feat: apply "rename 'gene' to 'cds' in code and public interfaces"

nextstrain · Jan 9, 2024 · 777f7bd · 777f7bd
1 parent 317ebee
commit 777f7bd
Show file tree

Hide file tree

Showing 34 changed files with 4,216 additions and 4,216 deletions.
diff --git a/data/nextstrain/flu/h1n1pdm/ha/CY121680/pathogen.json b/data/nextstrain/flu/h1n1pdm/ha/CY121680/pathogen.json
@@ -90,13 +90,13 @@
       "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,

diff --git a/data/nextstrain/flu/h1n1pdm/ha/MW626062/pathogen.json b/data/nextstrain/flu/h1n1pdm/ha/MW626062/pathogen.json
@@ -92,13 +92,13 @@
       "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,

diff --git a/data/nextstrain/flu/h1n1pdm/na/MW626056/pathogen.json b/data/nextstrain/flu/h1n1pdm/na/MW626056/pathogen.json
@@ -90,9 +90,9 @@
       "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,

diff --git a/data/nextstrain/flu/h3n2/ha/CY163680/pathogen.json b/data/nextstrain/flu/h3n2/ha/CY163680/pathogen.json
@@ -90,13 +90,13 @@
       "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,

diff --git a/data/nextstrain/flu/h3n2/ha/EPI1857216/pathogen.json b/data/nextstrain/flu/h3n2/ha/EPI1857216/pathogen.json
@@ -91,7 +91,7 @@
       "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
@@ -138,13 +138,13 @@
       "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,

diff --git a/data/nextstrain/flu/h3n2/na/EPI1857215/pathogen.json b/data/nextstrain/flu/h3n2/na/EPI1857215/pathogen.json
@@ -90,9 +90,9 @@
       "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,

diff --git a/data/nextstrain/flu/vic/ha/KX058884/pathogen.json b/data/nextstrain/flu/vic/ha/KX058884/pathogen.json
@@ -92,13 +92,13 @@
       "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,

diff --git a/data/nextstrain/flu/vic/na/CY073894/pathogen.json b/data/nextstrain/flu/vic/na/CY073894/pathogen.json
@@ -90,9 +90,9 @@
       "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,

diff --git a/data/nextstrain/flu/yam/ha/JN993010/pathogen.json b/data/nextstrain/flu/yam/ha/JN993010/pathogen.json
@@ -86,13 +86,13 @@
       "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,

diff --git a/data/nextstrain/mpox/all-clades/pathogen.json b/data/nextstrain/mpox/all-clades/pathogen.json
@@ -38,119 +38,119 @@
             "begin": 3,
             "end": 589
           },
-          "geneName": "OPG003"
+          "cdsName": "OPG003"
         },
         {
           "codonRange": {
             "begin": 3,
             "end": 589
           },
-          "geneName": "OPG003_dup"
+          "cdsName": "OPG003_dup"
         },
         {
           "codonRange": {
             "begin": 281,
             "end": 285
           },
-          "geneName": "OPG105"
+          "cdsName": "OPG105"
         },
         {
           "codonRange": {
             "begin": 227,
             "end": 229
           },
-          "geneName": "OPG164"
+          "cdsName": "OPG164"
         },
         {
           "codonRange": {
             "begin": 554,
             "end": 560
           },
-          "geneName": "OPG180"
+          "cdsName": "OPG180"
         },
         {
           "codonRange": {
             "begin": 42,
             "end": 101
           },
-          "geneName": "OPG197"
+          "cdsName": "OPG197"
         },
         {
           "codonRange": {
             "begin": 443,
             "end": 443
           },
-          "geneName": "OPG037"
+          "cdsName": "OPG037"
         },
         {
           "codonRange": {
             "begin": 57,
             "end": 443
           },
-          "geneName": "OPG037"
+          "cdsName": "OPG037"
         },
         {
           "codonRange": {
             "begin": 481,
             "end": 483
           },
-          "geneName": "OPG047"
+          "cdsName": "OPG047"
         },
         {
           "codonRange": {
             "begin": 482,
             "end": 483
           },
-          "geneName": "OPG047"
+          "cdsName": "OPG047"
         },
         {
           "codonRange": {
             "begin": 72,
             "end": 76
           },
-          "geneName": "OPG050"
+          "cdsName": "OPG050"
         },
         {
           "codonRange": {
             "begin": 369,
             "end": 371
           },
-          "geneName": "OPG153"
+          "cdsName": "OPG153"
         },
         {
           "codonRange": {
             "begin": 370,
             "end": 371
           },
-          "geneName": "OPG153"
+          "cdsName": "OPG153"
         },
         {
           "codonRange": {
             "begin": 166,
             "end": 169
           },
-          "geneName": "OPG191"
+          "cdsName": "OPG191"
         },
         {
           "codonRange": {
             "begin": 72,
             "end": 222
           },
-          "geneName": "OPG195"
+          "cdsName": "OPG195"
         },
         {
           "codonRange": {
             "begin": 208,
             "end": 222
           },
-          "geneName": "OPG195"
+          "cdsName": "OPG195"
         },
         {
           "codonRange": {
             "begin": 289,
             "end": 346
           },
-          "geneName": "OPG174"
+          "cdsName": "OPG174"
         }
       ],
       "scoreWeight": 20
@@ -183,23 +183,23 @@
       "ignoredStopCodons": [
         {
           "codon": 187,
-          "geneName": "OPG015_dup"
+          "cdsName": "OPG015_dup"
         },
         {
           "codon": 187,
-          "geneName": "OPG015"
+          "cdsName": "OPG015"
         },
         {
           "codon": 21,
-          "geneName": "OPG176"
+          "cdsName": "OPG176"
         },
         {
           "codon": 299,
-          "geneName": "OPG187"
+          "cdsName": "OPG187"
         },
         {
           "codon": 48,
-          "geneName": "OPG059"
+          "cdsName": "OPG059"
         }
       ],
       "scoreWeight": 20

diff --git a/data/nextstrain/mpox/clade-iib/pathogen.json b/data/nextstrain/mpox/clade-iib/pathogen.json
@@ -38,7 +38,7 @@
             "begin": 289,
             "end": 346
           },
-          "geneName": "OPG174"
+          "cdsName": "OPG174"
         }
       ],
       "scoreWeight": 20
@@ -71,15 +71,15 @@
       "ignoredStopCodons": [
         {
           "codon": 187,
-          "geneName": "OPG015_dup"
+          "cdsName": "OPG015_dup"
         },
         {
           "codon": 187,
-          "geneName": "OPG015"
+          "cdsName": "OPG015"
         },
         {
           "codon": 21,
-          "geneName": "OPG176"
+          "cdsName": "OPG176"
         }
       ],
       "scoreWeight": 40

diff --git a/data/nextstrain/mpox/lineage-b.1/pathogen.json b/data/nextstrain/mpox/lineage-b.1/pathogen.json
@@ -267,11 +267,11 @@
       "ignoredStopCodons": [
         {
           "codon": 187,
-          "geneName": "OPG015_dup"
+          "cdsName": "OPG015_dup"
         },
         {
           "codon": 187,
-          "geneName": "OPG015"
+          "cdsName": "OPG015"
         }
       ],
       "scoreWeight": 40