Merge pull request #123 from nextstrain/update-flu

flu: update subclade of H3N2/HA
nextstrain · Dec 20, 2023 · 609d7c6 · 609d7c6
2 parents f60dac9 + 25de54f
commit 609d7c6
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Showing 25 changed files with 131 additions and 4 deletions.
diff --git a/data/nextstrain/flu/h1n1pdm/ha/CY121680/pathogen.json b/data/nextstrain/flu/h1n1pdm/ha/CY121680/pathogen.json
@@ -80,6 +80,10 @@
   },
   "nucMutLabelMap": {},
   "nucMutLabelMapReverse": {},
+  "shortcuts": [
+    "flu-h1n1pdm-ha-broad",
+    "nextstrain/flu/h1n1pdm/ha/california-7-2009"
+  ],
   "aaMotifs": [
     {
       "name": "glycosylation",

diff --git a/data/nextstrain/flu/h1n1pdm/ha/MW626062/pathogen.json b/data/nextstrain/flu/h1n1pdm/ha/MW626062/pathogen.json
@@ -80,6 +80,12 @@
   },
   "nucMutLabelMap": {},
   "nucMutLabelMapReverse": {},
+  "shortcuts": [
+    "flu-h1n1pdm-ha",
+    "nextstrain/flu/h1n1pdm",
+    "nextstrain/flu/h1n1pdm/ha",
+    "nextstrain/flu/h1n1pdm/ha/wisconsin-588-2019"
+  ],
   "aaMotifs": [
     {
       "name": "glycosylation",

diff --git a/data/nextstrain/flu/h1n1pdm/na/MW626056/pathogen.json b/data/nextstrain/flu/h1n1pdm/na/MW626056/pathogen.json
@@ -79,6 +79,11 @@
   },
   "nucMutLabelMap": {},
   "nucMutLabelMapReverse": {},
+  "shortcuts": [
+    "flu-h1n1pdm-na",
+    "nextstrain/flu/h1n1pdm/na",
+    "nextstrain/flu/h1n1pdm/na/wisconsin-588-2019"
+  ],
   "aaMotifs": [
     {
       "name": "glycosylation",

diff --git a/data/nextstrain/flu/h3n2/ha/CY163680/CHANGELOG.md b/data/nextstrain/flu/h3n2/ha/CY163680/CHANGELOG.md
@@ -2,6 +2,7 @@
 
 Initial release for Nextclade v3!
 
+ - Addition of subclade H.1, H.2, H.3, and H.4
  - Aliasing of G.1.3.1.1 as subclade H
 
 Read more about Nextclade datasets in the documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html
diff --git a/data/nextstrain/flu/h3n2/ha/CY163680/pathogen.json b/data/nextstrain/flu/h3n2/ha/CY163680/pathogen.json
@@ -80,6 +80,10 @@
   },
   "nucMutLabelMap": {},
   "nucMutLabelMapReverse": {},
+  "shortcuts": [
+    "flu-h3n2-ha-broad",
+    "nextstrain/flu/h3n2/ha/wisconsin-67-2005"
+  ],
   "aaMotifs": [
     {
       "name": "glycosylation",

diff --git a/data/nextstrain/flu/h3n2/ha/CY163680/tree.json b/data/nextstrain/flu/h3n2/ha/CY163680/tree.json
diff --git a/data/nextstrain/flu/h3n2/ha/EPI1857216/CHANGELOG.md b/data/nextstrain/flu/h3n2/ha/EPI1857216/CHANGELOG.md
@@ -2,6 +2,7 @@
 
 Initial release for Nextclade v3!
 
