Merge pull request #119 from nextstrain/feat/apply-rename-default-gene

nextstrain · Dec 8, 2023 · 63ca00d · 63ca00d
2 parents e726dd3 + 2b97081
commit 63ca00d
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diff --git a/data/nextstrain/flu/h1n1pdm/ha/CY121680/pathogen.json b/data/nextstrain/flu/h1n1pdm/ha/CY121680/pathogen.json
@@ -11,7 +11,7 @@
     "cli": "3.0.0-alpha.0",
     "web": "3.0.0-alpha.0"
   },
-  "defaultGene": "HA1",
+  "defaultCds": "HA1",
   "files": {
     "changelog": "CHANGELOG.md",
     "examples": "sequences.fasta",
@@ -53,7 +53,7 @@
       "ignoredStopCodons": []
     }
   },
-  "geneOrderPreference": [
+  "cdsOrderPreference": [
     "HA1",
     "HA2"
   ],

diff --git a/data/nextstrain/flu/h1n1pdm/ha/MW626062/pathogen.json b/data/nextstrain/flu/h1n1pdm/ha/MW626062/pathogen.json
@@ -11,7 +11,7 @@
     "cli": "3.0.0-alpha.0",
     "web": "3.0.0-alpha.0"
   },
-  "defaultGene": "HA1",
+  "defaultCds": "HA1",
   "files": {
     "changelog": "CHANGELOG.md",
     "examples": "sequences.fasta",
@@ -53,7 +53,7 @@
       "ignoredStopCodons": []
     }
   },
-  "geneOrderPreference": [
+  "cdsOrderPreference": [
     "HA1",
     "HA2"
   ],

diff --git a/data/nextstrain/flu/h1n1pdm/mp/pathogen.json b/data/nextstrain/flu/h1n1pdm/mp/pathogen.json
@@ -42,7 +42,7 @@
       "ignoredStopCodons": []
     }
   },
-  "geneOrderPreference": [],
+  "cdsOrderPreference": [],
   "maintenance": {
     "website": [
       "https://nextstrain.org",
@@ -70,7 +70,7 @@
     "reference accession": "NC_026431",
     "reference name": "A/California/07/2009"
   },
-  "defaultGene": "M2",
+  "defaultCds": "M2",
   "version": {
     "tag": "unreleased"
   }

diff --git a/data/nextstrain/flu/h1n1pdm/na/MW626056/pathogen.json b/data/nextstrain/flu/h1n1pdm/na/MW626056/pathogen.json
@@ -11,7 +11,7 @@
     "cli": "3.0.0-alpha.0",
     "web": "3.0.0-alpha.0"
   },
-  "defaultGene": "NA",
+  "defaultCds": "NA",
   "files": {
     "changelog": "CHANGELOG.md",
     "examples": "sequences.fasta",
@@ -53,7 +53,7 @@
       "ignoredStopCodons": []
     }
   },
-  "geneOrderPreference": [
+  "cdsOrderPreference": [
     "NA"
   ],
   "maintenance": {

diff --git a/data/nextstrain/flu/h1n1pdm/np/pathogen.json b/data/nextstrain/flu/h1n1pdm/np/pathogen.json
@@ -42,7 +42,7 @@
       "ignoredStopCodons": []
     }
   },
-  "geneOrderPreference": [],
+  "cdsOrderPreference": [],
   "maintenance": {
     "website": [
       "https://nextstrain.org",
@@ -70,7 +70,7 @@
     "reference accession": "NC_026436",
     "reference name": "A/California/07/2009"
   },
-  "defaultGene": "NP",
+  "defaultCds": "NP",
   "version": {
     "tag": "unreleased"
   }

diff --git a/data/nextstrain/flu/h1n1pdm/ns/pathogen.json b/data/nextstrain/flu/h1n1pdm/ns/pathogen.json
@@ -42,7 +42,7 @@
       "ignoredStopCodons": []
     }
   },
-  "geneOrderPreference": [],
+  "cdsOrderPreference": [],
   "maintenance": {
     "website": [
       "https://nextstrain.org",
@@ -70,7 +70,7 @@
     "reference accession": "NC_026432",
     "reference name": "A/California/07/2009"
   },
-  "defaultGene": "NS1",
+  "defaultCds": "NS1",
   "version": {
     "tag": "unreleased"
   }

diff --git a/data/nextstrain/flu/h1n1pdm/pa/pathogen.json b/data/nextstrain/flu/h1n1pdm/pa/pathogen.json
@@ -42,7 +42,7 @@
       "ignoredStopCodons": []
     }
   },
-  "geneOrderPreference": [],
+  "cdsOrderPreference": [],
   "maintenance": {
     "website": [
       "https://nextstrain.org",
@@ -70,7 +70,7 @@
     "reference accession": "NC_026437",
     "reference name": "A/California/07/2009"
   },
-  "defaultGene": "PA",
+  "defaultCds": "PA",
   "version": {
     "tag": "unreleased"
   }

