diff --git a/constellations/__init__.py b/constellations/__init__.py index 2382b5c..96c428b 100644 --- a/constellations/__init__.py +++ b/constellations/__init__.py @@ -1,3 +1,3 @@ _program = "constellations" -__version__ = "v0.1.12" +__version__ = "v0.1.13" diff --git a/constellations/definitions/cA.23.1+E484K.json b/constellations/definitions/cA.23.1+E484K.json index 74f69ab..f79937b 100644 --- a/constellations/definitions/cA.23.1+E484K.json +++ b/constellations/definitions/cA.23.1+E484K.json @@ -36,7 +36,7 @@ ], "rules": { "min_alt": 5, - "max_ref": 3, + "max_ref": 4, "S:E484K": "alt" } } diff --git a/constellations/definitions/cA.23.1.json b/constellations/definitions/cA.23.1.json index c7c362e..3bb41a5 100644 --- a/constellations/definitions/cA.23.1.json +++ b/constellations/definitions/cA.23.1.json @@ -31,6 +31,6 @@ ], "rules": { "min_alt": 5, - "max_ref": 3 + "max_ref": 4 } } diff --git a/constellations/definitions/cAY.4.json b/constellations/definitions/cAY.4.json index ad83230..ab66566 100644 --- a/constellations/definitions/cAY.4.json +++ b/constellations/definitions/cAY.4.json @@ -47,7 +47,7 @@ "spike:T95I:0.967111" ], "rules": { - "min_alt": 12, + "min_alt": 10, "max_ref": 3, "orf1a:A2529V": "alt" } diff --git a/constellations/definitions/cB.1.1.318.json b/constellations/definitions/cB.1.1.318.json index b393f5c..5cc959f 100644 --- a/constellations/definitions/cB.1.1.318.json +++ b/constellations/definitions/cB.1.1.318.json @@ -41,7 +41,7 @@ "del:28895:3" ], "rules": { - "min_alt": 11, - "max_ref": 3 + "min_alt": 7, + "max_ref": 7 } -} \ No newline at end of file +} diff --git a/constellations/definitions/cB.1.1.7+E484K.json b/constellations/definitions/cB.1.1.7+E484K.json index 7640c3f..69226d5 100644 --- a/constellations/definitions/cB.1.1.7+E484K.json +++ b/constellations/definitions/cB.1.1.7+E484K.json @@ -43,8 +43,8 @@ "N:S235F" ], "rules": { - "min_alt": 15, - "max_ref": 3, + "min_alt": 10, + "max_ref": 7, "S:E484K": "alt" } } diff --git a/constellations/definitions/cB.1.1.7.json b/constellations/definitions/cB.1.1.7.json index 7e6e488..1fc2826 100644 --- a/constellations/definitions/cB.1.1.7.json +++ b/constellations/definitions/cB.1.1.7.json @@ -44,7 +44,7 @@ "N:S235F" ], "rules": { - "min_alt": 15, - "max_ref": 3 + "min_alt": 10, + "max_ref": 7 } } diff --git a/constellations/definitions/cB.1.351.json b/constellations/definitions/cB.1.351.json index d0af77c..7ce488a 100644 --- a/constellations/definitions/cB.1.351.json +++ b/constellations/definitions/cB.1.351.json @@ -40,7 +40,7 @@ "del:11287:9" ], "rules": { - "min_alt": 6, - "max_ref": 3 + "min_alt": 8, + "max_ref": 10 } } diff --git a/constellations/definitions/cB.1.427.json b/constellations/definitions/cB.1.427.json index 43c5d8e..297bd55 100644 --- a/constellations/definitions/cB.1.427.json +++ b/constellations/definitions/cB.1.427.json @@ -36,7 +36,7 @@ "orf1b:P976L:0.948544" ], "rules": { - "min_alt": 5, - "max_ref": 3 + "min_alt": 2, + "max_ref": 0 } } diff --git a/constellations/definitions/cB.1.429.json b/constellations/definitions/cB.1.429.json index 993b349..42b0864 100644 --- a/constellations/definitions/cB.1.429.json +++ b/constellations/definitions/cB.1.429.json @@ -38,6 +38,6 @@ ], "rules": { "min_alt": 6, - "max_ref": 3 + "max_ref": 2 } } diff --git a/constellations/definitions/cB.1.525.json b/constellations/definitions/cB.1.525.json index 69daf3f..74ec34f 100644 --- a/constellations/definitions/cB.1.525.json +++ b/constellations/definitions/cB.1.525.json @@ -42,7 +42,7 @@ "nuc:G29543T" ], "rules": { - "min_alt": 8, - "max_ref": 3 + "min_alt": 10, + "max_ref": 6 } -} \ No newline at end of file +} diff --git a/constellations/definitions/cB.1.526.json b/constellations/definitions/cB.1.526.json index 1e26102..f483d37 100644 --- a/constellations/definitions/cB.1.526.json +++ b/constellations/definitions/cB.1.526.json @@ -43,8 +43,8 @@ "nuc:A28271-" ], "rules": { - "min_alt": 11, - "max_ref": 7 + "min_alt": 13, + "max_ref": 12 } } diff --git a/constellations/definitions/cB.1.617.1.json b/constellations/definitions/cB.1.617.1.json index e41f8ed..d23be2d 100644 --- a/constellations/definitions/cB.1.617.1.json +++ b/constellations/definitions/cB.1.617.1.json @@ -33,7 +33,7 @@ "N:R203M" ], "rules": { - "min_alt": 5, - "max_ref": 3 + "min_alt": 4, + "max_ref": 2 } } diff --git a/constellations/definitions/cB.1.617.2+K417N.json b/constellations/definitions/cB.1.617.2+K417N.json index 70bdaa2..f6143da 100644 --- a/constellations/definitions/cB.1.617.2+K417N.json +++ b/constellations/definitions/cB.1.617.2+K417N.json @@ -40,8 +40,8 @@ "N:D377Y" ], "rules": { - "min_alt": 5, - "max_ref": 3, + "min_alt": 8, + "max_ref": 14, "S:K417N": "alt" } } diff --git a/constellations/definitions/cB.1.617.2.json b/constellations/definitions/cB.1.617.2.json index 0eba89f..74c53cf 100644 --- a/constellations/definitions/cB.1.617.2.json +++ b/constellations/definitions/cB.1.617.2.json @@ -45,7 +45,7 @@ "N:D377Y" ], "rules": { - "min_alt": 5, - "max_ref": 3 + "min_alt": 8, + "max_ref": 14 } } diff --git a/constellations/definitions/cB.1.617.3.json b/constellations/definitions/cB.1.617.3.json index 9cfdf0f..7a013f2 100644 --- a/constellations/definitions/cB.1.617.3.json +++ b/constellations/definitions/cB.1.617.3.json @@ -38,7 +38,7 @@ "N:D377Y" ], "rules": { - "min_alt": 9, + "min_alt": 5, "max_ref": 3 } -} \ No newline at end of file +} diff --git a/constellations/definitions/cB.1.621.json b/constellations/definitions/cB.1.621.json index ec76c58..def8bae 100644 --- a/constellations/definitions/cB.1.621.json +++ b/constellations/definitions/cB.1.621.json @@ -54,7 +54,7 @@ "nuc:T28618A:0.916667" ], "rules": { - "min_alt": 19, - "max_ref": 3 + "min_alt": 21, + "max_ref": 6 } } diff --git a/constellations/definitions/cBA.1.json b/constellations/definitions/cBA.1.json index 2b35463..c077c22 100644 --- a/constellations/definitions/cBA.1.json +++ b/constellations/definitions/cBA.1.json @@ -51,8 +51,8 @@ "note2": "Requires ancestral mutation so scorpio tie breaks correctly", "rules": { "default": { - "min_alt": 17, - "max_ref": 2 + "min_alt": 10, + "max_ref": 7 } } } diff --git a/constellations/definitions/cBA.2.86.json b/constellations/definitions/cBA.2.86.json new file mode 100644 index 0000000..4e320f2 --- /dev/null +++ b/constellations/definitions/cBA.2.86.json @@ -0,0 +1,81 @@ +{ + "label": "Omicron (BA.2.86-like)", + "description": "BA.2.86 lineage defining mutations", + "sources": [ + ], + "type": "variant", + "variant": { + "Pango_lineages": [ + "BA.2.86" + ], + "WHO_label": "Omicron", + "mrca_lineage": "BA.2.86", + "lineage_name": "BA.2.86", + "parent_lineage": "BA.2" + }, + "tags": [ + "BA.2.86" + ], + "sites": [ + "orf1a:A211D", + "orf1a:V1056L", + "orf1a:N2526S", + "nuc:C8293T", + "orf1a:A2710T", + "orf1a:V3593F", + "orf1a:T4175I", + "nuc:T13339C", + "nuc:T15756A", + "nuc:A18492G", + "spike:S50L", + "del:21765:6", + "spike:V127F", + "del:21991:3", + "spike:FR157SG", + "spike:L216F", + "spike:H245N", + "spike:A264D", + "spike:I332V", + "spike:G339H", + "spike:K356T", + "spike:R403K", + "spike:R408S", + "spike:K417N", + "spike:V445H", + "spike:G446S", + "spike:N450D", + "spike:L452W", + "spike:N460K", + "spike:N481K", + "spike:E484K", + "spike:F486P", + "spike:E554K", + "spike:A570V", + "spike:P621S", + "spike:P681R", + "spike:S939F", + "spike:P1143L", + "nuc:C25207T", + "m:D3H", + "m:T30A", + "nuc:C26681T", + "m:A104V", + "nuc:C27807T", + "n:Q229K" + ], + "intermediate": [ + "nuc:C12815T:0.500000", + "nuc:21608+12:0.500000", + "nuc:C21622T:0.750000", + "spike:R21T:0.750000", + "del:22194:3:0.750000", + "del:23008:3:0.625000", + "m:Q19E:0.750000" + ], + "rules": { + "min_alt": 