+ - Addition of subclade H.1, H.2, H.3, and H.4
  - Aliasing of G.1.3.1.1 as subclade H
 
 Read more about Nextclade datasets in the documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html
diff --git a/data/nextstrain/flu/h3n2/ha/EPI1857216/pathogen.json b/data/nextstrain/flu/h3n2/ha/EPI1857216/pathogen.json
@@ -80,6 +80,12 @@
   },
   "nucMutLabelMap": {},
   "nucMutLabelMapReverse": {},
+  "shortcuts": [
+    "flu-h3n2-ha",
+    "nextstrain/flu/h3n2",
+    "nextstrain/flu/h3n2/ha",
+    "nextstrain/flu/h3n2/ha/darwin-6-2021"
+  ],
   "phenotypeData": [
     {
       "name": "RBD",

diff --git a/data/nextstrain/flu/h3n2/ha/EPI1857216/tree.json b/data/nextstrain/flu/h3n2/ha/EPI1857216/tree.json
diff --git a/data/nextstrain/flu/h3n2/na/EPI1857215/pathogen.json b/data/nextstrain/flu/h3n2/na/EPI1857215/pathogen.json
@@ -79,6 +79,11 @@
   },
   "nucMutLabelMap": {},
   "nucMutLabelMapReverse": {},
+  "shortcuts": [
+    "flu-h3n2-na",
+    "nextstrain/flu/h3n2/na",
+    "nextstrain/flu/h3n2/na/darwin-6-2021"
+  ],
   "aaMotifs": [
     {
       "name": "glycosylation",

diff --git a/data/nextstrain/flu/vic/ha/KX058884/pathogen.json b/data/nextstrain/flu/vic/ha/KX058884/pathogen.json
@@ -80,6 +80,12 @@
   },
   "nucMutLabelMap": {},
   "nucMutLabelMapReverse": {},
+  "shortcuts": [
+    "flu-vic-ha",
+    "nextstrain/flu/vic",
+    "nextstrain/flu/vic/ha",
+    "nextstrain/flu/vic/ha/brisbane-60-2008"
+  ],
   "aaMotifs": [
     {
       "name": "glycosylation",

diff --git a/data/nextstrain/flu/vic/na/CY073894/pathogen.json b/data/nextstrain/flu/vic/na/CY073894/pathogen.json
@@ -79,6 +79,11 @@
   },
   "nucMutLabelMap": {},
   "nucMutLabelMapReverse": {},
+  "shortcuts": [
+    "flu-vic-na",
+    "nextstrain/flu/vic/na",
+    "nextstrain/flu/vic/na/brisbane-60-2008"
+  ],
   "aaMotifs": [
     {
       "name": "glycosylation",