diff --git a/data/nextstrain/flu/h1n1pdm/pb1/pathogen.json b/data/nextstrain/flu/h1n1pdm/pb1/pathogen.json
@@ -42,7 +42,7 @@
       "ignoredStopCodons": []
     }
   },
-  "geneOrderPreference": [],
+  "cdsOrderPreference": [],
   "maintenance": {
     "website": [
       "https://nextstrain.org",
@@ -70,7 +70,7 @@
     "reference accession": "NC_026435",
     "reference name": "A/California/07/2009"
   },
-  "defaultGene": "PB1",
+  "defaultCds": "PB1",
   "version": {
     "tag": "unreleased"
   }

diff --git a/data/nextstrain/flu/h1n1pdm/pb2/pathogen.json b/data/nextstrain/flu/h1n1pdm/pb2/pathogen.json
@@ -42,7 +42,7 @@
       "ignoredStopCodons": []
     }
   },
-  "geneOrderPreference": [],
+  "cdsOrderPreference": [],
   "maintenance": {
     "website": [
       "https://nextstrain.org",
@@ -70,7 +70,7 @@
     "reference accession": "NC_026438",
     "reference name": "A/California/07/2009"
   },
-  "defaultGene": "PB2",
+  "defaultCds": "PB2",
   "version": {
     "tag": "unreleased"
   }

diff --git a/data/nextstrain/flu/h3n2/ha/CY163680/pathogen.json b/data/nextstrain/flu/h3n2/ha/CY163680/pathogen.json
@@ -11,7 +11,7 @@
     "cli": "3.0.0-alpha.0",
     "web": "3.0.0-alpha.0"
   },
-  "defaultGene": "HA1",
+  "defaultCds": "HA1",
   "files": {
     "changelog": "CHANGELOG.md",
     "examples": "sequences.fasta",
@@ -53,7 +53,7 @@
       "ignoredStopCodons": []
     }
   },
-  "geneOrderPreference": [
+  "cdsOrderPreference": [
     "HA1",
     "HA2"
   ],

diff --git a/data/nextstrain/flu/h3n2/ha/EPI1857216/pathogen.json b/data/nextstrain/flu/h3n2/ha/EPI1857216/pathogen.json
@@ -11,7 +11,7 @@
     "cli": "3.0.0-alpha.0",
     "web": "3.0.0-alpha.0"
   },
-  "defaultGene": "HA1",
+  "defaultCds": "HA1",
   "files": {
     "changelog": "CHANGELOG.md",
     "examples": "sequences.fasta",
@@ -53,7 +53,7 @@
       "ignoredStopCodons": []
     }
   },
-  "geneOrderPreference": [
+  "cdsOrderPreference": [
     "HA1",
     "HA2"
   ],

diff --git a/data/nextstrain/flu/h3n2/mp/pathogen.json b/data/nextstrain/flu/h3n2/mp/pathogen.json
@@ -42,7 +42,7 @@
       "ignoredStopCodons": []
     }
   },
-  "geneOrderPreference": [],
+  "cdsOrderPreference": [],
   "maintenance": {
     "website": [
       "https://nextstrain.org",
@@ -70,7 +70,7 @@
     "reference accession": "NC_007367",
     "reference name": "A/NewYork/392/2004"
   },
-  "defaultGene": "M2",
+  "defaultCds": "M2",
   "version": {
     "tag": "unreleased"
   }

diff --git a/data/nextstrain/flu/h3n2/na/EPI1857215/pathogen.json b/data/nextstrain/flu/h3n2/na/EPI1857215/pathogen.json
@@ -11,7 +11,7 @@
     "cli": "3.0.0-alpha.0",
     "web": "3.0.0-alpha.0"
   },
-  "defaultGene": "NA",
+  "defaultCds": "NA",
   "files": {
     "changelog": "CHANGELOG.md",
     "examples": "sequences.fasta",
@@ -53,7 +53,7 @@
       "ignoredStopCodons": []
     }
   },
-  "geneOrderPreference": [
+  "cdsOrderPreference": [
     "NA"
   ],
   "maintenance": {

diff --git a/data/nextstrain/flu/h3n2/np/pathogen.json b/data/nextstrain/flu/h3n2/np/pathogen.json
@@ -42,7 +42,7 @@
       "ignoredStopCodons": []
     }
   },
-  "geneOrderPreference": [],
+  "cdsOrderPreference": [],
   "maintenance": {
     "website": [
       "https://nextstrain.org",
@@ -70,7 +70,7 @@
     "reference accession": "NC_007369",
     "reference name": "A/NewYork/392/2004"
   },
-  "defaultGene": "NP",
+  "defaultCds": "NP",
   "version": {
     "tag": "unreleased"
   }

diff --git a/data/nextstrain/flu/h3n2/ns/pathogen.json b/data/nextstrain/flu/h3n2/ns/pathogen.json
@@ -42,7 +42,7 @@
       "ignoredStopCodons": []
     }
   },
-  "geneOrderPreference": [],
+  "cdsOrderPreference": [],
   "maintenance": {
     "website": [
       "https://nextstrain.org",
@@ -70,7 +70,7 @@
     "reference accession": "NC_007370",
     "reference name": "A/NewYork/392/2004"
   },
-  "defaultGene": "NS1",
+  "defaultCds": "NS1",
   "version": {
     "tag": "unreleased"
   }

