nextclade: rename gene to cds in pathogen.json

nextstrain · Jan 9, 2024 · 63d5f68 · 63d5f68
1 parent b91fbe2
commit 63d5f68
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Showing 10 changed files with 28 additions and 28 deletions.
diff --git a/nextclade/dataset_config/h1n1pdm/ha/CY121680/pathogen.json b/nextclade/dataset_config/h1n1pdm/ha/CY121680/pathogen.json
@@ -11,13 +11,13 @@
         "nameShort": "Glyc.",
         "nameFriendly": "Glycosylation",
         "description": "N-linked glycosylation motifs (N-X-S/T with X any amino acid other than P)",
-        "includeGenes": [
+        "includeCdses": [
           {
-            "gene":"HA1",
+            "cds":"HA1",
             "ranges":[]
           },
           {
-            "gene":"HA2",
+            "cds":"HA2",
             "ranges":[{"begin":0, "end":186}]
           }
         ],

diff --git a/nextclade/dataset_config/h1n1pdm/ha/MW626062/pathogen.json b/nextclade/dataset_config/h1n1pdm/ha/MW626062/pathogen.json
@@ -13,13 +13,13 @@
         "nameShort": "Glyc.",
         "nameFriendly": "Glycosylation",
         "description": "N-linked glycosylation motifs (N-X-S/T with X any amino acid other than P)",
-        "includeGenes": [
+        "includeCdses": [
           {
-            "gene":"HA1",
+            "cds":"HA1",
             "ranges":[]
           },
           {
-            "gene":"HA2",
+            "cds":"HA2",
             "ranges":[{"begin":0, "end":186}]
           }
         ],

diff --git a/nextclade/dataset_config/h1n1pdm/na/MW626056/pathogen.json b/nextclade/dataset_config/h1n1pdm/na/MW626056/pathogen.json
@@ -12,9 +12,9 @@
         "nameShort": "Glyc.",
         "nameFriendly": "Glycosylation",
         "description": "N-linked glycosylation motifs (N-X-S/T with X any amino acid other than P)",
-        "includeGenes": [
+        "includeCdses": [
           {
-            "gene":"NA",
+            "cds":"NA",
             "ranges":[{"begin":33, "end":470}]
           }
         ],

diff --git a/nextclade/dataset_config/h3n2/ha/CY163680/pathogen.json b/nextclade/dataset_config/h3n2/ha/CY163680/pathogen.json
@@ -11,13 +11,13 @@
         "nameShort": "Glyc.",
         "nameFriendly": "Glycosylation",
         "description": "N-linked glycosylation motifs (N-X-S/T with X any amino acid other than P)",
-        "includeGenes": [
+        "includeCdses": [
           {
-            "gene":"HA1",
+            "cds":"HA1",
             "ranges":[]
           },
           {
-            "gene":"HA2",
+            "cds":"HA2",
             "ranges":[{"begin":0, "end":186}]
           }
         ],

diff --git a/nextclade/dataset_config/h3n2/ha/EPI1857216/pathogen.json b/nextclade/dataset_config/h3n2/ha/EPI1857216/pathogen.json
@@ -12,7 +12,7 @@
       "name": "RBD",
       "nameFriendly": "RBD mutations",
       "description": "This column displays the number of differences between the sequence and the reference at positions identified by Koel et al. (145, 155, 156, 158, 159, 189, and 193 in HA1)",
-      "gene": "HA1",
+      "cds": "HA1",
       "aaRange": {
         "begin": 100,
         "end": 200
@@ -43,13 +43,13 @@
       "nameShort": "Glyc.",
       "nameFriendly": "Glycosylation",
       "description": "N-linked glycosylation motifs (N-X-S/T with X any amino acid other than P)",
-      "includeGenes": [
+      "includeCdses": [
         {
-          "gene":"HA1",
+          "cds":"HA1",
           "ranges":[]
         },
         {
-          "gene":"HA2",
+          "cds":"HA2",
           "ranges":[{"begin":0, "end":186}]
         }
       ],

diff --git a/nextclade/dataset_config/h3n2/na/EPI1857215/pathogen.json b/nextclade/dataset_config/h3n2/na/EPI1857215/pathogen.json
@@ -12,9 +12,9 @@
         "nameShort": "Glyc.",
         "nameFriendly": "Glycosylation",
         "description": "N-linked glycosylation motifs (N-X-S/T with X any amino acid other than P)",
-        "includeGenes": [
+        "includeCdses": [
           {
-            "gene":"NA",
+            "cds":"NA",
             "ranges":[{"begin":33, "end":470}]
           }
         ],

diff --git a/nextclade/dataset_config/vic/ha/EPI1926632/pathogen.json b/nextclade/dataset_config/vic/ha/EPI1926632/pathogen.json
@@ -7,13 +7,13 @@
       "nameShort": "Glyc.",
       "nameFriendly": "Glycosylation",
       "description": "N-linked glycosylation motifs (N-X-S/T with X any amino acid other than P)",
-      "includeGenes": [
+      "includeCdses": [
         {
-          "gene":"HA1",
+          "cds":"HA1",
           "ranges":[]
         },
         {
-          "gene":"HA2",
+          "cds":"HA2",
           "ranges":[{"begin":0, "end":187}]
         }
       ],

diff --git a/nextclade/dataset_config/vic/ha/KX058884/pathogen.json b/nextclade/dataset_config/vic/ha/KX058884/pathogen.json
@@ -13,13 +13,13 @@
         "nameShort": "Glyc.",
         "nameFriendly": "Glycosylation",
         "description": "N-linked glycosylation motifs (N-X-S/T with X any amino acid other than P)",
-        "includeGenes": [
+        "includeCdses": [
           {
-            "gene":"HA1",
+            "cds":"HA1",
             "ranges":[]
           },
           {
-            "gene":"HA2",
+            "cds":"HA2",
             "ranges":[{"begin":0, "end":186}]
           }
         ],

diff --git a/nextclade/dataset_config/vic/na/CY073894/pathogen.json b/nextclade/dataset_config/vic/na/CY073894/pathogen.json
@@ -12,9 +12,9 @@
         "nameShort": "Glyc.",
         "nameFriendly": "Glycosylation",
         "description": "N-linked glycosylation motifs (N-X-S/T with X any amino acid other than P)",
-        "includeGenes": [
+        "includeCdses": [
           {
-            "gene":"NA",
+            "cds":"NA",
             "ranges":[{"begin":33, "end":466}]
           }
         ],

diff --git a/nextclade/dataset_config/yam/ha/JN993010/pathogen.json b/nextclade/dataset_config/yam/ha/JN993010/pathogen.json
@@ -7,13 +7,13 @@
         "nameShort": "Glyc.",
         "nameFriendly": "Glycosylation",
         "description": "N-linked glycosylation motifs (N-X-S/T with X any amino acid other than P)",
-        "includeGenes": [
+        "includeCdses": [
           {
-            "gene":"HA1",
+            "cds":"HA1",
             "ranges":[]
           },
           {
-            "gene":"HA2",
+            "cds":"HA2",
             "ranges":[{"begin":0, "end":186}]
           }
         ],