ebola: test ebola dataset with clades

data/nextstrain/ebola/zaire/genome_annotation.gff3

@@ -1,9 +1,14 @@
 ##gff-version 3
-##sequence-region KR075003.1 1 18958
-KR075003.1	feature	gene	470	2689	.	+	0	gene_name "NP"
-KR075003.1	feature	gene	3129	4151	.	+	0	gene_name "VP35"
-KR075003.1	feature	gene	4479	5459	.	+	0	gene_name "VP40"
-KR075003.1	feature	gene	6039	8069	.	+	0	gene_name "GP"
-KR075003.1	feature	gene	8509	9375	.	+	0	gene_name "VP30"
-KR075003.1	feature	gene	10345	11100	.	+	0	gene_name "VP24"
-KR075003.1	feature	gene	11581	18219	.	+	0	gene_name "L"
+#!gff-spec-version 1.21
+#!processor NCBI annotwriter
+##sequence-region NC_002549.1 1 18959
+##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=186538
+NC_002549.1	RefSeq	region	1	18959	.	+	.	ID=NC_002549.1:1..18959;Dbxref=taxon:186538;gbkey=Src;genome=genomic;isolate=Ebola virus/H.sapiens-tc/COD/1976/Yambuku-Mayinga;mol_type=viral cRNA
+NC_002549.1	RefSeq	CDS	470	2689	.	+	0	ID=cds-NP_066243.1;Dbxref=GenBank:NP_066243.1,GeneID:911830;Name=NP;gbkey=CDS;gene=NP;locus_tag=ZEBOVgp1;product=nucleoprotein;protein_id=NP_066243.1
+NC_002549.1	RefSeq	CDS	3129	4151	.	+	0	ID=cds-NP_066244.1;Dbxref=GenBank:NP_066244.1,GeneID:911827;Name=VP35;gbkey=CDS;gene=VP35;locus_tag=ZEBOVgp2;product=polymerase complex protein;protein_id=NP_066244.1
+NC_002549.1	RefSeq	CDS	4479	5459	.	+	0	ID=cds-NP_066245.1;Dbxref=GenBank:NP_066245.1,GeneID:911825;Name=VP40;gbkey=CDS;gene=VP40;locus_tag=ZEBOVgp3;product=matrix protein;protein_id=NP_066245.1
+NC_002549.1	RefSeq	CDS	6039	7133	.	+	0	ID=cds-NP_066247.1;Dbxref=GenBank:NP_066247.1,GeneID:911829;Name=GP;Note=sGP%2C small non-structural%2C secreted glycoprotein%3B sGP secreted as an anti-parallel oriented homodimer;gbkey=CDS;gene=GP;locus_tag=ZEBOVgp4;product=small secreted glycoprotein;protein_id=NP_066247.1
+NC_002549.1	RefSeq	CDS	8509	9375	.	+	0	ID=cds-NP_066249.1;Dbxref=GenBank:NP_066249.1,GeneID:911826;Name=VP30;Note=polymerase complex protein;gbkey=CDS;gene=VP30;locus_tag=ZEBOVgp5;product=minor nucleoprotein;protein_id=NP_066249.1
+NC_002549.1	RefSeq	CDS	10345	11100	.	+	0	ID=cds-NP_066250.1;Dbxref=GenBank:NP_066250.1,GeneID:911828;Name=VP24;gbkey=CDS;gene=VP24;locus_tag=ZEBOVgp6;product=membrane-associated protein;protein_id=NP_066250.1
+NC_002549.1	RefSeq	CDS	11581	18219	.	+	0	ID=cds-NP_066251.1;Dbxref=GenBank:NP_066251.1,GeneID:911824;Name=L;gbkey=CDS;gene=L;locus_tag=ZEBOVgp7;product=RNA-dependent RNA polymerase;protein_id=NP_066251.1
+

data/nextstrain/ebola/zaire/pathogen.json

@@ -1,48 +1,24 @@
 {
-  "compatibility": {
-    "cli": "3.0.0-alpha.0",
-    "web": "3.0.0-alpha.0"
-  },
+  "schemaVersion": "3.0.0",
   "files": {
-    "changelog": "CHANGELOG.md",
-    "examples": "sequences.fasta",
-    "genomeAnnotation": "genome_annotation.gff3",
+    "reference": "reference.fasta",
     "pathogenJson": "pathogen.json",
-    "readme": "README.md",
-    "reference": "reference.fasta"
-  },
-  "schemaVersion": "3.0.0",
-  "version": {
-    "tag": "unreleased"
+    "genomeAnnotation": "genome_annotation.gff3",
+    "treeJson": "tree.json",
+    "examples": "sequences.fasta"
   },
   "attributes": {
-    "name": "Zaire ebolavirus",
-    "reference name": "LBR/2014/Makona-Liberia-DQE14",
-    "reference accession": "KR075003.1",
-    "experimental": true
+    "name": {
+      "value": "Zika tutorial dataset"
+    },
+    "reference name": {
+      "value": "NC_035889.1"
+    },
+    "reference": {
+      "value": "NC_035889.1"
+    }
   },
-  "maintenance": {
-    "website": [
-      "https://nextstrain.org",
-      "https://clades.nextstrain.org"
-    ],
-    "documentation": [
-      "https://github.com/nextstrain/nextclade_data",
-      "https://docs.nextstrain.org/projects/nextclade"
-    ],
-    "source code": [
-      "https://github.com/nextstrain/nextclade_data",
-      "https://github.com/neherlab/nextclade_data_workflows"
-    ],
-    "issues": [
-      "https://github.com/nextstrain/nextclade_data",
-      "https://github.com/nextstrain/nextclade_data/issues"
-    ],
-    "organizations": [
-      "Nextstrain"
-    ],
-    "authors": [
-      "Nextstrain team <https://nextstrain.org>"
-    ]
+  "version": {
+    "tag": "unreleased"
   }
 }