diff --git a/data/nextstrain/flu/h3n2/pa/pathogen.json b/data/nextstrain/flu/h3n2/pa/pathogen.json
@@ -42,7 +42,7 @@
       "ignoredStopCodons": []
     }
   },
-  "geneOrderPreference": [],
+  "cdsOrderPreference": [],
   "maintenance": {
     "website": [
       "https://nextstrain.org",
@@ -70,7 +70,7 @@
     "reference accession": "NC_007371",
     "reference name": "A/NewYork/392/2004"
   },
-  "defaultGene": "PA",
+  "defaultCds": "PA",
   "version": {
     "tag": "unreleased"
   }

diff --git a/data/nextstrain/flu/h3n2/pb1/pathogen.json b/data/nextstrain/flu/h3n2/pb1/pathogen.json
@@ -42,7 +42,7 @@
       "ignoredStopCodons": []
     }
   },
-  "geneOrderPreference": [],
+  "cdsOrderPreference": [],
   "maintenance": {
     "website": [
       "https://nextstrain.org",
@@ -70,7 +70,7 @@
     "reference accession": "NC_007372",
     "reference name": "A/NewYork/392/2004"
   },
-  "defaultGene": "PB1",
+  "defaultCds": "PB1",
   "version": {
     "tag": "unreleased"
   }

diff --git a/data/nextstrain/flu/h3n2/pb2/pathogen.json b/data/nextstrain/flu/h3n2/pb2/pathogen.json
@@ -42,7 +42,7 @@
       "ignoredStopCodons": []
     }
   },
-  "geneOrderPreference": [],
+  "cdsOrderPreference": [],
   "maintenance": {
     "website": [
       "https://nextstrain.org",
@@ -70,7 +70,7 @@
     "reference accession": "NC_007373",
     "reference name": "A/NewYork/392/2004"
   },
-  "defaultGene": "PB2",
+  "defaultCds": "PB2",
   "version": {
     "tag": "unreleased"
   }

diff --git a/data/nextstrain/flu/vic/ha/KX058884/pathogen.json b/data/nextstrain/flu/vic/ha/KX058884/pathogen.json
@@ -11,7 +11,7 @@
     "cli": "3.0.0-alpha.0",
     "web": "3.0.0-alpha.0"
   },
-  "defaultGene": "HA1",
+  "defaultCds": "HA1",
   "files": {
     "changelog": "CHANGELOG.md",
     "examples": "sequences.fasta",
@@ -53,7 +53,7 @@
       "ignoredStopCodons": []
     }
   },
-  "geneOrderPreference": [
+  "cdsOrderPreference": [
     "HA1",
     "HA2"
   ],

diff --git a/data/nextstrain/flu/vic/na/CY073894/pathogen.json b/data/nextstrain/flu/vic/na/CY073894/pathogen.json
@@ -11,7 +11,7 @@
     "cli": "3.0.0-alpha.0",
     "web": "3.0.0-alpha.0"
   },
-  "defaultGene": "NA",
+  "defaultCds": "NA",
   "files": {
     "changelog": "CHANGELOG.md",
     "examples": "sequences.fasta",
@@ -53,7 +53,7 @@
       "ignoredStopCodons": []
     }
   },
-  "geneOrderPreference": [
+  "cdsOrderPreference": [
     "NA"
   ],
   "maintenance": {

diff --git a/data/nextstrain/flu/yam/ha/JN993010/pathogen.json b/data/nextstrain/flu/yam/ha/JN993010/pathogen.json
@@ -11,7 +11,7 @@
     "cli": "3.0.0-alpha.0",
     "web": "3.0.0-alpha.0"
   },
-  "defaultGene": "HA1",
+  "defaultCds": "HA1",
   "files": {
     "changelog": "CHANGELOG.md",
     "examples": "sequences.fasta",
@@ -53,7 +53,7 @@
       "ignoredStopCodons": []
     }
   },
-  "geneOrderPreference": [
+  "cdsOrderPreference": [
     "HA1",
     "HA2"
   ],

diff --git a/data/nextstrain/rsv/a/EPI_ISL_412866/pathogen.json b/data/nextstrain/rsv/a/EPI_ISL_412866/pathogen.json
@@ -11,7 +11,7 @@
     "cli": "3.0.0-alpha.0",
     "web": "3.0.0-alpha.0"
   },
-  "defaultGene": "F",
+  "defaultCds": "F",
   "files": {
     "changelog": "CHANGELOG.md",
     "examples": "sequences.fasta",
@@ -53,7 +53,7 @@
       "ignoredStopCodons": []
     }
   },
-  "geneOrderPreference": [
+  "cdsOrderPreference": [
     "F",
     "G",
     "L"