From 6b49827cf0e811cca9ce1cf6999e35fcb0bb2c86 Mon Sep 17 00:00:00 2001 From: Richard Neher Date: Sat, 1 Apr 2023 21:38:54 +0200 Subject: [PATCH] update flu datasets and fix B/vic annotation --- CHANGELOG.md | 10 + .../2023-04-02T12:00:00Z/files/genemap.gff | 5 + .../2023-04-02T12:00:00Z/files/primers.csv | 1 + .../2023-04-02T12:00:00Z/files/qc.json | 33 + .../files/reference.fasta | 2 + .../files/sequences.fasta | 1364 + .../2023-04-02T12:00:00Z/files/tag.json | 25 + .../2023-04-02T12:00:00Z/files/tree.json | 67993 +++++++++++++++ .../files/virus_properties.json | 26 + .../2023-04-02T12:00:00Z/files/genemap.gff | 5 + .../2023-04-02T12:00:00Z/files/primers.csv | 1 + .../2023-04-02T12:00:00Z/files/qc.json | 33 + .../files/reference.fasta | 27 + .../files/sequences.fasta | 1364 + .../2023-04-02T12:00:00Z/files/tag.json | 25 + .../2023-04-02T12:00:00Z/files/tree.json | 61876 ++++++++++++++ .../files/virus_properties.json | 26 + .../2023-04-02T12:00:00Z/files/genemap.gff | 4 + .../2023-04-02T12:00:00Z/files/primers.csv | 1 + .../2023-04-02T12:00:00Z/files/qc.json | 33 + .../files/reference.fasta | 25 + .../files/sequences.fasta | 1101 + .../2023-04-02T12:00:00Z/files/tag.json | 25 + .../2023-04-02T12:00:00Z/files/tree.json | 49377 +++++++++++ .../files/virus_properties.json | 22 + .../2023-04-02T12:00:00Z/files/genemap.gff | 5 + .../2023-04-02T12:00:00Z/files/primers.csv | 1 + .../2023-04-02T12:00:00Z/files/qc.json | 33 + .../files/reference.fasta | 26 + .../files/sequences.fasta | 1320 + .../2023-04-02T12:00:00Z/files/tag.json | 25 + .../2023-04-02T12:00:00Z/files/tree.json | 68404 ++++++++++++++++ .../files/virus_properties.json | 26 + .../2023-04-02T12:00:00Z/files/genemap.gff | 5 + .../2023-04-02T12:00:00Z/files/primers.csv | 1 + .../2023-04-02T12:00:00Z/files/qc.json | 33 + .../files/reference.fasta | 23 + .../files/sequences.fasta | 1320 + .../2023-04-02T12:00:00Z/files/tag.json | 25 + .../2023-04-02T12:00:00Z/files/tree.json | 62117 ++++++++++++++ .../files/virus_properties.json | 56 + .../2023-04-02T12:00:00Z/files/genemap.gff | 4 + .../2023-04-02T12:00:00Z/files/primers.csv | 1 + .../2023-04-02T12:00:00Z/files/qc.json | 33 + .../files/reference.fasta | 2 + .../files/sequences.fasta | 1144 + .../2023-04-02T12:00:00Z/files/tag.json | 25 + .../2023-04-02T12:00:00Z/files/tree.json | 52697 ++++++++++++ .../files/virus_properties.json | 22 + .../2023-04-02T12:00:00Z/files/genemap.gff | 5 + .../2023-04-02T12:00:00Z/files/primers.csv | 1 + .../2023-04-02T12:00:00Z/files/qc.json | 33 + .../files/reference.fasta | 28 + .../files/sequences.fasta | 1408 + .../2023-04-02T12:00:00Z/files/tag.json | 25 + .../2023-04-02T12:00:00Z/files/tree.json | 54466 ++++++++++++ .../files/virus_properties.json | 26 + .../2023-04-02T12:00:00Z/files/genemap.gff | 4 + .../2023-04-02T12:00:00Z/files/primers.csv | 1 + .../2023-04-02T12:00:00Z/files/qc.json | 33 + .../files/reference.fasta | 25 + .../files/sequences.fasta | 1188 + .../2023-04-02T12:00:00Z/files/tag.json | 25 + .../2023-04-02T12:00:00Z/files/tree.json | 51436 ++++++++++++ .../files/virus_properties.json | 22 + 65 files changed, 479478 insertions(+) create mode 100644 data/datasets/flu_h1n1pdm_ha/references/CY121680/versions/2023-04-02T12:00:00Z/files/genemap.gff create mode 100644 data/datasets/flu_h1n1pdm_ha/references/CY121680/versions/2023-04-02T12:00:00Z/files/primers.csv create mode 100644 data/datasets/flu_h1n1pdm_ha/references/CY121680/versions/2023-04-02T12:00:00Z/files/qc.json create mode 100644 data/datasets/flu_h1n1pdm_ha/references/CY121680/versions/2023-04-02T12:00:00Z/files/reference.fasta create mode 100644 data/datasets/flu_h1n1pdm_ha/references/CY121680/versions/2023-04-02T12:00:00Z/files/sequences.fasta create mode 100644 data/datasets/flu_h1n1pdm_ha/references/CY121680/versions/2023-04-02T12:00:00Z/files/tag.json create mode 100644 data/datasets/flu_h1n1pdm_ha/references/CY121680/versions/2023-04-02T12:00:00Z/files/tree.json create mode 100644 data/datasets/flu_h1n1pdm_ha/references/CY121680/versions/2023-04-02T12:00:00Z/files/virus_properties.json create mode 100644 data/datasets/flu_h1n1pdm_ha/references/MW626062/versions/2023-04-02T12:00:00Z/files/genemap.gff create mode 100644 data/datasets/flu_h1n1pdm_ha/references/MW626062/versions/2023-04-02T12:00:00Z/files/primers.csv create mode 100644 data/datasets/flu_h1n1pdm_ha/references/MW626062/versions/2023-04-02T12:00:00Z/files/qc.json create mode 100644 data/datasets/flu_h1n1pdm_ha/references/MW626062/versions/2023-04-02T12:00:00Z/files/reference.fasta create mode 100644 data/datasets/flu_h1n1pdm_ha/references/MW626062/versions/2023-04-02T12:00:00Z/files/sequences.fasta create mode 100644 data/datasets/flu_h1n1pdm_ha/references/MW626062/versions/2023-04-02T12:00:00Z/files/tag.json create mode 100644 data/datasets/flu_h1n1pdm_ha/references/MW626062/versions/2023-04-02T12:00:00Z/files/tree.json create mode 100644 