diff --git a/data/nextstrain/flu/h1n1pdm/ha/CY121680/pathogen.json b/data/nextstrain/flu/h1n1pdm/ha/CY121680/pathogen.json index a74a5aa1..a7a9f602 100644 --- a/data/nextstrain/flu/h1n1pdm/ha/CY121680/pathogen.json +++ b/data/nextstrain/flu/h1n1pdm/ha/CY121680/pathogen.json @@ -90,13 +90,13 @@ "nameShort": "Glyc.", "nameFriendly": "Glycosylation", "description": "N-linked glycosylation motifs (N-X-S/T with X any amino acid other than P)", - "includeGenes": [ + "includeCdses": [ { - "gene": "HA1", + "cds": "HA1", "ranges": [] }, { - "gene": "HA2", + "cds": "HA2", "ranges": [ { "begin": 0, diff --git a/data/nextstrain/flu/h1n1pdm/ha/MW626062/pathogen.json b/data/nextstrain/flu/h1n1pdm/ha/MW626062/pathogen.json index 08209501..3021ad5c 100644 --- a/data/nextstrain/flu/h1n1pdm/ha/MW626062/pathogen.json +++ b/data/nextstrain/flu/h1n1pdm/ha/MW626062/pathogen.json @@ -92,13 +92,13 @@ "nameShort": "Glyc.", "nameFriendly": "Glycosylation", "description": "N-linked glycosylation motifs (N-X-S/T with X any amino acid other than P)", - "includeGenes": [ + "includeCdses": [ { - "gene": "HA1", + "cds": "HA1", "ranges": [] }, { - "gene": "HA2", + "cds": "HA2", "ranges": [ { "begin": 0, diff --git a/data/nextstrain/flu/h1n1pdm/na/MW626056/pathogen.json b/data/nextstrain/flu/h1n1pdm/na/MW626056/pathogen.json index f70e8431..fdc9746d 100644 --- a/data/nextstrain/flu/h1n1pdm/na/MW626056/pathogen.json +++ b/data/nextstrain/flu/h1n1pdm/na/MW626056/pathogen.json @@ -90,9 +90,9 @@ "nameShort": "Glyc.", "nameFriendly": "Glycosylation", "description": "N-linked glycosylation motifs (N-X-S/T with X any amino acid other than P)", - "includeGenes": [ + "includeCdses": [ { - "gene": "NA", + "cds": "NA", "ranges": [ { "begin": 33, diff --git a/data/nextstrain/flu/h3n2/ha/CY163680/pathogen.json b/data/nextstrain/flu/h3n2/ha/CY163680/pathogen.json index af3b5f4d..a622f5e5 100644 --- a/data/nextstrain/flu/h3n2/ha/CY163680/pathogen.json +++ b/data/nextstrain/flu/h3n2/ha/CY163680/pathogen.json @@ -90,13 +90,13 @@ "nameShort": "Glyc.", "nameFriendly": "Glycosylation", "description": "N-linked glycosylation motifs (N-X-S/T with X any amino acid other than P)", - "includeGenes": [ + "includeCdses": [ { - "gene": "HA1", + "cds": "HA1", "ranges": [] }, { - "gene": "HA2", + "cds": "HA2", "ranges": [ { "begin": 0, diff --git a/data/nextstrain/flu/h3n2/ha/EPI1857216/pathogen.json b/data/nextstrain/flu/h3n2/ha/EPI1857216/pathogen.json index 25d0a30e..e60cf7fa 100644 --- a/data/nextstrain/flu/h3n2/ha/EPI1857216/pathogen.json +++ b/data/nextstrain/flu/h3n2/ha/EPI1857216/pathogen.json @@ -91,7 +91,7 @@ "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", + "cds": "HA1", "aaRange": { "begin": 100, "end": 200 @@ -138,13 +138,13 @@ "nameShort": "Glyc.", "nameFriendly": "Glycosylation", "description": "N-linked glycosylation motifs (N-X-S/T with X any amino acid other than P)", - "includeGenes": [ + "includeCdses": [ { - "gene": "HA1", + "cds": "HA1", "ranges": [] }, { - "gene": "HA2", + "cds": "HA2", "ranges": [ { "begin": 0, diff --git a/data/nextstrain/flu/h3n2/na/EPI1857215/pathogen.json b/data/nextstrain/flu/h3n2/na/EPI1857215/pathogen.json index 349aa973..20b76a9d 100644 --- a/data/nextstrain/flu/h3n2/na/EPI1857215/pathogen.json +++ b/data/nextstrain/flu/h3n2/na/EPI1857215/pathogen.json @@ -90,9 +90,9 @@ "nameShort": "Glyc.", "nameFriendly": "Glycosylation", "description": "N-linked glycosylation motifs (N-X-S/T with X any amino acid other than P)", - "includeGenes": [ + "includeCdses": [ { - "gene": "NA", + "cds": "NA", "ranges": [ { "begin": 33, diff --git a/data/nextstrain/flu/vic/ha/KX058884/pathogen.json b/data/nextstrain/flu/vic/ha/KX058884/pathogen.json index bf3170df..0690e4b4 100644 --- a/data/nextstrain/flu/vic/ha/KX058884/pathogen.json +++ b/data/nextstrain/flu/vic/ha/KX058884/pathogen.json @@ -92,13 +92,13 @@ "nameShort": "Glyc.", "nameFriendly": "Glycosylation", "description": "N-linked glycosylation motifs (N-X-S/T with X any amino acid other than P)", - "includeGenes": [ + "includeCdses": [ { - "gene": "HA1", + "cds": "HA1", "ranges": [] }, { - "gene": "HA2", + "cds": "HA2", "ranges": [ { "begin": 0, diff --git a/data/nextstrain/flu/vic/na/CY073894/pathogen.json b/data/nextstrain/flu/vic/na/CY073894/pathogen.json index 5cb7d0a7..35ea1fa2 100644 --- a/data/nextstrain/flu/vic/na/CY073894/pathogen.json +++ b/data/nextstrain/flu/vic/na/CY073894/pathogen.json @@ -90,9 +90,9 @@ "nameShort": "Glyc.", "nameFriendly": "Glycosylation", "description": "N-linked glycosylation motifs (N-X-S/T with X any amino acid other than P)", - "includeGenes": [ + "includeCdses": [ { - "gene": "NA", + "cds": "NA", "ranges": [ { "begin": 33, diff --git a/data/nextstrain/flu/yam/ha/JN993010/pathogen.json b/data/nextstrain/flu/yam/ha/JN993010/pathogen.json index 0d56d0a7..95c3975f 100644 --- a/data/nextstrain/flu/yam/ha/JN993010/pathogen.json +++ b/data/nextstrain/flu/yam/ha/JN993010/pathogen.json @@ -86,13 +86,13 @@ "nameShort": "Glyc.", "nameFriendly": "Glycosylation", "description": "N-linked glycosylation motifs (N-X-S/T with X any amino acid other than P)", - "includeGenes": [ + "includeCdses": [ { - "gene": "HA1", + "cds": "HA1", "ranges": [] }, { - "gene": "HA2", + "cds": "HA2", "ranges": [ { "begin": 0, diff --git