flu: add B(vic) non-HA/NA datasets

data/nextstrain/collection.json

@@ -57,6 +57,12 @@
     "nextstrain/measles/N450/WHO-2012",
     "nextstrain/dengue/all",
     "nextstrain/yellow-fever/prM-E",
-    "nextstrain/hmpv/all-clades/NC_039199"
+    "nextstrain/hmpv/all-clades/NC_039199",
+    "nextstrain/flu/vic/pa",
+    "nextstrain/flu/vic/pb1",
+    "nextstrain/flu/vic/np",
+    "nextstrain/flu/vic/mp",
+    "nextstrain/flu/vic/pb2",
+    "nextstrain/flu/vic/ns"
   ]
 }

data/nextstrain/flu/vic/mp/CHANGELOG.md

@@ -0,0 +1,3 @@
+## Unreleased
+
+Initial release of all segments for Influenza B(Vic). Datasets for segments other than HA and NA are "reference-only" and are based on B/Brisbane/2008.

data/nextstrain/flu/vic/mp/README.md

@@ -0,0 +1,16 @@
+# Influenza B(Vic) MP based on reference "B/Brisbane/60/2008"
+
+| Key                  | Value                |
+| -------------------- | -------------------- |
+| authors                | [Richard Neher](https://neherlab.org), [Nextstrain](https://nextstrain.org)                         |
+| name                 | Influenza B(Vic) MP                      |
+| reference            | B/Brisbane/60/2008                    |
+| dataset path         | flu/vic/mp                     |
+| reference accession  | CY115152  |
+
+## Features
+This dataset only provides a reference for alignment and an annotation for translation.
+
+## What is Nextclade dataset
+
+Read more about Nextclade datasets in Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html

data/nextstrain/flu/vic/mp/genome_annotation.gff3

@@ -0,0 +1,8 @@
+##gff-version 3
+#!gff-spec-version 1.21
+#!processor NCBI annotwriter
+##sequence-region CY115152.1 1 1147
+##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=604436
+CY115152.1	Genbank	region	1	1147	.	+	.	ID=CY115152.1:1..1147;Dbxref=taxon:604436;Name=7;collection-date=2008;country=Australia: Brisbane;gbkey=Src;lab-host=Egg passage(s);mol_type=viral cRNA;nat-host=human;segment=7;strain=B/Brisbane/60/2008
+CY115152.1	Genbank	CDS	3	749	.	+	0	Name=M1;gene=M1;gbkey=CDS;protein_id=AFH57910.1;ID=cds-AFH57910.1;product=matrix protein 1;Dbxref=NCBI_GP:AFH57910.1
+CY115152.1	Genbank	CDS	749	1078	.	+	0	Name=BM2;gbkey=CDS;gene=BM2;protein_id=AFH57911.1;product=BM2 protein;ID=cds-AFH57911.1;Dbxref=NCBI_GP:AFH57911.1

data/nextstrain/flu/vic/mp/pathogen.json

@@ -0,0 +1,75 @@
+{
+  "schemaVersion": "3.0.0",
+  "alignmentParams": {
+    "excessBandwidth": 9,
+    "terminalBandwidth": 100,
+    "allowedMismatches": 4,
+    "gapAlignmentSide": "right",
+    "minSeedCover": 0.1
+  },
+  "compatibility": {
+    "cli": "3.0.0-alpha.0",
+    "web": "3.0.0-alpha.0"
+  },
+  "files": {
+    "changelog": "CHANGELOG.md",
+    "genomeAnnotation": "genome_annotation.gff3",
+    "pathogenJson": "pathogen.json",
+    "readme": "README.md",
+    "examples":"sequences.fasta",
+    "reference": "reference.fasta"
+  },
+  "qc": {
+    "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": []
+    }
+  },
+  "cdsOrderPreference": [],
+  "maintenance": {
+    "website": [
+      "https://nextstrain.org",
+      "https://clades.nextstrain.org"
+    ],
+    "documentation": [
+      "https://github.com/nextstrain/seasonal-flu"
+    ],
+    "source code": [
+      "https://github.com/nextstrain/seasonal_flu"
+    ],
+    "issues": [
+      "https://github.com/nextstrain/seasonal_flu/issues"
+    ],
+    "organizations": [
+      "Nextstrain"
+    ],
+    "authors": [
+      "Nextstrain team <https://nextstrain.org>"
+    ]
+  },
+  "attributes": {
+    "name": "Influenza B(Vic) MP (segment 7)",
+    "segment": "mp",
+    "reference accession": "CY115152",
+    "reference name": "B/Brisbane/60/2008"
+  },
+  "defaultCds": "M1"
+}

data/nextstrain/flu/vic/mp/reference.fasta

@@ -0,0 +1,21 @@
+>CY115152.1 Influenza B virus (B/Brisbane/60/2008) matrix protein 1 (M1) and BM2 protein (BM2) genes, complete cds
+AAATGTCGCTGTTTGGAGACACAATTGCCTACCTGCTTTCATTGACAGAAGATGGAGAAG
+GCAAAGCAGAACTAGCAGAAAAATTACACTGTTGGTTTGGTGGGAAAGAATTTGACCTAG
+ACTCTGCCTTGGAATGGATAAAAAACAAAAGATGCTTAACTGATATACAAAAAGCACTAA
+TTGGTGCCTCTATATGCTTTTTAAAACCCAAAGACCAGGAAAGAAAAAGAAGATTCATCA
+CAGAGCCCTTATCAGGAATGGGAACAACAGCAACAAAAAAGAAAGGCCTGATTCTGGCTG
+AGAGAAAAATGAGAAGATGTGTGAGCTTTCATGAAGCATTTGAAATAGCAGAAGGCCATG
+AAAGCTCAGCGCTACTATACTGTCTCATGGTCATGTACCTGAATCCTGGAAATTATTCAA
+TGCAAGTAAAACTAGGAACGCTCTGTGCTTTATGCGAGAAACAAGCATCACATTCACACA
+GGGCTCATAGCAGAGCAGCGAGATCTTCAGTGCCTGGAGTGAGACGAGAAATGCAGATGG
+TCTCAGCTATGAACACAGCAAAAACAATGAATGGAATGGGAAAAGGAGAAGACGTCCAAA
+AGCTGGCAGAAGAGTTGCAAAGCAACATTGGAGTGCTGAGATCTCTTGGGGCAAGCCAAA
+AGAATGGGGAAGGGATTGCAAAGGATGTAATGGAAGTGCTAAAGCAGAGCTCCATGGGAA
+ATTCAGCTCTTGTGAAGAAATATCTATAATGCTCGAACCATTTCAGATTCTTACAATTTG
+TTCTTTTATCTTATCAGCTCTCCATTTCATGGCTTGGACAATAGGGCATTTGAATCAAAT
+AAAAAGAGGAATAAACATGAAAATACGAATAAAAGGTCCAAACAAAGAGACAATAAACAG
+AGAGGTATCAATTTTGAGACACAGTTACCAAAAAGAAATCCAGGCCAAAGAAACAATGAA
+GGAAGTACTCTCTGACAACATGGAGGTATTGAATGACCACATAATAATTGAGGGGCTTTC
+TGCCGAAGAGATAATAAAAATGGGTGAAACAGTTTTGGAGATAGAAGAATTGCATTAAAT
+TCAATTTTACTGTATTTCTTACTATGCATTTAAGCAAATTGTAATCAATGTCAGCAAATA
+AACTGGA