sites": [
"ORF1a:T1246I",
=====================================
constellations/definitions/cP.2.json
=====================================
@@ -10,14 +10,15 @@
"P.2"
],
"mrca_lineage": "P.2",
- "PHE_label": "VUI-21JAN-01",
+ "PHE_label": "V-21JAN-01",
"WHO_label": "Zeta",
"representative_genome": ""
},
"tags": [
"P.2",
"VUI-21JAN-01",
- "VUI202101/01"
+ "VUI202101/01",
+ "V-21JAN-01"
],
"sites": [
"ORF1ab:L205V",
=====================================
constellations/definitions/cP.3.json
=====================================
@@ -10,15 +10,16 @@
"Pango_lineages": [
"P.3"
],
- "mrca_lineage": "P.3",
- "PHE_label": "VUI-21MAR-02",
+ "mrca_lineage": "P.3",
+ "PHE_label": "V-21MAR-02",
"WHO_label": "Theta",
"representative_genome": ""
},
"tags": [
"P.3",
"VUI-21MAR-02",
- "VUI202103/02"
+ "VUI202103/02",
+ "V-21MAR-02"
],
"sites": [
"nsp3:D736G",
=====================================
constellations/definitions/cXBB-parent1.json
=====================================
@@ -0,0 +1,31 @@
+{
+ "label": "XBB-parent1",
+ "description": "Majority parent of XBB recombinant lineage",
+ "sources": [
+ ],
+ "type": "variant",
+ "variant": {
+ "mrca_lineage": "",
+ "lineage_name": "XBB-parent1",
+ "parent_lineage": "BA.2",
+ "representative_genome": ""
+ },
+ "tags": [
+ "XBB"
+ ],
+ "note": "Shared mutations with BA.2.75 parent",
+ "note": "Likely breakpoint: ~ S:446",
+ "sites": [
+ "spike:G339H",
+ "spike:G446S",
+ "spike:N460K",
+ "e:T11A",
+ "nuc:C25416T"
+ ],
+ "rules": {
+ "default": {
+ "min_alt": 2,
+ "max_ref": 2
+ }
+ }
+}
=====================================
constellations/definitions/cXBB-parent2.json
=====================================
@@ -0,0 +1,27 @@
+{
+ "label": "XBB-parent2",
+ "description": "Minority parent of XBB recombinant lineage",
+ "sources": [
+ ],
+ "type": "variant",
+ "variant": {
+ "mrca_lineage": "",
+ "lineage_name": "XBB-parent2",
+ "parent_lineage": "XBB-parent1",
+ "representative_genome": ""
+ },
+ "tags": [
+ "XBB"
+ ],
+ "note": "Shared mutations with BA.2.10.1 parent",
+ "note": "Likely breakpoint: ~ S:446",
+ "sites": [
+ "orf1b:S959P"
+ ],
+ "rules": {
+ "default": {
+ "min_alt": 0,
+ "max_ref": 1
+ }
+ }
+}
=====================================
constellations/definitions/cXBB.1.16.json
=====================================
@@ -0,0 +1,32 @@
+{
+ "label": "Omicron (XBB.1.16-like)",
+ "description": "XBB.1.16 lineage defining mutations",
+ "sources": [
+ ],
+ "type": "variant",
+ "variant": {
+ "Pango_lineages": [
+ "XBB.1.16"
+ ],
+ "WHO_label": "Omicron",
+ "parent_lineage": "XBB.1",
+ "mrca_lineage": "XBB.1.16",
+ "lineage_name": "XBB.1.16",
+ "representative_genome": ""
+ },
+ "tags": [
+ "XBB.1.16"
+ ],
+ "note": "Unique mutations for XBB.1.16 sublineage",
+ "sites": [
+ "orf1b:D1746Y",
+ "spike:E180V",
+ "nuc:T28297C",
+ "nuc:A28447G",
+ "nuc:C29386T"
+ ],
+ "rules": {
+ "min_alt": 3,
+ "max_ref": 1
+ }
+}