a/data/nextstrain/mpox/all-clades/pathogen.json b/data/nextstrain/mpox/all-clades/pathogen.json index e3f51617..06a19bfd 100644 --- a/data/nextstrain/mpox/all-clades/pathogen.json +++ b/data/nextstrain/mpox/all-clades/pathogen.json @@ -38,119 +38,119 @@ "begin": 3, "end": 589 }, - "geneName": "OPG003" + "cdsName": "OPG003" }, { "codonRange": { "begin": 3, "end": 589 }, - "geneName": "OPG003_dup" + "cdsName": "OPG003_dup" }, { "codonRange": { "begin": 281, "end": 285 }, - "geneName": "OPG105" + "cdsName": "OPG105" }, { "codonRange": { "begin": 227, "end": 229 }, - "geneName": "OPG164" + "cdsName": "OPG164" }, { "codonRange": { "begin": 554, "end": 560 }, - "geneName": "OPG180" + "cdsName": "OPG180" }, { "codonRange": { "begin": 42, "end": 101 }, - "geneName": "OPG197" + "cdsName": "OPG197" }, { "codonRange": { "begin": 443, "end": 443 }, - "geneName": "OPG037" + "cdsName": "OPG037" }, { "codonRange": { "begin": 57, "end": 443 }, - "geneName": "OPG037" + "cdsName": "OPG037" }, { "codonRange": { "begin": 481, "end": 483 }, - "geneName": "OPG047" + "cdsName": "OPG047" }, { "codonRange": { "begin": 482, "end": 483 }, - "geneName": "OPG047" + "cdsName": "OPG047" }, { "codonRange": { "begin": 72, "end": 76 }, - "geneName": "OPG050" + "cdsName": "OPG050" }, { "codonRange": { "begin": 369, "end": 371 }, - "geneName": "OPG153" + "cdsName": "OPG153" }, { "codonRange": { "begin": 370, "end": 371 }, - "geneName": "OPG153" + "cdsName": "OPG153" }, { "codonRange": { "begin": 166, "end": 169 }, - "geneName": "OPG191" + "cdsName": "OPG191" }, { "codonRange": { "begin": 72, "end": 222 }, - "geneName": "OPG195" + "cdsName": "OPG195" }, { "codonRange": { "begin": 208, "end": 222 }, - "geneName": "OPG195" + "cdsName": "OPG195" }, { "codonRange": { "begin": 289, "end": 346 }, - "geneName": "OPG174" + "cdsName": "OPG174" } ], "scoreWeight": 20 @@ -183,23 +183,23 @@ "ignoredStopCodons": [ { "codon": 187, - "geneName": "OPG015_dup" + "cdsName": "OPG015_dup" }, { "codon": 187, - "geneName": "OPG015" + "cdsName": "OPG015" }, { "codon": 21, - "geneName": "OPG176" + "cdsName": "OPG176" }, { "codon": 299, - "geneName": "OPG187" + "cdsName": "OPG187" }, { "codon": 48, - "geneName": "OPG059" + "cdsName": "OPG059" } ], "scoreWeight": 20 diff --git a/data/nextstrain/mpox/clade-iib/pathogen.json b/data/nextstrain/mpox/clade-iib/pathogen.json index 934126a1..ee466470 100644 --- a/data/nextstrain/mpox/clade-iib/pathogen.json +++ b/data/nextstrain/mpox/clade-iib/pathogen.json @@ -38,7 +38,7 @@ "begin": 289, "end": 346 }, - "geneName": "OPG174" + "cdsName": "OPG174" } ], "scoreWeight": 20 @@ -71,15 +71,15 @@ "ignoredStopCodons": [ { "codon": 187, - "geneName": "OPG015_dup" + "cdsName": "OPG015_dup" }, { "codon": 187, - "geneName": "OPG015" + "cdsName": "OPG015" }, { "codon": 21, - "geneName": "OPG176" + "cdsName": "OPG176" } ], "scoreWeight": 40 diff --git a/data/nextstrain/mpox/lineage-b.1/pathogen.json b/data/nextstrain/mpox/lineage-b.1/pathogen.json index 6b453c98..5b40438e 100644 --- a/data/nextstrain/mpox/lineage-b.1/pathogen.json +++ b/data/nextstrain/mpox/lineage-b.1/pathogen.json @@ -267,11 +267,11 @@ "ignoredStopCodons": [ { "codon": 187, - "geneName": "OPG015_dup" + "cdsName": "OPG015_dup" }, { "codon": 187, - "geneName": "OPG015" + "cdsName": "OPG015" } ], "scoreWeight": 40 diff --git a/data/nextstrain/sars-cov-2/BA.2.86/pathogen.json b/data/nextstrain/sars-cov-2/BA.2.86/pathogen.json index c8d27170..2784af23 100644 --- a/data/nextstrain/sars-cov-2/BA.2.86/pathogen.json +++ b/data/nextstrain/sars-cov-2/BA.2.86/pathogen.json @@ -59,2247 +59,2247 @@ "begin": 141, "end": 143 }, - "geneName": "S" + "cdsName": "S" }, { "codonRange": { "begin": 210, "end": 214 }, - "geneName": "S" + "cdsName": "S" }, { "codonRange": { "begin": 211, "end": 214 }, - "geneName": "S" + "cdsName": "S" }, { "codonRange": { "begin": 212, "end": 214 }, - "geneName": "S" + "cdsName": "S" }, { "codonRange": { "begin": 74, "end": 76 }, - "geneName": "E" + "cdsName": "E" }, { "codonRange": { "begin": 1, "end": 276 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 15, "end": 276 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 27, "end": 276 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 28, "end": 276 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 28, "end": 42 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 29, "end": 43 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 47, "end": 276 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 56, "end": 276 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 65, "end": 276 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 94, "end": 276 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 103, "end": 276 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 104, "end": 276 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 135, "end": 276 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 146, "end": 276 }, - 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"geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 89, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 90, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 91, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 92, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 93, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 94, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 95, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 96, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 97, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 98, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" } ] }, @@ -2331,359 +2331,359 @@ "ignoredStopCodons": [ { "codon": 417, - "geneName": "N" + "cdsName": "N" }, { "codon": 238, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codon": 240, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codon": 241, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codon": 244, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codon": 251, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codon": 253, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codon": 260, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codon": 263, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codon": 265, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codon": 7, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 12, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 22, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 26, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 30, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 42, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 45, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 48, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 50, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 53, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 54, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 55, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 58, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 20, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 34, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 37, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 39, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 40, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 43, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 52, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 61, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 71, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 74, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 75, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 76, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 79, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 80, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 82, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 84, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 88, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 89, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 90, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 91, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 93, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 94, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 96, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 112, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 116, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 117, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 120, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 2, - "geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 4, - 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"geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 53, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 58, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 59, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 63, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 67, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 71, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 89, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 90, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 91, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 94, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 102, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 104, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 105, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 109, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 6, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codon": 19, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codon": 33, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codon": 64, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codon": 76, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codon": 85, - "geneName": "ORF9b" + "cdsName": "ORF9b" } ] } @@ -6768,7 +6768,7 @@ "end": 531 }, "description": "This column displays the predicted impact of RBD mutations on ACE2 binding, relative to a BA.2.86 baseline.\nA score is in log10 space. Hence a score of +1 should be interpreted as 10x higher affinity.\nThe score assumes that mutations do not interact. The underlying data looked at the impact of each mutation independently.