From a38cdd82587d616d095d0cc7ef011a505ce8356b Mon Sep 17 00:00:00 2001 From: ivan-tests-stuff Date: Sat, 20 Jan 2024 01:56:04 +0100 Subject: [PATCH] Test dataset addition --- data/community/org/user/dummy/CHANGELOG.md | 5 + data/community/org/user/dummy/README.md | 23 ++++ .../org/user/dummy/genome_annotation.gff3 | 3 + data/community/org/user/dummy/pathogen.json | 35 ++++++ data/community/org/user/dummy/reference.fasta | 2 + data/community/org/user/dummy/sequences.fasta | 18 +++ data/community/org/user/dummy/tree.json | 108 ++++++++++++++++++ 7 files changed, 194 insertions(+) create mode 100644 data/community/org/user/dummy/CHANGELOG.md create mode 100644 data/community/org/user/dummy/README.md create mode 100644 data/community/org/user/dummy/genome_annotation.gff3 create mode 100644 data/community/org/user/dummy/pathogen.json create mode 100644 data/community/org/user/dummy/reference.fasta create mode 100644 data/community/org/user/dummy/sequences.fasta create mode 100644 data/community/org/user/dummy/tree.json diff --git a/data/community/org/user/dummy/CHANGELOG.md b/data/community/org/user/dummy/CHANGELOG.md new file mode 100644 index 00000000..5d7c67a6 --- /dev/null +++ b/data/community/org/user/dummy/CHANGELOG.md @@ -0,0 +1,5 @@ +## Unreleased + +Initial release for Nextclade v3! + +Read more about Nextclade datasets in the documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html diff --git a/data/community/org/user/dummy/README.md b/data/community/org/user/dummy/README.md new file mode 100644 index 00000000..a68c812e --- /dev/null +++ b/data/community/org/user/dummy/README.md @@ -0,0 +1,23 @@ +# Nextclade dataset for "dummy1" based on reference "DU1MMY" (.ignore/files) + + +## Dataset attributes + +| attribute | value | +| -------------------- | ---------------------------------------- | +| name | dummy1 | +| refName | DU1MMY | +| refAccession | DU1MMY | + + +## Authors and contacts + +Source code: + +Author1: + +Author2: + +## What is Nextclade dataset + +Read more about Nextclade datasets in Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html diff --git a/data/community/org/user/dummy/genome_annotation.gff3 b/data/community/org/user/dummy/genome_annotation.gff3 new file mode 100644 index 00000000..9be0562c --- /dev/null +++ b/data/community/org/user/dummy/genome_annotation.gff3 @@ -0,0 +1,3 @@ +#DUMMY +ref dummy region 1 120 . + . ID=ref +ref dummy CDS 1 15 . + 0 Name=HA1;gene=HA1 diff --git a/data/community/org/user/dummy/pathogen.json b/data/community/org/user/dummy/pathogen.json new file mode 100644 index 00000000..11de9c71 --- /dev/null +++ b/data/community/org/user/dummy/pathogen.json @@ -0,0 +1,35 @@ +{ + "attributes": { + "name": "dummy1", + "refAccession": "DU1MMY", + "refName": "DU1MMY" + }, + "cdsOrderPreference": [ + "HA1" + ], + "compatibility": { + "cli": "3.0.0-alpha.0", + "web": "3.0.0-alpha.0" + }, + "defaultCds": "HA1", + "deprecated": false, + "enabled": true, + "experimental": true, + "files": { + "changelog": "CHANGELOG.md", + "examples": "sequences.fasta", + "genomeAnnotation": "genome_annotation.gff3", + "pathogenJson": "pathogen.json", + "readme": "README.md", + "reference": "reference.fasta", + "treeJson": "tree.json" + }, + "meta": { + "bugs": "https://github.com/nextstrain/nextclade_data/issues", + "source