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data/datasets/flu_vic_na/references/CY073894/versions/2023-04-02T12:00:00Z/files/virus_properties.json diff --git a/CHANGELOG.md b/CHANGELOG.md index 85a756c1..ca546b4a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,15 @@ # CHANGELOG +## 2023-04-02 + +### New dataset version (tag `2023-04-02T12:00:00Z`) + +#### Influenza virus datasets + +All Influenza virus datasets were updated with more recent sequences. The trees now include more older reference viruses for more robust designation of older clades. +The B/Vic annotation of the HA segment was fixed -- it was previously off by 3 nucleotides resulting in amino acid numbering being off by one. + + ## 2023-03-28 ### Internal diff --git a/data/datasets/flu_h1n1pdm_ha/references/CY121680/versions/2023-04-02T12:00:00Z/files/genemap.gff b/data/datasets/flu_h1n1pdm_ha/references/CY121680/versions/2023-04-02T12:00:00Z/files/genemap.gff new file mode 100644 index 00000000..a3952a1f --- /dev/null +++ b/data/datasets/flu_h1n1pdm_ha/references/CY121680/versions/2023-04-02T12:00:00Z/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" diff --git a/data/datasets/flu_h1n1pdm_ha/references/CY121680/versions/2023-04-02T12:00:00Z/files/primers.csv b/data/datasets/flu_h1n1pdm_ha/references/CY121680/versions/2023-04-02T12:00:00Z/files/primers.csv new file mode 100644 index 00000000..a3d2810a --- /dev/null +++ b/data/datasets/flu_h1n1pdm_ha/references/CY121680/versions/2023-04-02T12:00:00Z/files/primers.csv @@ -0,0 +1 @@ +Country (Institute),Target,Oligonucleotide,Sequence diff --git a/data/datasets/flu_h1n1pdm_ha/references/CY121680/versions/2023-04-02T12:00:00Z/files/qc.json b/data/datasets/flu_h1n1pdm_ha/references/CY121680/versions/2023-04-02T12:00:00Z/files/qc.json new file mode 100644 index 00000000..a0219afe --- /dev/null +++ b/data/datasets/flu_h1n1pdm_ha/references/CY121680/versions/2023-04-02T12:00:00Z/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": [] + } +} diff --git a/data/datasets/flu_h1n1pdm_ha/references/CY121680/versions/2023-04-02T12:00:00Z/files/reference.fasta b/data/datasets/flu_h1n1pdm_ha/references/CY121680/versions/2023-04-02T12:00:00Z/files/reference.fasta new file mode 100644 index 00000000..a3b664be --- /dev/null +++ b/data/datasets/flu_h1n1pdm_ha/references/CY121680/versions/2023-04-02T12:00:00Z/files/reference.fasta @@ -0,0 +1,2 @@ +>CY121680.1 Influenza A virus (A/California/07/2009(H1N1)) hemagglutinin (HA) gene, complete cds +GGAAAACAAAAGCAACAAAAATGAAGGCAATACTAGTAGTTCTGCTATATACATTTGCAACCGCAAATGCAGACACATTATGTATAGGTTATCATGCGAACAATTCAACAGACACTGTAGACACAGTACTAGAAAAGAATGTAACAGTAACACACTCTGTTAACCTTCTAGAAGACAAGCATAACGGGAAACTATGCAAACTAAGAGGGGTAGCCCCATTGCATTTGGGTAAATGTAACATTGCTGGCTGGATCCTGGGAAATCCAGAGTGTGAATCACTCTCCACAGCAAGCTCATGGTCCTACATTGTGGAAACACCTAGTTCAGACAATGGAACGTGTTACCCAGGAGATTTCATCGATTATGAGGAGCTAAGAGAGCAATTGAGCTCAGTGTCATCATTTGAAAGGTTTGAGATATTCCCCAAGACAAGTTCATGGCCCAATCATGACTCGAACAAAGGTGTAACGGCAGCATGTCCTCATGCTGGAGCAAAAAGCTTCTACAAAAATTTAATATGGCTAGTTAAAAAAGGAAATTCATACCCAAAGCTCAGCAAATCCTACATTAATGATAAAGGGAAAGAAGTCCTCGTGCTATGGGGCATTCACCATCCATCTACTAGTGCTGACCAACAAAGTCTCTATCAGAATGCAGATGCATATGTTTTTGTGGGGTCATCAAGATACAGCAAGAAGTTCAAGCCGGAAATAGCAATAAGACCCAAAGTGAGGGATCGAGAAGGGAGAATGAACTATTACTGGACACTAGTAGAGCCGGGAGACAAAATAACATTCGAAGCAACTGGAAATCTAGTGGTACCGAGATATGCATTCGCAATGGAAAGAAATGCTGGATCTGGTATTATCATTTCAGATACACCAGTCCACGATTGCAATACAACTTGTCAAACACCCAAGGGTGCTATAAACACCAGCCTCCCATTTCAGAATATACATCCGATCACAATTGGAAAATGTCCAAAATATGTAAAAAGCACAAAATTGAGACTGGCCACAGGATTGAGGAATATCCCGTCTATTCAATCTAGAGGCCTATTTGGGGCCATTGCCGGTTTCATTGAAGGGGGGTGGACAGGGATGGTAGATGGATGGTACGGTTATCACCATCAAAATGAGCAGGGGTCAGGATATGCAGCCGACCTGAAGAGCACACAGAATGCCATTGACGAGATTACTAACAAAGTAAATTCTGTTATTGAAAAGATGAATACACAGTTCACAGCAGTAGGTAAAGAGTTCAACCACCTGGAAAAAAGAATAGAGAATTTAAATAAAAAAGTTGATGATGGTTTCCTGGACATTTGGACTTACAATGCCGAACTGTTGGTTCTATTGGAAAATGAAAGAACTTTGGACTACCACGATTCAAATGTGAAGAACTTATATGAAAAGGTAAGAAGCCAGCTAAAAAACAATGCCAAGGAAATTGGAAACGGCTGCTTTGAATTTTACCACAAATGCGATAACACGTGCATGGAAAGTGTCAAAAATGGGACTTATGACTACCCAAAATACTCAGAGGAAGCAAAATTAAACAGAGAAGAAATAGATGGGGTAAAGCTGGAATCAACAAGGATTTACCAGATTTTGGCGATCTATTCAACTGTCGCCAGTTCATTGGTACTGGTAGTCTCCCTGGGGGCAATCAGTTTCTGGATGTGCTCTAATGGGTCTCTACAGTGTAGAATATGTATTTAACATTAGGATTTCAGAAGCATGAGAAAAACAC diff --git a/data/datasets/flu_h1n1pdm_ha/references/CY121680/versions/2023-04-02T12:00:00Z/files/sequences.fasta b/data/datasets/flu_h1n1pdm_ha/references/CY121680/versions/2023-04-02T12:00:00Z/files/sequences.fasta new file mode 100644 index 00000000..08f9b5a3 --- /dev/null +++ b/data/datasets/flu_h1n1pdm_ha/references/CY121680/versions/2023-04-02T12:00:00Z/files/sequences.fasta @@ -0,0 +1,1364 @@ +>A/Massachusetts/17/2023 +ggaaaataaaagcaacaaaaatgaaggcaatactagtagctatgctgtatacatttacaa +ccgcaaatgcagacacattatgtataggttatcatgcgaacaattcaacagacactgtgg +acacagtactagaaaagaatgtaacagtaacacactctgtcaatcttctagaagacaagc +ataacggaaaactatgcaaactaagaggggtagccccattgcatttgggtcaatgtaaca +ttgctggctggatcttgggaaatccagagtgtgaaacactctccacagcaagatcatggt +cctacattgtggaaacatctaattcagacaatggaacgtgttacccaggagatttcatca +attatgaggagctaagagagcaattgagctcagtgtcatcatttgaaaggtttgaaatat +tccccaagacaagttcatggcctaatcatgactcggacaatggtgtaacggcagcatgtt +ctcacgctggagcaagaagcttctacaaaaacttgatatggctggttaaaaaaggaaaat 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"A1300G" + ], + "HA2": [ + "K83R" + ] + }, + "labels": { + "aa": "HA2: K83R" + } + } + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } +} \ No newline at end of file diff --git a/data/datasets/flu_h1n1pdm_ha/references/CY121680/versions/2023-04-02T12:00:00Z/files/virus_properties.json b/data/datasets/flu_h1n1pdm_ha/references/CY121680/versions/2023-04-02T12:00:00Z/files/virus_properties.json new file mode 100644 index 00000000..a9af3dfd --- /dev/null +++ b/data/datasets/flu_h1n1pdm_ha/references/CY121680/versions/2023-04-02T12:00:00Z/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]" + ] + } + ] +} \ No newline at end of file diff --git a/data/datasets/flu_h1n1pdm_ha/references/MW626062/versions/2023-04-02T12:00:00Z/files/genemap.gff b/data/datasets/flu_h1n1pdm_ha/references/MW626062/versions/2023-04-02T12:00:00Z/files/genemap.gff new file mode 100644 index 00000000..825fe437 --- /dev/null +++ b/data/datasets/flu_h1n1pdm_ha/references/MW626062/versions/2023-04-02T12:00:00Z/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" diff --git a/data/datasets/flu_h1n1pdm_ha/references/MW626062/versions/2023-04-02T12:00:00Z/files/primers.csv b/data/datasets/flu_h1n1pdm_ha/references/MW626062/versions/2023-04-02T12:00:00Z/files/primers.csv new file mode 100644 index 00000000..a3d2810a --- /dev/null +++ b/data/datasets/flu_h1n1pdm_ha/references/MW626062/versions/2023-04-02T12:00:00Z/files/primers.csv @@ -0,0 +1 @@ +Country (Institute),Target,Oligonucleotide,Sequence diff --git a/data/datasets/flu_h1n1pdm_ha/references/MW626062/versions/2023-04-02T12:00:00Z/files/qc.json b/data/datasets/flu_h1n1pdm_ha/references/MW626062/versions/2023-04-02T12:00:00Z/files/qc.json new file mode 100644 index 00000000..a0219afe --- /dev/null +++ b/data/datasets/flu_h1n1pdm_ha/references/MW626062/versions/2023-04-02T12:00:00Z/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": [] + } +} diff --git a/data/datasets/flu_h1n1pdm_ha/references/MW626062/versions/2023-04-02T12:00:00Z/files/reference.fasta b/data/datasets/flu_h1n1pdm_ha/references/MW626062/versions/2023-04-02T12:00:00Z/files/reference.fasta new file mode 100644 index 00000000..546126e1 --- /dev/null +++ b/data/datasets/flu_h1n1pdm_ha/references/MW626062/versions/2023-04-02T12:00:00Z/files/reference.fasta @@ -0,0 +1,27 @@ +>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 diff --git a/data/datasets/flu_h1n1pdm_ha/references/MW626062/versions/2023-04-02T12:00:00Z/files/sequences.fasta b/data/datasets/flu_h1n1pdm_ha/references/MW626062/versions/2023-04-02T12:00:00Z/files/sequences.fasta new file mode 100644 index 00000000..b062c686 --- /dev/null +++ b/data/datasets/flu_h1n1pdm_ha/references/MW626062/versions/2023-04-02T12:00:00Z/files/sequences.fasta @@ -0,0 +1,1364 @@ +>A/NewYork/4/2021 +ggaaaacaaaagcaacaaaaatgaaggcaatactagtagttatgctgtatacatttacaa +ccgcaaatgcagacacattatgtataggttatcatgcgaacaattcaacagacactgtgg +acacagtactagaaaagaatgtaacagtaacacactctgtcaatcttctagaagacaagc +ataacggaaaactatgcaaactaagaggggtagccccattgcatttgggtcaatgtaaca +ttgctggctggatcctgggaaatccagagtgtgaatcactctccacagcaagatcatggt +cctacattgtggaaacatctaattcagacaatggaacgtgttacccaggagatttcatca +attatgaggagctaagagagcaattgagctcagtgtcatcatttgaaaggtttgaaatat +tccccaagacaagttcatggcctaatcatgactcggacaatggtgtaacggcagcatgtc +ctcacgctggagcaaaaagcttctacaaaaacttgatatggctggttaaaaaaggaaaat +catacccaaagatcaaccaaacctacattaatgataaagggaaagaagtcctcgtgctgt +ggggcattcaccatccacccactattactgaccaagaaagtctttatcagaatgcagatg 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"EPI_ISL": { + "value": "EPI2293227" + }, + "short_clade": { + "value": "5a.2a" + }, + "accessionID": { + "value": "A/Yakutia/164-rl7V/2022" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "A20T", + "G954A", + "A1001G", + "G1145A", + "A1493T", + "G1744A" + ], + "HA1": [ + "V295I" + ] + }, + "labels": { + "aa": "HA1: V295I" + } + } + }, + { + "name": "A/StPetersburg/RII-4537S/2022", + "node_attrs": { + "div": 0.05637000000000001, + "date": { + "value": "2022-12-05" + }, + "country": { + "value": "russia" + }, + "region": { + "value": "west_asia" + }, + "clade_membership": { + "value": "6B.1A.5a.2a" + }, + "EPI_ISL": { + "value": "EPI2262739" + }, + "short_clade": { + "value": "5a.2a" + }, + "accessionID": { + "value": "A/StPetersburg/RII-4537S/2022" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "A840C" + ], + "HA1": [ + "M257L" + ] + }, + "labels": { + "aa": "HA1: M257L" + } + } + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } +} \ No newline at end of file diff --git a/data/datasets/flu_h1n1pdm_ha/references/MW626062/versions/2023-04-02T12:00:00Z/files/virus_properties.json