From 5b7b3539ee396816578ca9fd6f3820950338ccf3 Mon Sep 17 00:00:00 2001 From: Rachel Colquhoun Date: Tue, 1 Feb 2022 16:12:07 +0000 Subject: [PATCH 1/5] remove ref counts for BA.3 --- constellations/definitions/cB.1.1.529.json | 4 +--- constellations/definitions/cBA.1.json | 10 ++++++---- constellations/definitions/cBA.2.json | 10 ++++++---- 3 files changed, 13 insertions(+), 11 deletions(-) diff --git a/constellations/definitions/cB.1.1.529.json b/constellations/definitions/cB.1.1.529.json index d833c0a..fecfbea 100644 --- a/constellations/definitions/cB.1.1.529.json +++ b/constellations/definitions/cB.1.1.529.json @@ -47,8 +47,6 @@ "spike:D796Y", "spike:Q954H", "spike:N969K", - "nuc:C25000T", - "nuc:C25584T", "e:T9I", "m:Q19E", "m:A63T", @@ -62,7 +60,7 @@ "note": "Common mutations to the sublineages found", "rules": { "default": { - "min_alt": 25, + "min_alt": 23, "max_ref": 5, "spike:D614G": "not ref" }, diff --git a/constellations/definitions/cBA.1.json b/constellations/definitions/cBA.1.json index 2cb22db..042791f 100644 --- a/constellations/definitions/cBA.1.json +++ b/constellations/definitions/cBA.1.json @@ -36,20 +36,22 @@ "spike:T547K", "spike:N856K", "spike:L981F", + "nuc:C25000T", + "nuc:C25584T", "m:D3G" ], "note": "Unique mutations for sublineage", "note2": "Requires ancestral mutation so scorpio tie breaks correctly", "rules": { "default": { - "min_alt": 10, + "min_alt": 12, "max_ref": 3, - "spike:D614G": "not ref" + "nuc:T5386G": "not ref" }, "Probable": { - "min_alt": 6, + "min_alt": 8, "max_ref": 8, - "spike:D614G": "not ref" + "nuc:T5386G": "not ref" } } } diff --git a/constellations/definitions/cBA.2.json b/constellations/definitions/cBA.2.json index 4cbad40..b1166b8 100644 --- a/constellations/definitions/cBA.2.json +++ b/constellations/definitions/cBA.2.json @@ -40,6 +40,8 @@ "spike:T376A", "spike:D405N", "spike:R408S", + "nuc:C25000T", + "nuc:C25584T", "nuc:C26060T", "nuc:C26858T", "orf6:D61L", @@ -48,14 +50,14 @@ "note": "Unique mutations for sublineage", "rules": { "default": { - "min_alt": 16, + "min_alt": 18, "max_ref": 3, - "spike:D614G": "not ref" + "nuc:C10198T": "not ref" }, "Probable": { - "min_alt": 10, + "min_alt": 12, "max_ref": 8, - "spike:D614G": "not ref" + "nuc:C10198T": "not ref" } } } From 293d975c13a06573e768c324955394cda557403d Mon Sep 17 00:00:00 2001 From: Rachel Colquhoun Date: Tue, 1 Feb 2022 16:29:25 +0000 Subject: [PATCH 2/5] remove ref counts for BA.3 --- constellations/definitions/cB.1.1.529.json | 5 ++--- constellations/definitions/cBA.1.json | 8 +++++--- constellations/definitions/cBA.2.json | 1 + 3 files changed, 8 insertions(+), 6 deletions(-) diff --git a/constellations/definitions/cB.1.1.529.json b/constellations/definitions/cB.1.1.529.json index fecfbea..9707512 100644 --- a/constellations/definitions/cB.1.1.529.json +++ b/constellations/definitions/cB.1.1.529.json @@ -23,7 +23,6 @@ "orf1ab:T3255I", "orf1ab:P3395H", "orf1ab:SGF3675-", - "nuc:T13195C", "orf1ab:P4715L", "orf1ab:I5967V", "spike:G142D", @@ -60,12 +59,12 @@ "note": "Common mutations to the sublineages found", "rules": { "default": { - "min_alt": 23, + "min_alt": 22, "max_ref": 5, "spike:D614G": "not ref" }, "Probable": { - "min_alt": 15, + "min_alt": 12, "max_ref": 14 } } diff --git a/constellations/definitions/cBA.1.json b/constellations/definitions/cBA.1.json index 042791f..5470517 100644 --- a/constellations/definitions/cBA.1.json +++ b/constellations/definitions/cBA.1.json @@ -19,10 +19,12 @@ ], "sites": [ "orf1ab:K856R", - "del:6513:3", "nuc:T5386G", + "del:6513:3", "orf1ab:A2710T", + "orf1ab:L3674F", "orf1ab:I3758V", + "nuc:C13195T", "nuc:C15240T", "spike:A67V", "del:21765:6", @@ -44,12 +46,12 @@ "note2": "Requires ancestral mutation so scorpio tie breaks correctly", "rules": { "default": { - "min_alt": 12, + "min_alt": 14, "max_ref": 3, "nuc:T5386G": "not ref" }, "Probable": { - "min_alt": 8, + "min_alt": 10, "max_ref": 8, "nuc:T5386G": "not ref" } diff --git a/constellations/definitions/cBA.2.json b/constellations/definitions/cBA.2.json index b1166b8..537ba96 100644 --- a/constellations/definitions/cBA.2.json +++ b/constellations/definitions/cBA.2.json @@ -30,6 +30,7 @@ "nuc:G10447A", "nuc:C15714T", "nuc:C12880T", + "nuc:C15714T", "orf1ab:R5716C", "orf1ab:T6564I", "nuc:A20055G", From f18502dd2cd1ab25e6929c82ebdabbaeafb32d19 Mon Sep 17 00:00:00 2001 From: Rachel Colquhoun Date: Tue, 8 Feb 2022 21:00:29 +0000 Subject: [PATCH 3/5] update min alt for lambda is appears to be too low --- constellations/definitions/cC.37.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/constellations/definitions/cC.37.json b/constellations/definitions/cC.37.json index 22831fe..5e7bca0 100644 --- a/constellations/definitions/cC.37.json +++ b/constellations/definitions/cC.37.json @@ -38,7 +38,7 @@ "N:G214C" ], "rules": { - "min_alt": 5, + "min_alt": 9, "max_ref": 3 } } From 26a016b80e42dd7ebcaf1cf2088be6a42de2eedd Mon Sep 17 00:00:00 2001 From: Rachel Colquhoun Date: Tue, 8 Feb 2022 21:00:41 +0000 Subject: [PATCH 4/5] increment version --- constellations/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/constellations/__init__.py b/constellations/__init__.py index ecb4329..65ef258 100644 --- a/constellations/__init__.py +++ b/constellations/__init__.py @@ -1,3 +1,3 @@ _program = "constellations" -__version__ = "v0.1.2" +__version__ = "v0.1.3" From 378449720a569b198b540f1ea7bf988872b53b1d Mon Sep 17 00:00:00 2001 From: Rachel Colquhoun Date: Tue, 8 Feb 2022 21:29:34 +0000 Subject: [PATCH 5/5] fix --- constellations/definitions/cBA.1.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/constellations/definitions/cBA.1.json b/constellations/definitions/cBA.1.json index 5470517..f627fa8 100644 --- a/constellations/definitions/cBA.1.json +++ b/constellations/definitions/cBA.1.json @@ -24,7 +24,7 @@ "orf1ab:A2710T", "orf1ab:L3674F", "orf1ab:I3758V", - "nuc:C13195T", + "nuc:T13195C", "nuc:C15240T", "spike:A67V", "del:21765:6",