flu: update h3n2

data/datasets/flu_h3n2_ha/references/EPI1857216/versions/2023-11-18T12:00:00Z/files/genemap.gff

@@ -0,0 +1,5 @@
+##gff-version 3
+##sequence-region EPI1857216 1 1718
+EPI1857216	feature	gene	1	48	.	+	.	gene_name="SigPep"
+EPI1857216	feature	gene	49	1035	.	+	.	gene_name="HA1"
+EPI1857216	feature	gene	1036	1698	.	+	.	gene_name="HA2"

data/datasets/flu_h3n2_ha/references/EPI1857216/versions/2023-11-18T12:00:00Z/files/primers.csv

@@ -0,0 +1 @@
+Country (Institute),Target,Oligonucleotide,Sequence

data/datasets/flu_h3n2_ha/references/EPI1857216/versions/2023-11-18T12:00:00Z/files/qc.json

@@ -0,0 +1,33 @@
+{
+  "schemaVersion": "1.2.0",
+  "privateMutations": {
+    "enabled": true,
+    "typical": 5,
+    "cutoff": 15,
+    "weightLabeledSubstitutions": 2,
+    "weightReversionSubstitutions": 1,
+    "weightUnlabeledSubstitutions": 1
+  },
+  "missingData": {
+    "enabled": false,
+    "missingDataThreshold": 100,
+    "scoreBias": 10
+  },
+  "snpClusters": {
+    "enabled": false,
+    "windowSize": 100,
+    "clusterCutOff": 5,
+    "scoreWeight": 50
+  },
+  "mixedSites": {
+    "enabled": true,
+    "mixedSitesThreshold": 4
+  },
+  "frameShifts": {
+    "enabled": true
+  },
+  "stopCodons": {
+    "enabled": true,
+    "ignoredStopCodons": []
+  }
+}

data/datasets/flu_h3n2_ha/references/EPI1857216/versions/2023-11-18T12:00:00Z/files/reference.fasta

@@ -0,0 +1,23 @@
+>EPI_ISL_1563628 | A/Darwin/6/2021 | A / H3N2 |  | 2021-03-16
+atgaagactatcattgctttgagcaacattctatgtcttgttttcgctcaaaaaatacctggaaatgacaatagcacggc
+aacgctgtgccttgggcaccatgcagtaccaaacggaacgatagtgaaaacaatcacaaatgaccgaattgaagttacta
+atgctactgagttggttcagaattcatcaataggtgaaatatgcggcagtcctcatcagatccttgatggagggaactgc
+acactaatagatgctctattgggggaccctcagtgtgacggctttcaaaataaggaatgggacctttttgttgaaagaag
+cagagccaacagcaactgttacccttatgatgtgccggattatgcctcccttaggtcactagttgcctcatccggcacac
+tggagtttaaaaatgaaagcttcaattggactggagtcaaacaaaacggaacaagttctgcgtgcataaggggatctagt
+agtagtttttttagtagattaaattggttgaccagcttaaacaacatatatccagcacagaacgtgactatgccaaacaa
+ggaacaatttgacaaattgtacatttggggggttcaccacccggatacggacaagaaccaaatctccctgtttgctcaat
+catcaggaagaatcacagtatctaccaaaagaagccaacaagctgtaatcccaaatatcggatctagacccagaataagg
+gatatccctagcagaataagcatctattggacaatagtaaaaccgggagacatacttttgattaacagcacagggaatct
+aattgctcctaggggttacttcaaaatacgaagtgggaaaagctcaataatgagatcagatgcacccattggcaaatgta
+agtctgaatgcatcactccaaatggaagcattcccaatgacaaaccgttccaaaatgtaaacaggatcacatacggggcc
+tgtcccagatatgttaagcaaagcaccctgaaattggcaacaggaatgcgaaatgtaccagagaaacaaaccagaggcat
+atttggcgcaatagcgggtttcatagaaaatggatgggagggaatggtggatggttggtacggtttcaggcatcaaaatt
+ctgagggaagaggacaagcagcagatctcaaaagcactcaagcagcaatcgatcaaatcaatgggaagctgaatcgattg
+atcggaaaaaccaacgagaaattccatcagattgaaaaagaattctcagaagtagaaggaagagttcaagaccttgagaa
+atatgttgaggacactaaaatagatctctggtcatacaacgcggagcttcttgttgccctggagaaccaacatacgattg
+acctaactgactcagaaatgaacaaactgtttgaaaaaacaaagaagcaactgagggaaaatgctgaggatatgggaaat
+ggttgtttcaaaatataccacaaatgtgacaatgcctgcataggatcaataagaaatgaaacttatgaccacaatgtgta
+cagggatgaagcattaaacaaccggttccagatcaagggagttgagctgaagtcagggtacaaagattggatcctatgga
+tttcctttgccatgtcatgttttttgctttgtattgctttgttggggttcatcatgtgggcctgccaaaagggcaacatt
+agatgcaacatttgcatttgagtgcattaattaaaaac

data/datasets/flu_h3n2_ha/references/EPI1857216/versions/2023-11-18T12:00:00Z/files/tag.json

@@ -0,0 +1,25 @@
+{
+  "tag": "2023-11-18T12:00:00Z",
+  "comment": "Addition of experimental lineages",
+  "compatibility": {
+    "nextcladeCli": {
+      "min": "1.3.0",
+      "max": null
+    },
+    "nextcladeWeb": {
+      "min": "1.6.0",
+      "max": null
+    }
+  },
+  "enabled": true,
+  "files": {
+    "geneMap": "genemap.gff",
+    "primers": "primers.csv",
+    "qc": "qc.json",
+    "reference": "reference.fasta",
+    "sequences": "sequences.fasta",
+    "tree": "tree.json",
+    "virusPropertiesJson": "virus_properties.json"
+  },
+  "metadata": {}
+}

data/datasets/flu_h3n2_ha/references/EPI1857216/versions/2023-11-18T12:00:00Z/files/virus_properties.json

@@ -0,0 +1,56 @@
+{
+  "schemaVersion": "1.10.0",
+  "nucMutLabelMap": {},
+  "nucMutLabelMapReverse": {},
+  "phenotypeData":[
+    {
+      "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",
+      "aaRange": {
+        "begin": 100,
+        "end": 200
+      },
+      "ignore": {
+        "clades": ["outgroup"]
+      },
+      "data": [
+        {
+          "name": "differences",
+          "weight": 1,
+          "locations": {
+            "145": {"default":1},
+            "155": {"default":1},
+            "156": {"default":1},
+            "158": {"default":1},
+            "159": {"default":1},
+            "189": {"default":1},
+            "193": {"default":1}
+          }
+        }
+      ]
+    }
+  ],
+  "aaMotifs": [
+    {
+      "name": "glycosylation",
+      "nameShort": "Glyc.",
+      "nameFriendly": "Glycosylation",
+      "description": "N-linked glycosylation motifs (N-X-S/T with X any amino acid other than P)",
+      "includeGenes": [
+        {
+          "gene":"HA1",
+          "ranges":[]
+        },
+        {
+          "gene":"HA2",
+          "ranges":[{"begin":0, "end":186}]
+        }
+      ],
+      "motifs": [
+        "N[^P][ST]"
+      ]
+    }
+  ]
+}