b/data/datasets/flu_h1n1pdm_ha/references/MW626062/versions/2023-04-02T12:00:00Z/files/virus_properties.json new file mode 100644 index 00000000..a9af3dfd --- /dev/null +++ b/data/datasets/flu_h1n1pdm_ha/references/MW626062/versions/2023-04-02T12:00:00Z/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]" + ] + } + ] +} \ No newline at end of file diff --git a/data/datasets/flu_h1n1pdm_na/references/MW626056/versions/2023-04-02T12:00:00Z/files/genemap.gff b/data/datasets/flu_h1n1pdm_na/references/MW626056/versions/2023-04-02T12:00:00Z/files/genemap.gff new file mode 100644 index 00000000..f026596c --- /dev/null +++ b/data/datasets/flu_h1n1pdm_na/references/MW626056/versions/2023-04-02T12:00:00Z/files/genemap.gff @@ -0,0 +1,4 @@ +##gff-version 3 +##sequence-region MW626056.1 1 1433 +MW626056.1 annotation remark 1 1433 . . . accessions=MW626056;data_file_division=VRL;date=23-FEB-2021;keywords=;molecule_type=cRNA;organism=Influenza A virus;references=location: %5B0:1433%5D%0Aauthors: Jernigan%2CD.%2C Wentworth%2CD.%2C Barnes%2CJ.%2C Garten%2CR. and Xu%2CX.%0Atitle: Influenza Sequencing Activity group%0Ajournal: Unpublished%0Amedline id: %0Apubmed id: %0Acomment:,location: %5B0:1433%5D%0Aauthors: Jernigan%2CD.%2C Wentworth%2CD.%2C Barnes%2CJ.%2C Garten%2CR. and Xu%2CX.%0Atitle: Direct Submission%0Ajournal: Submitted %2817-FEB-2021%29 WHO Collaborating Center for Surveillance%2C Epidemiology and Control of Influenza%2C Influenza Division%2C Centers for Disease Control and Prevention%2C 1600 Clifton Road%2C N.E.%2C Atlanta%2C GA 30333%2C USA%0Amedline id: %0Apubmed id: %0Acomment:;sequence_version=1;source=Influenza A virus;structured_comment=OrderedDict%28%5B%28%27FluData%27%2C OrderedDict%28%5B%28%27EPI_ISOLATE_ID%27%2C %27EPI_ISL_628888%27%29%2C %28%27NAME%27%2C %27A/Wisconsin/588/2019%27%29%2C %28%27TYPE%27%2C %27H1N1%27%29%2C %28%27Segment_name%27%2C %27NA%27%29%2C %28%27HOST_AGE%27%2C %2766%27%29%2C %28%27HOST_GENDER%27%2C %27M%27%29%2C %28%27PASSAGE%27%2C %27C2S1 %282020-05-15%29%27%29%2C %28%27LOCATION%27%2C %27United States / Wisconsin%27%29%2C %28%27COLLECT_DATE%27%2C %2719-Dec-2019%27%29%2C %28%27Lineage%27%2C %27A%28H1N1%29pdm09%27%29%2C %28%27SPECIMEN_ID%27%2C %2719VR015562 ORIGINAL%27%29%2C %28%27SENDER_LAB%27%2C %27Wisconsin State Laboratory of Hygiene +MW626056.1 feature gene 9 1418 . + . codon_start=1;gene=NA;gene_name=NA;product=neuraminidase;protein_id=QRV63257.1; diff --git a/data/datasets/flu_h1n1pdm_na/references/MW626056/versions/2023-04-02T12:00:00Z/files/primers.csv b/data/datasets/flu_h1n1pdm_na/references/MW626056/versions/2023-04-02T12:00:00Z/files/primers.csv new file mode 100644 index 00000000..a3d2810a --- /dev/null +++ b/data/datasets/flu_h1n1pdm_na/references/MW626056/versions/2023-04-02T12:00:00Z/files/primers.csv @@ -0,0 +1 @@ +Country (Institute),Target,Oligonucleotide,Sequence diff --git a/data/datasets/flu_h1n1pdm_na/references/MW626056/versions/2023-04-02T12:00:00Z/files/qc.json b/data/datasets/flu_h1n1pdm_na/references/MW626056/versions/2023-04-02T12:00:00Z/files/qc.json new file mode 100644 index 00000000..a0219afe --- /dev/null +++ b/data/datasets/flu_h1n1pdm_na/references/MW626056/versions/2023-04-02T12:00:00Z/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": [] + } +} diff --git a/data/datasets/flu_h1n1pdm_na/references/MW626056/versions/2023-04-02T12:00:00Z/files/reference.fasta b/data/datasets/flu_h1n1pdm_na/references/MW626056/versions/2023-04-02T12:00:00Z/files/reference.fasta new file mode 100644 index 00000000..02ca3b74 --- /dev/null +++ b/data/datasets/flu_h1n1pdm_na/references/MW626056/versions/2023-04-02T12:00:00Z/files/reference.fasta @@ -0,0 +1,25 @@ +>MW626056.1 Influenza A virus 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b/data/datasets/flu_h1n1pdm_na/references/MW626056/versions/2023-04-02T12:00:00Z/files/virus_properties.json new file mode 100644 index 00000000..27ec895a --- /dev/null +++ b/data/datasets/flu_h1n1pdm_na/references/MW626056/versions/2023-04-02T12:00:00Z/files/virus_properties.json @@ -0,0 +1,22 @@ +{ + "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":"NA", + "ranges":[{"begin":33, "end":470}] + } + ], + "motifs": [ + "N[^P][ST]" + ] + } + ] +} diff --git a/data/datasets/flu_h3n2_ha/references/CY163680/versions/2023-04-02T12:00:00Z/files/genemap.gff b/data/datasets/flu_h3n2_ha/references/CY163680/versions/2023-04-02T12:00:00Z/files/genemap.gff new file mode 100644 index 00000000..579ff7ff --- /dev/null +++ b/data/datasets/flu_h3n2_ha/references/CY163680/versions/2023-04-02T12:00:00Z/files/genemap.gff @@ -0,0 +1,5 @@ +##gff-version 3 +##sequence-region CY163680.1 1 1737 +CY163680.1 feature gene 18 65 . + . gene_name="SigPep" +CY163680.1 feature gene 66 1052 . + . gene_name="HA1" +CY163680.1 feature gene 1053 1715 . + . gene_name="HA2" diff --git a/data/datasets/flu_h3n2_ha/references/CY163680/versions/2023-04-02T12:00:00Z/files/primers.csv b/data/datasets/flu_h3n2_ha/references/CY163680/versions/2023-04-02T12:00:00Z/files/primers.csv