diff --git a/data_output/index.json b/data_output/index.json
@@ -381,6 +381,10 @@
         },
         {
           "path": "nextstrain/flu/h1n1pdm/ha/CY121680",
+          "shortcuts": [
+            "flu-h1n1pdm-ha-broad",
+            "nextstrain/flu/h1n1pdm/ha/california-7-2009"
+          ],
           "enabled": true,
           "attributes": {
             "name": "Influenza A H1N1pdm HA",
@@ -448,6 +452,12 @@
         },
         {
           "path": "nextstrain/flu/h1n1pdm/ha/MW626062",
+          "shortcuts": [
+            "flu-h1n1pdm-ha",
+            "nextstrain/flu/h1n1pdm",
+            "nextstrain/flu/h1n1pdm/ha",
+            "nextstrain/flu/h1n1pdm/ha/wisconsin-588-2019"
+          ],
           "enabled": true,
           "attributes": {
             "name": "Influenza A H1N1pdm HA",
@@ -515,6 +525,11 @@
         },
         {
           "path": "nextstrain/flu/h1n1pdm/na/MW626056",
+          "shortcuts": [
+            "flu-h1n1pdm-na",
+            "nextstrain/flu/h1n1pdm/na",
+            "nextstrain/flu/h1n1pdm/na/wisconsin-588-2019"
+          ],
           "enabled": true,
           "attributes": {
             "name": "Influenza A H1N1pdm NA",
@@ -582,6 +597,10 @@
         },
         {
           "path": "nextstrain/flu/h3n2/ha/CY163680",
+          "shortcuts": [
+            "flu-h3n2-ha-broad",
+            "nextstrain/flu/h3n2/ha/wisconsin-67-2005"
+          ],
           "enabled": true,
           "attributes": {
             "name": "Influenza A H3N2 HA",
@@ -649,6 +668,12 @@
         },
         {
           "path": "nextstrain/flu/h3n2/ha/EPI1857216",
+          "shortcuts": [
+            "flu-h3n2-ha",
+            "nextstrain/flu/h3n2",
+            "nextstrain/flu/h3n2/ha",
+            "nextstrain/flu/h3n2/ha/darwin-6-2021"
+          ],
           "enabled": true,
           "attributes": {
             "name": "Influenza A H3N2 HA",
@@ -717,6 +742,11 @@
         },
         {
           "path": "nextstrain/flu/h3n2/na/EPI1857215",
+          "shortcuts": [
+            "flu-h3n2-na",
+            "nextstrain/flu/h3n2/na",
+            "nextstrain/flu/h3n2/na/darwin-6-2021"
+          ],
           "enabled": true,
           "attributes": {
             "name": "Influenza A H3N2 NA",
@@ -784,6 +814,12 @@
         },
         {
           "path": "nextstrain/flu/vic/ha/KX058884",
+          "shortcuts": [
+            "flu-vic-ha",
+            "nextstrain/flu/vic",
+            "nextstrain/flu/vic/ha",
+            "nextstrain/flu/vic/ha/brisbane-60-2008"
+          ],
           "enabled": true,
           "attributes": {
             "name": "Influenza B Victoria HA",
@@ -851,6 +887,11 @@
         },
         {
           "path": "nextstrain/flu/vic/na/CY073894",
+          "shortcuts": [
+            "flu-vic-na",
+            "nextstrain/flu/vic/na",
+            "nextstrain/flu/vic/na/brisbane-60-2008"
+          ],
           "enabled": true,
           "attributes": {
             "name": "Influenza B Victoria NA",

diff --git a/data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/pathogen.json b/data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/pathogen.json
@@ -80,6 +80,10 @@
   },
   "nucMutLabelMap": {},
   "nucMutLabelMapReverse": {},
+  "shortcuts": [
+    "flu-h1n1pdm-ha-broad",
+    "nextstrain/flu/h1n1pdm/ha/california-7-2009"
+  ],
   "aaMotifs": [
     {
       "name": "glycosylation",

diff --git a/data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/pathogen.json b/data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/pathogen.json
@@ -80,6 +80,12 @@
   },
   "nucMutLabelMap": {},
   "nucMutLabelMapReverse": {},
+  "shortcuts": [
+    "flu-h1n1pdm-ha",
+    "nextstrain/flu/h1n1pdm",
+    "nextstrain/flu/h1n1pdm/ha",
+    "nextstrain/flu/h1n1pdm/ha/wisconsin-588-2019"
+  ],
   "aaMotifs": [
     {
       "name": "glycosylation",

diff --git a/data_output/nextstrain/flu/h1n1pdm/na/MW626056/unreleased/pathogen.json b/data_output/nextstrain/flu/h1n1pdm/na/MW626056/unreleased/pathogen.json
@@ -79,6 +79,11 @@
   },
   "nucMutLabelMap": {},
   "nucMutLabelMapReverse": {},
+  "shortcuts": [
+    "flu-h1n1pdm-na",
+    "nextstrain/flu/h1n1pdm/na",
+    "nextstrain/flu/h1n1pdm/na/wisconsin-588-2019"
+  ],
   "aaMotifs": [
     {
       "name": "glycosylation",

diff --git a/data_output/nextstrain/flu/h3n2/ha/CY163680/unreleased/CHANGELOG.md b/data_output/nextstrain/flu/h3n2/ha/CY163680/unreleased/CHANGELOG.md
@@ -2,6 +2,7 @@
 
 Initial release for Nextclade v3!
 
