flu: update datasets

CHANGELOG.md

@@ -1,5 +1,12 @@
 # CHANGELOG
 
+## 2023-11-18
+
+### New Influenza datasets version (tag `2023-11-18T12:00:00Z`)
+
+ - new subclades for several lineages
+ - new alias for A/H3N2 HA
+
 ## 2023-10-26
 
 ### New SARS-CoV-2 dataset version (tag `2023-10-26T12:00:00Z`)

data/datasets/flu_h1n1pdm_ha/references/CY121680/versions/2023-11-18T12:00:00Z/files/genemap.gff

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+##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/2023-11-18T12:00:00Z/files/primers.csv

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

data/datasets/flu_h1n1pdm_ha/references/CY121680/versions/2023-11-18T12:00:00Z/files/qc.json

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+{
+  "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/2023-11-18T12:00:00Z/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/2023-11-18T12:00:00Z/files/tag.json

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+{
+  "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_h1n1pdm_ha/references/CY121680/versions/2023-11-18T12:00:00Z/files/virus_properties.json

@@ -0,0 +1,26 @@
+{
+    "schemaVersion": "1.10.0",
+    "nucMutLabelMap": {},
+    "nucMutLabelMapReverse": {},
+    "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]"
+        ]
+      }
+    ]
+}

data/datasets/flu_h1n1pdm_ha/references/MW626062/versions/2023-11-18T12:00:00Z/files/genemap.gff

@@ -0,0 +1,5 @@
+##gff-version 3
+##sequence-region MW626062.1 1 1752
+MW626062.1	feature	gene	21	71	.	+	.	gene_name="SigPep"
+MW626062.1	feature	gene	72	1052	.	+	.	gene_name="HA1"
+MW626062.1	feature	gene	1053	1718	.	+	.	gene_name="HA2"

data/datasets/flu_h1n1pdm_ha/references/MW626062/versions/2023-11-18T12:00:00Z/files/primers.csv

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

data/datasets/flu_h1n1pdm_ha/references/MW626062/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_h1n1pdm_ha/references/MW626062/versions/2023-11-18T12:00:00Z/files/reference.fasta

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+>MW626062.1 Influenza A virus (A/Wisconsin/588/2019(H1N1)) segment 4 hemagglutinin (HA) gene, complete cds
+GGAAAACAAAAGCAACAAAAATGAAGGCAATACTAGTAGTTATGCTGTATACATTTACAACCGCAAATGC
+AGACACATTATGTATAGGTTATCATGCGAACAATTCAACAGACACTGTGGACACAGTACTAGAAAAGAAT
+GTAACAGTAACACACTCTGTCAATCTTCTGGAAGACAAGCATAACGGAAAACTATGCAAACTAAGAGGGG
+TAGCCCCATTGCATTTGGGTAAATGTAACATTGCTGGCTGGATCCTGGGAAATCCAGAGTGTGAATCACT
+CTCCACAGCAAGATCATGGTCCTACATTGTGGAAACATCTAATTCAGACAATGGAACGTGTTACCCAGGA
+GATTTCATCAATTATGAGGAGCTAAGAGAGCAATTGAGCTCAGTGTCATCATTTGAAAGGTTTGAAATAT
+TCCCCAAGACAAGTTCATGGCCTAATCATGACTCGGACAATGGTGTAACGGCAGCATGTCCTCACGCTGG
+AGCAAAAAGCTTCTACAAAAACTTGATATGGCTGGTTAAAAAAGGAAAATCATACCCAAAGATCAACCAA
+ACCTACATTAATGATAAAGGGAAAGAAGTCCTCGTGCTGTGGGGCATTCACCATCCACCTACTATTGCTG
+ACCAACAAAGTCTCTATCAGAATGCAGATGCATATGTTTTTGTGGGGACATCAAGATACAGCAAGAAGTT
+CAAGCCGGAAATAGCAACAAGACCCAAAGTGAGGGATCAAGAAGGGAGAATGAACTATTACTGGACACTA
+GTAGAACCGGGAGACAAAATAACATTCGAAGCAACTGGTAATCTAGTGGCACCGAGATATGCATTCACAA
+TGGAAAGAGATGCTGGATCTGGTATTATCATTTCAGATACACCAGTCCACGATTGCAATACAACTTGTCA
+GACACCCGAGGGTGCTATAAACACCAGCCTCCCATTTCAGAATGTACATCCGATCACAATTGGGAAATGT
+CCAAAGTATGTAAAAAGCACAAAATTGAGACTGGCCACAGGATTGAGGAATGTCCCGTCTATTCAATCTA
+GAGGCCTATTCGGGGCCATTGCTGGCTTCATCGAAGGGGGGTGGACAGGGATGGTAGATGGATGGTACGG
+TTATCACCATCAAAATGAGCAGGGGTCAGGATATGCAGCCGATCTGAAGAGCACACAAAATGCCATTGAT
+AAGATTACTAACAAAGTAAATTCTGTTATTGAAAAGATGAATACACAGTTCACAGCAGTTGGTAAAGAGT
+TCAACCACCTTGAAAAAAGAATAGAGAATCTAAATAAAAAGGTTGATGATGGTTTCCTGGACATTTGGAC
+TTACAATGCCGAACTGTTGGTTCTACTGGAAAACGAAAGAACTTTGGACTATCACGATTCAAATGTGAAG
+AACTTGTATGAAAAAGTAAGAAACCAGTTAAAAAACAATGCCAAGGAAATTGGAAACGGCTGCTTTGAAT
+TTTACCACAAATGCGACAACACATGCATGGAAAGTGTCAAGAATGGGACTTATGACTACCCAAAATACTC
+AGAGGAAGCAAAATTAAACAGAGAAAAAATAGATGGAGTAAAGCTGGACTCAACAAGGATCTACCAGATT
+TTGGCGATCTATTCAACTGTTGCCAGTTCATTGGTACTGGTAGTCTCCCTGGGGGCAATCAGCTTCTGGA
+TGTGCTCTAATGGGTCTCTACAGTGTAGAATATGTATTTAACATTAGGATTTCAGAATCATGAGAAAAAC
+AC