new file mode 100644 index 00000000..a3d2810a --- /dev/null +++ b/data/datasets/flu_h3n2_ha/references/CY163680/versions/2023-04-02T12:00:00Z/files/primers.csv @@ -0,0 +1 @@ +Country (Institute),Target,Oligonucleotide,Sequence diff --git a/data/datasets/flu_h3n2_ha/references/CY163680/versions/2023-04-02T12:00:00Z/files/qc.json b/data/datasets/flu_h3n2_ha/references/CY163680/versions/2023-04-02T12:00:00Z/files/qc.json new file mode 100644 index 00000000..a0219afe --- /dev/null +++ b/data/datasets/flu_h3n2_ha/references/CY163680/versions/2023-04-02T12:00:00Z/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": [] + } +} diff --git a/data/datasets/flu_h3n2_ha/references/CY163680/versions/2023-04-02T12:00:00Z/files/reference.fasta b/data/datasets/flu_h3n2_ha/references/CY163680/versions/2023-04-02T12:00:00Z/files/reference.fasta new file mode 100644 index 00000000..a4df05fb --- /dev/null +++ b/data/datasets/flu_h3n2_ha/references/CY163680/versions/2023-04-02T12:00:00Z/files/reference.fasta @@ -0,0 +1,26 @@ +>CY163680.1 Influenza A virus (A/Wisconsin/67/2005(H3N2)) hemagglutinin (HA) gene, complete cds +GGATAATTCTATTAACCATGAAGACTATCATTGCTTTGAGCTACATTCTATGTCTGGTTTTCGCTCAAAA +ACTTCCCGGAAATGACAACAGCACGGCAACGCTGTGCCTTGGGCACCATGCAGTACCAAACGGAACGATA +GTGAAAACAATCACGAATGACCAAATTGAAGTTACTAATGCTACTGAGCTGGTTCAGAGTTCCTCAACAG +GTGGAATATGCGACAGTCCTCATCAGATCCTTGATGGAGAAAACTGCACACTAATAGATGCTCTATTGGG +AGACCCTCAGTGTGATGGCTTCCAAAATAAGAAATGGGACCTTTTTGTTGAACGCAGCAAAGCCTACAGC +AACTGTTACCCTTATGATGTGCCGGATTATGCCTCCCTTAGGTCACTAGTTGCCTCATCCGGCACACTGG +AGTTTAACGATGAAAGCTTCAATTGGACTGGAGTCACTCAAAATGGAACAAGCTCTTCTTGCAAAAGGAG +ATCTAATAACAGTTTCTTTAGTAGATTGAATTGGTTGACCCACTTAAAATTCAAATACCCAGCATTGAAC +GTGACTATGCCAAACAATGAAAAATTTGACAAATTGTACATTTGGGGGGTTCACCACCCGGTTACGGACA +ATGACCAAATCTTCCTGTATGCTCAAGCATCAGGAAGAATCACAGTCTCTACCAAAAGAAGCCAACAAAC 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any amino acid other than P)", + "includeGenes": [ + { + "gene":"HA1", + "ranges":[] + }, + { + "gene":"HA2", + "ranges":[{"begin":0, "end":186}] + } + ], + "motifs": [ + "N[^P][ST]" + ] + } + ] +} \ No newline at end of file diff --git a/data/datasets/flu_h3n2_ha/references/EPI1857216/versions/2023-04-02T12:00:00Z/files/genemap.gff b/data/datasets/flu_h3n2_ha/references/EPI1857216/versions/2023-04-02T12:00:00Z/files/genemap.gff new file mode 100644 index 00000000..f33ff5bc --- /dev/null +++ b/data/datasets/flu_h3n2_ha/references/EPI1857216/versions/2023-04-02T12:00:00Z/files/genemap.gff @@ -0,0 +1,5 @@ +##gff-version 3 +##sequence-region EPI1857216 1 1718 +EPI1857216 feature gene 1 48 . + . gene_name="SigPep" +EPI1857216 feature gene 49 1035 . + . gene_name="HA1" +EPI1857216 feature gene 1036 1698 . + . gene_name="HA2" diff --git a/data/datasets/flu_h3n2_ha/references/EPI1857216/versions/2023-04-02T12:00:00Z/files/primers.csv b/data/datasets/flu_h3n2_ha/references/EPI1857216/versions/2023-04-02T12:00:00Z/files/primers.csv new file mode 100644 index 00000000..a3d2810a --- /dev/null +++ b/data/datasets/flu_h3n2_ha/references/EPI1857216/versions/2023-04-02T12:00:00Z/files/primers.csv @@ -0,0 +1 @@ +Country (Institute),Target,Oligonucleotide,Sequence diff --git a/data/datasets/flu_h3n2_ha/references/EPI1857216/versions/2023-04-02T12:00:00Z/files/qc.json b/data/datasets/flu_h3n2_ha/references/EPI1857216/versions/2023-04-02T12:00:00Z/files/qc.json new file mode 100644 index 00000000..a0219afe --- /dev/null +++ b/data/datasets/flu_h3n2_ha/references/EPI1857216/versions/2023-04-02T12:00:00Z/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": [] + } +} diff --git a/data/datasets/flu_h3n2_ha/references/EPI1857216/versions/2023-04-02T12:00:00Z/files/reference.fasta b/data/datasets/flu_h3n2_ha/references/EPI1857216/versions/2023-04-02T12:00:00Z/files/reference.fasta new file mode 100644 index 00000000..ee3b943f --- /dev/null +++ b/data/datasets/flu_h3n2_ha/references/EPI1857216/versions/2023-04-02T12:00:00Z/files/reference.fasta @@ -0,0 +1,23 @@ +>EPI_ISL_1563628 | A/Darwin/6/2021 | A / H3N2 | | 2021-03-16 +atgaagactatcattgctttgagcaacattctatgtcttgttttcgctcaaaaaatacctggaaatgacaatagcacggc +aacgctgtgccttgggcaccatgcagtaccaaacggaacgatagtgaaaacaatcacaaatgaccgaattgaagttacta 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[ + { + "name": "GISAID" + } + ], + "maintainers": [ + { + "name": "Cornelius Roemer", + "url": "https://neherlab.org" + }, + { + "name": "Richard Neher", + "url": "https://neherlab.org" + } + ], + "display_defaults": { + "color_by": "clade_membership", + "distance_measure": "div", + "branch_label": "clade" + }, + "genome_annotations": { + "SigPep": { + "seqid": "EPI_ISL_1563628", + "type": "gene", + "start": 1, + "end": 48, + "strand": "+" + }, + "HA1": { + "seqid": "EPI_ISL_1563628", + "type": "gene", + "start": 49, + "end": 1035, + "strand": "+" + }, + "HA2": { + "seqid": "EPI_ISL_1563628", + "type": "gene", + "start": 1036, + "end": 