+ - Addition of subclade H.1, H.2, H.3, and H.4
  - Aliasing of G.1.3.1.1 as subclade H
 
 Read more about Nextclade datasets in the documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html
diff --git a/data_output/nextstrain/flu/h3n2/ha/CY163680/unreleased/pathogen.json b/data_output/nextstrain/flu/h3n2/ha/CY163680/unreleased/pathogen.json
@@ -80,6 +80,10 @@
   },
   "nucMutLabelMap": {},
   "nucMutLabelMapReverse": {},
+  "shortcuts": [
+    "flu-h3n2-ha-broad",
+    "nextstrain/flu/h3n2/ha/wisconsin-67-2005"
+  ],
   "aaMotifs": [
     {
       "name": "glycosylation",

diff --git a/data_output/nextstrain/flu/h3n2/ha/CY163680/unreleased/tree.json b/data_output/nextstrain/flu/h3n2/ha/CY163680/unreleased/tree.json
diff --git a/data_output/nextstrain/flu/h3n2/ha/EPI1857216/unreleased/CHANGELOG.md b/data_output/nextstrain/flu/h3n2/ha/EPI1857216/unreleased/CHANGELOG.md
@@ -2,6 +2,7 @@
 
 Initial release for Nextclade v3!
 
+ - Addition of subclade H.1, H.2, H.3, and H.4
  - Aliasing of G.1.3.1.1 as subclade H
 
 Read more about Nextclade datasets in the documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html
diff --git a/data_output/nextstrain/flu/h3n2/ha/EPI1857216/unreleased/pathogen.json b/data_output/nextstrain/flu/h3n2/ha/EPI1857216/unreleased/pathogen.json
@@ -80,6 +80,12 @@
   },
   "nucMutLabelMap": {},
   "nucMutLabelMapReverse": {},
+  "shortcuts": [
+    "flu-h3n2-ha",
+    "nextstrain/flu/h3n2",
+    "nextstrain/flu/h3n2/ha",
+    "nextstrain/flu/h3n2/ha/darwin-6-2021"
+  ],
   "phenotypeData": [
     {
       "name": "RBD",

diff --git a/data_output/nextstrain/flu/h3n2/ha/EPI1857216/unreleased/tree.json b/data_output/nextstrain/flu/h3n2/ha/EPI1857216/unreleased/tree.json
diff --git a/data_output/nextstrain/flu/h3n2/na/EPI1857215/unreleased/pathogen.json b/data_output/nextstrain/flu/h3n2/na/EPI1857215/unreleased/pathogen.json
@@ -79,6 +79,11 @@
   },
   "nucMutLabelMap": {},
   "nucMutLabelMapReverse": {},
+  "shortcuts": [
+    "flu-h3n2-na",
+    "nextstrain/flu/h3n2/na",
+    "nextstrain/flu/h3n2/na/darwin-6-2021"
+  ],
   "aaMotifs": [
     {
       "name": "glycosylation",

diff --git a/data_output/nextstrain/flu/vic/ha/KX058884/unreleased/pathogen.json b/data_output/nextstrain/flu/vic/ha/KX058884/unreleased/pathogen.json
@@ -80,6 +80,12 @@
   },
   "nucMutLabelMap": {},
   "nucMutLabelMapReverse": {},
+  "shortcuts": [
+    "flu-vic-ha",
+    "nextstrain/flu/vic",
+    "nextstrain/flu/vic/ha",
+    "nextstrain/flu/vic/ha/brisbane-60-2008"
+  ],
   "aaMotifs": [
     {
       "name": "glycosylation",

diff --git a/data_output/nextstrain/flu/vic/na/CY073894/unreleased/pathogen.json b/data_output/nextstrain/flu/vic/na/CY073894/unreleased/pathogen.json
@@ -79,6 +79,11 @@
   },
   "nucMutLabelMap": {},
   "nucMutLabelMapReverse": {},
+  "shortcuts": [
+    "flu-vic-na",
+    "nextstrain/flu/vic/na",
+    "nextstrain/flu/vic/na/brisbane-60-2008"
+  ],
   "aaMotifs": [
     {
       "name": "glycosylation",