37, + "max_ref": 3 + }, + "notes": "Relative to BA.2 constellation definition, missing the following (mostly due to additional mutations changing the amino acid): orf1ab:L3201F, spike:G339D, spike:E484A, spike:Q493R, spike:P681H, m:Q19E" +} + diff --git a/constellations/definitions/cBA.2.json b/constellations/definitions/cBA.2.json index 8997dd8..b6e2aaf 100644 --- a/constellations/definitions/cBA.2.json +++ b/constellations/definitions/cBA.2.json @@ -54,8 +54,8 @@ "note": "Unique mutations for sublineage", "rules": { "default": { - "min_alt": 23, - "max_ref": 4 + "min_alt": 11, + "max_ref": 2 } } } diff --git a/constellations/definitions/cBA.3.json b/constellations/definitions/cBA.3.json index ee448af..9c6ab74 100644 --- a/constellations/definitions/cBA.3.json +++ b/constellations/definitions/cBA.3.json @@ -43,7 +43,7 @@ "note": "Unique mutations for sublineage", "rules": { "default": { - "min_alt": 13, + "min_alt": 16, "max_ref": 2 } } diff --git a/constellations/definitions/cBA.4.json b/constellations/definitions/cBA.4.json index 4370d5f..eb22d90 100644 --- a/constellations/definitions/cBA.4.json +++ b/constellations/definitions/cBA.4.json @@ -55,8 +55,8 @@ "note": "Unique mutations for sublineage", "rules": { "default": { - "min_alt": 29, - "max_ref": 5, + "min_alt": 16, + "max_ref": 2, "m:D3N":"ref", "s:Q493":"ref", "orf6:D61":"not ref", diff --git a/constellations/definitions/cBA.5.json b/constellations/definitions/cBA.5.json index 80c096b..7a764fc 100644 --- a/constellations/definitions/cBA.5.json +++ b/constellations/definitions/cBA.5.json @@ -52,7 +52,7 @@ "note": "Unique mutations for sublineage", "rules": { "default": { - "min_alt": 25, + "min_alt": 20, "max_ref": 4, "s:Q493":"ref", "nuc:C26858":"ref", diff --git a/constellations/definitions/cC.37.json b/constellations/definitions/cC.37.json index 0711719..876a746 100644 --- a/constellations/definitions/cC.37.json +++ b/constellations/definitions/cC.37.json @@ -40,7 +40,7 @@ "N:G214C" ], "rules": { - "min_alt": 9, - "max_ref": 3 + "min_alt": 6, + "max_ref": 4 } } diff --git a/constellations/definitions/cP.1.json b/constellations/definitions/cP.1.json index bd2dbd3..944acb6 100644 --- a/constellations/definitions/cP.1.json +++ b/constellations/definitions/cP.1.json @@ -39,7 +39,7 @@ "N:P80R" ], "rules": { - "min_alt": 8, - "max_ref": 3 + "min_alt": 3, + "max_ref": 8 } } diff --git a/constellations/definitions/cP.2.json b/constellations/definitions/cP.2.json index 031e398..da5fd4d 100644 --- a/constellations/definitions/cP.2.json +++ b/constellations/definitions/cP.2.json @@ -30,7 +30,7 @@ "N:M234I" ], "rules": { - "min_alt": 5, - "max_ref": 1 + "min_alt": 3, + "max_ref": 3 } } diff --git a/constellations/definitions/cP.3.json b/constellations/definitions/cP.3.json index 275326c..4c07520 100644 --- a/constellations/definitions/cP.3.json +++ b/constellations/definitions/cP.3.json @@ -41,7 +41,7 @@ "nuc:T24187A" ], "rules": { - "min_alt": 9, - "max_ref": 3 + "min_alt": 11, + "max_ref": 7 } -} \ No newline at end of file +} diff --git a/constellations/definitions/cXBB.1.16.json b/constellations/definitions/cXBB.1.16.json index 9840907..c75a149 100644 --- a/constellations/definitions/cXBB.1.16.json +++ b/constellations/definitions/cXBB.1.16.json @@ -26,7 +26,7 @@ "nuc:C29386T" ], "rules": { - "min_alt": 3, - "max_ref": 1 + "min_alt": 2, + "max_ref": 2 } } diff --git a/constellations/definitions/cXBB.json b/constellations/definitions/cXBB.json index 6395fe7..3771e27 100644 --- a/constellations/definitions/cXBB.json +++ b/constellations/definitions/cXBB.json @@ -29,13 +29,12 @@ "spike:V445P", "spike:F486S", "spike:F490S", - "nuc:C15738T", "nuc:T15939C", "nuc:T17859C" ], "rules": { - "min_alt": 5, - "max_ref": 3 + "min_alt": 3, + "max_ref": 4 } }