1698, + "strand": "+" + }, + "nuc": { + "seqid": "EPI_ISL_1563628", + "type": "source", + "start": 1, + "end": 1718, + "strand": "+" + } + }, + "colorings": [ + { + "key": "clade_membership", + "title": "Clade", + "type": "categorical" + }, + { + "key": "gt", + "title": "Genotype", + "type": "categorical" + }, + { + "key": "short_clade", + "title": 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}, + "country": { + "value": "estonia" + }, + "short_clade": { + "value": "2a.1b" + }, + "region": { + "value": "europe" + }, + "accessionID": { + "value": "A/Estonia/172023/2022" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "G1407A", + "G1572A" + ] + } + } + }, + { + "name": "A/Sydney/5/2023", + "node_attrs": { + "div": 0.04238999999999999, + "EPI_ISL": { + "value": "EPI2384108" + }, + "date": { + "value": "2023-01-05" + }, + "clade_membership": { + "value": "3C.2a1b.2a.2a.1b" + }, + "country": { + "value": "australia" + }, + "short_clade": { + "value": "2a.1b" + }, + "region": { + "value": "oceania" + }, + "accessionID": { + "value": "A/Sydney/5/2023" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "C666T", + "T810G", + "G1356T" + ] + } + } + }, + { + "name": "A/Catalonia/NSVH198263989/2023", + "node_attrs": { + "div": 0.04238999999999999, + "EPI_ISL": { + "value": "EPI2295994" + }, + "date": { + "value": "2023-01-10" + }, + "clade_membership": { + "value": 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"div": 0.04120999999999999, + "clade_membership": { + "value": "3C.2a1b.2a.2a.1b" + }, + "short_clade": { + "value": "2a.1b" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "C699T" + ] + } + }, + "children": [ + { + "name": "A/Slovakia/23-256/2023", + "node_attrs": { + "div": 0.04120999999999999, + "EPI_ISL": { + "value": "EPI2469113" + }, + "date": { + "value": "2023-01-10" + }, + "clade_membership": { + "value": "3C.2a1b.2a.2a.1b" + }, + "country": { + "value": "slovakia" + }, + "short_clade": { + "value": "2a.1b" + }, + "region": { + "value": "europe" + }, + "accessionID": { + "value": "A/Slovakia/23-256/2023" + } + }, + "branch_attrs": { + "mutations": {} + } + }, + { + "name": "A/Utah/IVYG43P90K8/2022", + "node_attrs": { + "div": 0.04179999999999999, + "EPI_ISL": { + "value": "EPI2418230" + }, + "date": { + "value": "2022-12-16" + }, + "clade_membership": { + "value": "3C.2a1b.2a.2a.1b" + }, + "country": { + "value": "usa" + }, + "short_clade": { + "value": "2a.1b" + }, + "region": { + "value": "north_america" + }, + "accessionID": { + "value": "A/Utah/IVYG43P90K8/2022" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "T1621C" + ], + "HA2": [ + "F196L" + ] + }, + "labels": { + "aa": "HA2: F196L" + } + } + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } +} \ No newline at end of file diff --git a/data/datasets/flu_h3n2_ha/references/EPI1857216/versions/2023-04-02T12:00:00Z/files/virus_properties.json b/data/datasets/flu_h3n2_ha/references/EPI1857216/versions/2023-04-02T12:00:00Z/files/virus_properties.json new file mode 100644 index 00000000..6b5cd7dd --- /dev/null +++ b/data/datasets/flu_h3n2_ha/references/EPI1857216/versions/2023-04-02T12:00:00Z/files/virus_properties.json @@ -0,0 +1,56 @@ +{ + "schemaVersion": "1.10.0", + "nucMutLabelMap": {}, + "nucMutLabelMapReverse": {}, + "phenotypeData":[ + { + "name": "RBD", + "nameFriendly": "RBD mutations", + "description": "This column displays the number of differences between the sequence and the reference at positions identified by Koel et al. (145, 155, 156, 158, 159, 189, and 193 in HA1)", + "gene": "HA1", + "aaRange": { + "begin": 100, + "end": 200 + }, + "ignore": { + "clades": ["outgroup"] + }, + "data": [ + { + "name": "differences", + "weight": 1, + "locations": { + "145": {"default":1}, + "155": {"default":1}, + "156": {"default":1}, + "158": {"default":1}, + "159": {"default":1}, + "189": {"default":1}, + "193": {"default":1} + } + } + ] + } + ], + "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]" + ] + } + ] +} diff --git a/data/datasets/flu_h3n2_na/references/EPI1857215/versions/2023-04-02T12:00:00Z/files/genemap.gff b/data/datasets/flu_h3n2_na/references/EPI1857215/versions/2023-04-02T12:00:00Z/files/genemap.gff new file mode 100644 index 00000000..cdeefd62 --- /dev/null +++ b/data/datasets/flu_h3n2_na/references/EPI1857215/versions/2023-04-02T12:00:00Z/files/genemap.gff @@ -0,0 +1,4 @@ +##gff-version 3 +##sequence-region EPI1857215 1 1433 +EPI1857215 annotation remark 1 1439 . . . accessions=EPI1857215; +EPI1857215 feature gene 8 1417 . + . codon_start=1;gene=NA;gene_name=NA;product=neuraminidase; diff --git a/data/datasets/flu_h3n2_na/references/EPI1857215/versions/2023-04-02T12:00:00Z/files/primers.csv b/data/datasets/flu_h3n2_na/references/EPI1857215/versions/2023-04-02T12:00:00Z/files/primers.csv new file mode 100644 index 00000000..a3d2810a --- /dev/null +++ b/data/datasets/flu_h3n2_na/references/EPI1857215/versions/2023-04-02T12:00:00Z/files/primers.csv @@ -0,0 +1 @@ +Country (Institute),Target,Oligonucleotide,Sequence diff --git a/data/datasets/flu_h3n2_na/references/EPI1857215/versions/2023-04-02T12:00:00Z/files/qc.json b/data/datasets/flu_h3n2_na/references/EPI1857215/versions/2023-04-02T12:00:00Z/files/qc.json new file mode 100644 index 00000000..a0219afe --- /dev/null +++ b/data/datasets/flu_h3n2_na/references/EPI1857215/versions/2023-04-02T12:00:00Z/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": [] + } +} diff --git a/data/datasets/flu_h3n2_na/references/EPI1857215/versions/2023-04-02T12:00:00Z/files/reference.fasta b/data/datasets/flu_h3n2_na/references/EPI1857215/versions/2023-04-02T12:00:00Z/files/reference.fasta new file mode 100644 index 00000000..a656dd57 --- /dev/null +++ b/data/datasets/flu_h3n2_na/references/EPI1857215/versions/2023-04-02T12:00:00Z/files/reference.fasta @@ -0,0 +1,2 @@ +>EPI1857215 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b/data/datasets/flu_h3n2_na/references/EPI1857215/versions/2023-04-02T12:00:00Z/files/virus_properties.json @@ -0,0 +1,22 @@ +{ + "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":"NA", + "ranges":[{"begin":33, "end":470}] + } + ], + "motifs": [ + "N[^P][ST]" + ] + } + ] +} \ No newline at end of file diff --git a/data/datasets/flu_vic_ha/references/KX058884/versions/2023-04-02T12:00:00Z/files/genemap.gff b/data/datasets/flu_vic_ha/references/KX058884/versions/2023-04-02T12:00:00Z/files/genemap.gff new file mode 100644 index 00000000..6b0fe595 --- /dev/null +++ b/data/datasets/flu_vic_ha/references/KX058884/versions/2023-04-02T12:00:00Z/files/genemap.gff @@ -0,0 +1,5 @@ +##gff-version 3 +##sequence-region KX058884.1 1 1885 +KX058884.1 feature gene 34 78 . + . gene_name="SigPep" +KX058884.1 feature gene 79 1119 . + . gene_name="HA1" +KX058884.1 feature gene 1120 1791 . + . gene_name="HA2" diff --git a/data/datasets/flu_vic_ha/references/KX058884/versions/2023-04-02T12:00:00Z/files/primers.csv b/data/datasets/flu_vic_ha/references/KX058884/versions/2023-04-02T12:00:00Z/files/primers.csv new file mode 100644 index 00000000..a3d2810a --- /dev/null +++ b/data/datasets/flu_vic_ha/references/KX058884/versions/2023-04-02T12:00:00Z/files/primers.csv @@ -0,0 +1 @@ +Country (Institute),Target,Oligonucleotide,Sequence diff --git a/data/datasets/flu_vic_ha/references/KX058884/versions/2023-04-02T12:00:00Z/files/qc.json b/data/datasets/flu_vic_ha/references/KX058884/versions/2023-04-02T12:00:00Z/files/qc.json new file mode 100644 index 00000000..a0219afe --- /dev/null +++ b/data/datasets/flu_vic_ha/references/KX058884/versions/2023-04-02T12:00:00Z/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": [] + } +} diff --git a/data/datasets/flu_vic_ha/references/KX058884/versions/2023-04-02T12:00:00Z/files/reference.fasta b/data/datasets/flu_vic_ha/references/KX058884/versions/2023-04-02T12:00:00Z/files/reference.fasta new file mode 100644 index 00000000..6d22e3ea --- /dev/null +++ b/data/datasets/flu_vic_ha/references/KX058884/versions/2023-04-02T12:00:00Z/files/reference.fasta @@ -0,0 +1,28 @@ +>KX058884.1 Influenza B virus (B/Brisbane/60/2008) segment 4 hemagglutinin (HA) gene, complete cds +AGCAGAAGCAGAGCATTTTCTAATATCCACAAAATGAAGGCAATAATTGTACTACTCATGGTAGTAACAT +CCAATGCAGATCGAATCTGCACTGGGATAACATCGTCAAACTCACCACATGTCGTCAAAACTGCTACTCA +AGGGGAGGTCAATGTGACTGGTGTAATACCACTGACAACAACACCCACCAAATCTCATTTTGCAAATCTC +AAAGGAACAGAAACCAGGGGGAAACTATGCCCAAAATGCCTCAACTGCACAGATCTGGACGTAGCCTTGG +GCAGACCAAAATGCACGGGGAAAATACCCTCGGCAAGAGTTTCAATACTCCATGAAGTCAGACCTGTTAC +ATCTGGGTGCTTTCCTATAATGCACGACAGAACAAAAATTAGACAGCTGCCTAACCTTCTCCGAGGATAC +GAACATATCAGGTTATCAACCCATAACGTTATCAATGCAGAAAATGCACCAGGAGGACCCTACAAAATTG +GAACCTCAGGGTCTTGCCCTAACATTACCAATGGAAACGGATTTTTCGCAACAATGGCTTGGGCCGTCCC +AAAAAACGACAAAAACAAAACAGCAACAAATCCATTAACAATAGAAGTACCATACATTTGTACAGAAGGA +GAAGACCAAATTACCGTTTGGGGGTTCCACTCTGACAACGAGGCCCAAATGGCAAAGCTCTATGGGGACT +CAAAGCCCCAGAAGTTCACCTCATCTGCCAACGGAGTGACCACACATTACGTTTCACAGATTGGTGGCTT +CCCAAATCAAACAGAAGACGGAGGACTACCACAAAGTGGTAGAATTGTTGTTGATTACATGGTGCAAAAA +TCTGGGAAAACAGGAACAATTACCTATCAAAGGGGTATTTTATTGCCTCAAAAGGTGTGGTGCGCAAGTG +GCAGGAGCAAGGTAATAAAAGGATCCTTGCCTTTAATTGGAGAAGCAGATTGCCTCCACGAAAAATACGG +TGGATTAAACAAAAGCAAGCCTTACTACACAGGGGAACATGCAAAGGCCATAGGAAATTGCCCAATATGG +GTGAAAACACCCTTGAAGCTGGCCAATGGAACCAAATATAGACCTCCTGCAAAACTATTAAAGGAAAGGG +GTTTCTTCGGAGCTATTGCTGGTTTCTTAGAAGGAGGATGGGAAGGAATGATTGCAGGTTGGCACGGATA +CACATCCCATGGGGCACATGGAGTAGCGGTGGCAGCAGACCTTAAGAGCACTCAAGAGGCCATAAACAAG +ATAACAAAAAATCTCAACTCTTTGAGTGAGCTGGAAGTAAAGAATCTTCAAAGACTAAGCGGTGCCATGG +ATGAACTCCACAACGAAATACTAGAACTAGATGAGAAAGTGGATGATCTCAGAGCTGATACAATAAGCTC +ACAAATAGAACTCGCAGTCCTGCTTTCCAATGAAGGAATAATAAACAGTGAAGATGAACATCTCTTGGCG +CTTGAAAGAAAGCTGAAGAAAATGCTGGGCCCCTCTGCTGTAGAGATAGGGAATGGATGCTTTGAAACCA +AACACAAGTGCAACCAGACCTGTCTCGACAGAATAGCTGCTGGTACCTTTGATGCAGGAGAATTTTCTCT +CCCCACCTTTGATTCACTGAATATTACTGCTGCATCTTTAAATGACGATGGATTGGATAATCATACTATA +CTGCTTTACTACTCAACTGCTGCCTCCAGTTTGGCTGTAACACTGATGATAGCTATCTTTGTTGTTTATA +TGGTCTCCAGAGACAATGTTTCTTGCTCCATCTGTCTATAAGGGAAGTTAAGCCCTGTATTTTCCTTTAT +TGTAGTGCTTGTTTACTTGTTGTCATTACAAAGAAACGTTATTGAAAAATGCTCTTGTTACTACT diff --git a/data/datasets/flu_vic_ha/references/KX058884/versions/2023-04-02T12:00:00Z/files/sequences.fasta b/data/datasets/flu_vic_ha/references/KX058884/versions/2023-04-02T12:00:00Z/files/sequences.fasta new file mode 100644 index 00000000..b3320069 --- /dev/null +++ b/data/datasets/flu_vic_ha/references/KX058884/versions/2023-04-02T12:00:00Z/files/sequences.fasta @@ -0,0 +1,1408 @@ +>B/Connecticut/1/2021 +attttctaatatccacaaaatgaaggcaataattgtactactcatggtagtaacatccaa +tgcagatcgaatctgcactgggataacatcgtcaaactcaccacatgtcgtcaaaactgc +tactcaaggggaggtcaatgtgactggtgtaataccactgacaacaacacccaccaaatc +tcattttgcaaatctcaaaggaacagaaaccagggggaaactatgcccaaaatgcctaaa +ctgcacagatctggatgtagccttgggcagaccaaaatgcacagggaaaataccctctgc +aagggtttcaatactccatgaagtcagacctgttacgtctgggtgctttcctataatgca +tgatagaacaaaaattagacagctgcctaaccttctccgaggatacgaacatgtcaggtt 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newline at end of file diff --git a/data/datasets/flu_vic_ha/references/KX058884/versions/2023-04-02T12:00:00Z/files/virus_properties.json b/data/datasets/flu_vic_ha/references/KX058884/versions/2023-04-02T12:00:00Z/files/virus_properties.json new file mode 100644 index 00000000..a9af3dfd --- /dev/null +++ b/data/datasets/flu_vic_ha/references/KX058884/versions/2023-04-02T12:00:00Z/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]" + ] + } + ] +} \ No newline at end of file diff --git a/data/datasets/flu_vic_na/references/CY073894/versions/2023-04-02T12:00:00Z/files/genemap.gff b/data/datasets/flu_vic_na/references/CY073894/versions/2023-04-02T12:00:00Z/files/genemap.gff new file mode 100644 index 00000000..a1ce3b32 --- /dev/null +++ b/data/datasets/flu_vic_na/references/CY073894/versions/2023-04-02T12:00:00Z/files/genemap.gff @@ -0,0 +1,4 @@ +##gff-version 3 +##sequence-region CY073894.1 1 1401 +CY073894.1 annotation remark 1 1401 . . . accessions=CY073894;data_file_division=VRL;date=25-JUL-2016;keywords=;molecule_type=cRNA;organism=Influenza B virus %28B/Brisbane/60/2008%29;references=location: %5B0:1401%5D%0Aauthors: Sabaiduc%2CS.%2C Skowronski%2CD.%2C Petric%2CM. and Chan%2CT.%0Atitle: %0Ajournal: Unpublished%0Amedline id: %0Apubmed id: %0Acomment:,location: %5B0:1401%5D%0Aauthors: Sabaiduc%2CS.%2C Skowronski%2CD.%2C Gardy%2CJ.%2C Petric%2CM. and Chan%2CT.%0Atitle: Direct Submission%0Ajournal: Submitted %2816-SEP-2010%29 Genome Research Laboratory%2C British Columbia Centre for Disease Control%2C 655 West 12th Ave.%2C Vancouver%2C BC V5Z4R4%2C Canada%0Amedline id: %0Apubmed id: %0Acomment:;sequence_version=1;source=Influenza B virus %28B/Brisbane/60/2008%29;taxonomy=Viruses,Riboviria,Orthornavirae,Negarnaviricota,Polyploviricotina,Insthoviricetes,Articulavirales,Orthomyxoviridae,Betainfluenzavirus;topology=linear +CY073894.1 feature gene 1 1401 . + . codon_start=1;gene=NA;gene_name=NA;product=neuraminidase;protein_id=ADN32819.1;translation=MLPSTIQTLTLFLTSGGVLLSLYVSASLSYLLYSDILLKFSPTEITAPTMPLDCANASNVQAVNRSATKGVTLLLPEPEWTYPRLSCPGSTFQKALLISPHRFGETKGNSAPLIIREPFIACGPNECKHFALTHYAAQPGGYYNGTRGDRNKLRHLISVKLGKIPTVENSIFHMAAWSGSACHDGKEWTYIGVDGPDNNALLKVKYGEAYTDTYHSYANKILRTQESACNCIGGNCYLMITDGSASGVSECRFLKIREGRIIKEIFPTGRVKHTEECTCGFASNKTIECACRDNSYTAKRPFVKLNVETDTAEIRLMCTDTYLDTPRPNDGSITGPCESNGDKGSGGIKGGFVHQRMESKIGRWYSRTMSKTERMGMGLYVKYDGDPWADSDALAFSGVMVSMKEPGWYSFGFEIKDKKCDVPCIGIEMVHDGGKETWHSAATAIYCLMGSGQLLWDTVTGVDMAL diff --git a/data/datasets/flu_vic_na/references/CY073894/versions/2023-04-02T12:00:00Z/files/primers.csv b/data/datasets/flu_vic_na/references/CY073894/versions/2023-04-02T12:00:00Z/files/primers.csv new file mode 100644 index 00000000..a3d2810a --- /dev/null +++ b/data/datasets/flu_vic_na/references/CY073894/versions/2023-04-02T12:00:00Z/files/primers.csv @@ -0,0 +1 @@ +Country (Institute),Target,Oligonucleotide,Sequence diff --git a/data/datasets/flu_vic_na/references/CY073894/versions/2023-04-02T12:00:00Z/files/qc.json b/data/datasets/flu_vic_na/references/CY073894/versions/2023-04-02T12:00:00Z/files/qc.json new file mode 100644 index 00000000..a0219afe --- /dev/null +++ b/data/datasets/flu_vic_na/references/CY073894/versions/2023-04-02T12:00:00Z/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": [] + } +} diff --git a/data/datasets/flu_vic_na/references/CY073894/versions/2023-04-02T12:00:00Z/files/reference.fasta b/data/datasets/flu_vic_na/references/CY073894/versions/2023-04-02T12:00:00Z/files/reference.fasta new file mode 100644 index 00000000..1bdc8402 --- /dev/null +++ b/data/datasets/flu_vic_na/references/CY073894/versions/2023-04-02T12:00:00Z/files/reference.fasta @@ -0,0 +1,25 @@ +>CY073894.1 Influenza B virus (B/Brisbane/60/2008) segment 6 sequence +ATGCTACCTTCAACTATACAAACGTTAACCCTATTTCTCACATCAGGGGGAGTATTATTA +TCACTATATGTGTCAGCTTCATTATCATACTTACTATATTCGGATATATTGCTAAAATTC 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