code": "https://github.com/nextstrain/nextclade_data" + }, + "schemaVersion": "3.0.0", + "version": { + "tag": "unreleased" + } +} diff --git a/data/community/org/user/dummy/reference.fasta b/data/community/org/user/dummy/reference.fasta new file mode 100644 index 00000000..37b29889 --- /dev/null +++ b/data/community/org/user/dummy/reference.fasta @@ -0,0 +1,2 @@ +>Dummy1/Ref +AAAAAAAAAAAAAAAGTCGCTGATCGATCGGCTAGCTGCTCGATCGATCGGCTAGCTATTCATTTTCGATCTCCTCTCGCGATCGTATAGCTACGCATCGACTACTGCATCACTGACTTG diff --git a/data/community/org/user/dummy/sequences.fasta b/data/community/org/user/dummy/sequences.fasta new file mode 100644 index 00000000..44b88a43 --- /dev/null +++ b/data/community/org/user/dummy/sequences.fasta @@ -0,0 +1,18 @@ +>ref +AAAAAAAAAAAAAAAGTCGCTGATCGATCGGCTAGCTGCTCGATCGATCGGCTAGCTATTCATTTTCGATCTCCTCTCGCGATCGTATAGCTACGCATCGACTACTGCATCACTGACTTG +>A +GGAAAAAAAAAAAAAGTCGCTGATCGATCGGCTAGCTGCTCGATCGATCGGCTAGCTATTCATTTTCGATCTCCTCTCGCGATCGTATAGCTACGCATCGACTACTGCATCACTGACTTG +>A1 +GAAAAAAGAAAAAAAGTCGCTGATCGATCGGCTAGCTGCTCGATCGATCGGCTAGCTATTCATTTTCGATCTCCTCTCGCGATCGTATAGCTACGCATCGACTACTGCATCACTGACTTG +>B1 +AACCAACCAAAAAAAGTCGCTGATCGATCGGCTAGCTGCTCGATCGATCGGCTAGCTATTCATTTTCGATCTCCTCTCGCGATCGTATAGCTACGCATCGACTACTGCATCACTGACTTG +>B2 +AACCAACCAAAAAAAGTCGCTGATCGATCGGCTAGCTGCTCGATCGATCGGCTAGCTATTCATTTTCGATCTCCTCTCGCGATCGTATAGCTACGCATCGACTACTGCATCACTGACTTG +>C +AACAGAAAAAAAAAAGTCGCTGATCGATCGGCTAGCTGCTCGATCGATCGGCTAGCTATTCATTTTCGATCTCCTCTCGCGATCGTATAGCTACGCATCGACTACTGCATCACTGACTTG +>BC1 +AACAAAAAAAGAAAAGTCGCTGATCGATCGGCTAGCTGCTCGATCGATCGGCTAGCTATTCATTTTCGATCTCCTCTCGCGATCGTATAGCTACGCATCGACTACTGCATCACTGACTTG +>BC2 +AACAAAAAAAGATAAGTCGCTGATCGATCGGCTAGCTGCTCGATCGATCGGCTAGCTATTCATTTTCGATCTCCTCTCGCGATCGTATAGCTACGCATCGACTACTGCATCACTGACTTG +>BC3 +AACAAAAAAAGATCAGTCGCTGATCGATCGGCTAGCTGCTCGATCGATCGGCTAGCTATTCATTTTCGATCTCCTCTCGCGATCGTATAGCTACGCATCGACTACTGCATCACTGACTTG diff --git a/data/community/org/user/dummy/tree.json b/data/community/org/user/dummy/tree.json new file mode 100644 index 00000000..b2a20d5e --- /dev/null +++ b/data/community/org/user/dummy/tree.json @@ -0,0 +1,108 @@ +{ + "meta": { + "title": "Dummy nextclade reference tree", + "data_provenance": [ + { + "name": "fictional data" + } + ] + }, + "tree": { + "name": "NODE_0000000", + "node_attrs": { + "div": 0, + "clade_membership": { + "value": "unassigned" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [] + } + }, + "children": [ + { + "name": "A", + "node_attrs": { + "div": 0.016666666666666666, + "clade_membership": { + "value": "unassigned" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "A1G", + "A2G" + ], + "HA1": [ + "K1G" + ] + } + }, + "children": [] + }, + { + "name": "NODE_0000001", + "node_attrs": { + "div": 0.008333333333333333, + "clade_membership": { + "value": "unassigned" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "A3C" + ], + "HA1": [ + "K1N" + ] + } + }, + "children": [ + { + "name": "B", + "node_attrs": { + "div": 0.016666666666666666, + "clade_membership": { + "value": "unassigned" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "A4C" + ], + "HA1": [ + "K2Q" + ] + } + }, + "children": [] + }, + { + "name": "C", + "node_attrs": { + "div": 0.016666666666666666, + "clade_membership": { + "value": "unassigned" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "A5G" + ], + "HA1": [ + "K2R" + ] + } + }, + "children": [] + } + ] + } + ] + } +}