Merge pull request #64 from nextstrain/fix-flu

flu: fix clade 2a.3b and add glyc to old data sets

CHANGELOG.md

@@ -1,5 +1,14 @@
 # CHANGELOG
 
+## 2023-02-01
+
+### Seasonal flu datasets
+
+#### New dataset version (tag `2023-02-01T12:00:00Z`)
+
+ - removes a synonymous mutation from the definition of A/H3N2 clade 2a.3b. Some viruses that should be in this clade didn't have this change.
+ - adds glycosylation to the remaining flu data sets
+
 ## 2023-01-27
 
 ### Seasonal flu datasets

data/datasets/flu_h1n1pdm_ha/references/CY121680/versions/2023-02-01T12:00:00Z/files/genemap.gff

@@ -0,0 +1,5 @@
+##gff-version 3
+##sequence-region CY121680.1 1 1752
+CY121680.1	feature	gene	21	71	.	+	.	gene_name="SigPep"
+CY121680.1	feature	gene	72	1052	.	+	.	gene_name="HA1"
+CY121680.1	feature	gene	1053	1718	.	+	.	gene_name="HA2"

data/datasets/flu_h1n1pdm_ha/references/CY121680/versions/2023-02-01T12:00:00Z/files/primers.csv

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

data/datasets/flu_h1n1pdm_ha/references/CY121680/versions/2023-02-01T12:00:00Z/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_h1n1pdm_ha/references/CY121680/versions/2023-02-01T12:00:00Z/files/reference.fasta

@@ -0,0 +1,2 @@
+>CY121680.1 Influenza A virus (A/California/07/2009(H1N1)) hemagglutinin (HA) gene, complete cds
+GGAAAACAAAAGCAACAAAAATGAAGGCAATACTAGTAGTTCTGCTATATACATTTGCAACCGCAAATGCAGACACATTATGTATAGGTTATCATGCGAACAATTCAACAGACACTGTAGACACAGTACTAGAAAAGAATGTAACAGTAACACACTCTGTTAACCTTCTAGAAGACAAGCATAACGGGAAACTATGCAAACTAAGAGGGGTAGCCCCATTGCATTTGGGTAAATGTAACATTGCTGGCTGGATCCTGGGAAATCCAGAGTGTGAATCACTCTCCACAGCAAGCTCATGGTCCTACATTGTGGAAACACCTAGTTCAGACAATGGAACGTGTTACCCAGGAGATTTCATCGATTATGAGGAGCTAAGAGAGCAATTGAGCTCAGTGTCATCATTTGAAAGGTTTGAGATATTCCCCAAGACAAGTTCATGGCCCAATCATGACTCGAACAAAGGTGTAACGGCAGCATGTCCTCATGCTGGAGCAAAAAGCTTCTACAAAAATTTAATATGGCTAGTTAAAAAAGGAAATTCATACCCAAAGCTCAGCAAATCCTACATTAATGATAAAGGGAAAGAAGTCCTCGTGCTATGGGGCATTCACCATCCATCTACTAGTGCTGACCAACAAAGTCTCTATCAGAATGCAGATGCATATGTTTTTGTGGGGTCATCAAGATACAGCAAGAAGTTCAAGCCGGAAATAGCAATAAGACCCAAAGTGAGGGATCGAGAAGGGAGAATGAACTATTACTGGACACTAGTAGAGCCGGGAGACAAAATAACATTCGAAGCAACTGGAAATCTAGTGGTACCGAGATATGCATTCGCAATGGAAAGAAATGCTGGATCTGGTATTATCATTTCAGATACACCAGTCCACGATTGCAATACAACTTGTCAAACACCCAAGGGTGCTATAAACACCAGCCTCCCATTTCAGAATATACATCCGATCACAATTGGAAAATGTCCAAAATATGTAAAAAGCACAAAATTGAGACTGGCCACAGGATTGAGGAATATCCCGTCTATTCAATCTAGAGGCCTATTTGGGGCCATTGCCGGTTTCATTGAAGGGGGGTGGACAGGGATGGTAGATGGATGGTACGGTTATCACCATCAAAATGAGCAGGGGTCAGGATATGCAGCCGACCTGAAGAGCACACAGAATGCCATTGACGAGATTACTAACAAAGTAAATTCTGTTATTGAAAAGATGAATACACAGTTCACAGCAGTAGGTAAAGAGTTCAACCACCTGGAAAAAAGAATAGAGAATTTAAATAAAAAAGTTGATGATGGTTTCCTGGACATTTGGACTTACAATGCCGAACTGTTGGTTCTATTGGAAAATGAAAGAACTTTGGACTACCACGATTCAAATGTGAAGAACTTATATGAAAAGGTAAGAAGCCAGCTAAAAAACAATGCCAAGGAAATTGGAAACGGCTGCTTTGAATTTTACCACAAATGCGATAACACGTGCATGGAAAGTGTCAAAAATGGGACTTATGACTACCCAAAATACTCAGAGGAAGCAAAATTAAACAGAGAAGAAATAGATGGGGTAAAGCTGGAATCAACAAGGATTTACCAGATTTTGGCGATCTATTCAACTGTCGCCAGTTCATTGGTACTGGTAGTCTCCCTGGGGGCAATCAGTTTCTGGATGTGCTCTAATGGGTCTCTACAGTGTAGAATATGTATTTAACATTAGGATTTCAGAAGCATGAGAAAAACAC

data/datasets/flu_h1n1pdm_ha/references/CY121680/versions/2023-02-01T12:00:00Z/files/tag.json

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+{
+  "tag": "2023-02-01T12:00:00Z",
+  "comment": "New WHO clade names, data from GISAID",
+  "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": {}
+}