=====================================
constellations/definitions/cXBB.1.5.json
=====================================
@@ -0,0 +1,31 @@
+{
+ "label": "Omicron (XBB.1.5-like)",
+ "description": "XBB.1.5 lineage defining mutations",
+ "sources": [
+ ],
+ "type": "variant",
+ "variant": {
+ "Pango_lineages": [
+ "XBB.1.5"
+ ],
+ "WHO_label": "Omicron",
+ "parent_lineage": "XBB.1",
+ "mrca_lineage": "XBB.1.5",
+ "lineage_name": "XBB.1.5",
+ "representative_genome": ""
+ },
+ "tags": [
+ "XBB.1.5"
+ ],
+ "note": "Unique mutations for XBB.1.5 sublineage",
+ "sites": [
+ "nuc:T17124C",
+ "spike:G252V",
+ "spike:F486P"
+ ],
+ "rules": {
+ "min_alt": 2,
+ "max_ref": 0,
+ "spike:F486":"alt"
+ }
+}
=====================================
constellations/definitions/cXBB.1.json
=====================================
@@ -0,0 +1,30 @@
+{
+ "label": "Omicron (XBB.1-like)",
+ "description": "XBB.1 lineage defining mutations",
+ "sources": [
+ ],
+ "type": "variant",
+ "variant": {
+ "Pango_lineages": [
+ "XBB.1"
+ ],
+ "WHO_label": "Omicron",
+ "parent_lineage": "XBB",
+ "mrca_lineage": "XBB.1",
+ "lineage_name": "XBB.1",
+ "representative_genome": ""
+ },
+ "tags": [
+ "XBB.1"
+ ],
+ "note": "Unique mutations for XBB.1 sublineage",
+ "sites": [
+ "spike:R408S",
+ "spike:K417N",
+ "orf8:G8*"
+ ],
+ "rules": {
+ "min_alt": 2,
+ "max_ref": 0
+ }
+}
=====================================
constellations/definitions/cXBB.json
=====================================
@@ -0,0 +1,41 @@
+{
+ "label": "Omicron (XBB-like)",
+ "description": "XBB recombinant lineage defining mutations",
+ "sources": [
+ ],
+ "type": "variant",
+ "variant": {
+ "Pango_lineages": [
+ "XBB"
+ ],
+ "WHO_label": "Omicron",
+ "parent_lineage": "XBB-parent2",
+ "mrca_lineage": "XBB",
+ "lineage_name": "XBB",
+ "representative_genome": ""
+ },
+ "tags": [
+ "XBB"
+ ],
+ "note": "Unique mutations for XBB sublineage",
+ "sites": [
+ "spike:V83A",
+ "spike:Y144-",
+ "spike:H146Q",
+ "spike:Q183E",
+ "spike:V213E",
+ "spike:R346T",
+ "spike:L368I",
+ "spike:V445P",
+ "spike:F486S",
+ "spike:F490S",
+
+ "nuc:C15738T",
+ "nuc:T15939C",
+ "nuc:T17859C"
+ ],
+ "rules": {
+ "min_alt": 5,
+ "max_ref": 3
+ }
+}
=====================================
constellations/definitions/cXE.json
=====================================
@@ -9,14 +9,16 @@
"XE"
],
"WHO_label": "Omicron",
- "parent_lineage": "XE-parent2",
- "mrca_lineage": "XE",
+ "parent_lineage": "XE-parent2",
+ "mrca_lineage": "XE",
+ "PHE_label": "V-22APR-02",
"lineage_name": "XE",
"representative_genome": ""
},
"tags": [
"XE",
- "GL2"
+ "GL2",
+ "V-22APR-02"
],
"note": "Unique mutations for XE sublineage",
"sites": [
@@ -28,7 +30,7 @@
"nuc:C14599T"
],
"rules": {
- "min_alt": 2,
+ "min_alt": 3,
"max_ref": 0
}
}
View it on GitLab: https://salsa.debian.org/med-team/constellations/-/commit/b5559d69cd86694b163e85a088cf54fb0ffa7e5c
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