\nThe score is calculated using the same data and logic as Bloom lab's ACE2 binding calculator (see https://doi.org/10.1101/2022.09.20.508745).", - "gene": "S", + "cds": "S", "ignore": { "clades": [ "outgroup" diff --git a/data/nextstrain/sars-cov-2/BA.2/pathogen.json b/data/nextstrain/sars-cov-2/BA.2/pathogen.json index 82ebb736..99d8b078 100644 --- a/data/nextstrain/sars-cov-2/BA.2/pathogen.json +++ b/data/nextstrain/sars-cov-2/BA.2/pathogen.json @@ -59,2247 +59,2247 @@ "begin": 141, "end": 143 }, - "geneName": "S" + "cdsName": "S" }, { "codonRange": { "begin": 210, "end": 214 }, - "geneName": "S" + "cdsName": "S" }, { "codonRange": { "begin": 211, "end": 214 }, - "geneName": "S" + "cdsName": "S" }, { "codonRange": { "begin": 212, "end": 214 }, - "geneName": "S" + "cdsName": "S" }, { "codonRange": { "begin": 74, "end": 76 }, - "geneName": "E" + "cdsName": "E" }, { "codonRange": { "begin": 1, "end": 276 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 15, "end": 276 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 27, "end": 276 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 28, "end": 276 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 28, "end": 42 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 29, "end": 43 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 47, "end": 276 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 56, "end": 276 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 65, "end": 276 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 94, "end": 276 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 103, "end": 276 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 104, "end": 276 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 135, "end": 276 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 146, "end": 276 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 147, "end": 276 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 148, "end": 276 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 256, "end": 276 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 249, "end": 276 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 257, "end": 276 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 258, "end": 276 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 259, "end": 276 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 260, "end": 276 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 263, "end": 276 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 264, "end": 276 }, - 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"geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 88, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 89, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 90, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 91, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 92, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 93, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 94, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 95, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 96, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 97, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 98, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" } ] }, @@ -2331,359 +2331,359 @@ "ignoredStopCodons": [ { "codon": 417, - "geneName": "N" + "cdsName": "N" }, { "codon": 238, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codon": 240, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codon": 241, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codon": 244, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codon": 251, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codon": 253, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codon": 260, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codon": 263, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codon": 265, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codon": 7, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 12, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 22, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 26, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 30, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 42, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 45, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 48, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 50, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 53, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 54, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 55, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 58, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 20, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 34, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 37, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 39, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 40, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 43, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 52, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 61, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 71, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 74, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 75, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 76, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 79, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 80, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 82, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 84, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 88, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 89, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 90, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 91, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 93, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 94, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 96, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 112, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 116, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 117, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 120, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 2, - "geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 4, - "geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 9, - "geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 11, - "geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 13, - "geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 18, - "geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 28, - "geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 30, - "geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 32, - "geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 34, - "geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 38, - "geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 7, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 17, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 18, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 22, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 26, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 28, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 44, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 49, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 53, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 58, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 59, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 63, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 67, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 71, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 89, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 90, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 91, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 94, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 102, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 104, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 105, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 109, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 6, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codon": 19, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codon": 33, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codon": 64, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codon": 76, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codon": 85, - "geneName": "ORF9b" + "cdsName": "ORF9b" } ] } @@ -6633,7 +6633,7 @@ "end": 531 }, "description": "This column displays predicted neutralizing antibody escape relative to BA.2.\nThe remaining antibody fraction can be calculated as exp(-escape_score). An escape value of 0 means all binding is retained. A value of 1 means e^(-1)=0.4 of binding is retained. A value of 2 means ~17% of binding is retained etc.\nNote that the score does not distinguish between amino acids that are subsituted, so S:346T has the same score as S:346I.\nNote that only RBD mutations are considered, defined as mutations between S:330 and S:531. Mutations outside this range are ignored.\nAll reversions are ignored as they are assumed to be artefacts.\nThe score assumes that mutations do not interact. The underlying data looked at the impact of each mutation independently.\nThe score is calculated using the same logic as Bloom lab's antibody escape calculator (see https://doi.org/10.1093/ve/veac021) using data generated by Yunlong Cao's group (see https://doi.org/10.1101/2022.09.15.507787).", - "gene": "S", + "cds": "S", "ignore": { "clades": [ "outgroup" @@ -218772,7 +218772,7 @@ "end": 531 }, "description": "This column displays the predicted impact of RBD mutations on ACE2 binding, relative to a BA.2 baseline.\nA score is in log10 space. Hence a score of +1 should be interpreted as 10x higher affinity.\nThe score assumes that mutations do not interact. The underlying data looked at the impact of each mutation independently.\nThe score is calculated using the same data and logic as Bloom lab's ACE2 binding calculator (see https://doi.org/10.1101/2022.09.20.508745).", - "gene": "S", + "cds": "S", "ignore": { "clades": [ "outgroup" diff --git a/data/nextstrain/sars-cov-2/XBB/pathogen.json b/data/nextstrain/sars-cov-2/XBB/pathogen.json index 5e989967..07760a4c 100644 --- a/data/nextstrain/sars-cov-2/XBB/pathogen.json +++ b/data/nextstrain/sars-cov-2/XBB/pathogen.json @@ -59,2247 +59,2247 @@ "begin": 141, "end": 143 }, - "geneName": "S" + "cdsName": "S" }, { "codonRange": { "begin": 210, "end": 214 }, - "geneName": "S" + "cdsName": "S" }, { "codonRange": { "begin": 211, "end": 214 }, - "geneName": "S" + "cdsName": "S" }, { "codonRange": { "begin": 212, "end": 214 }, - "geneName": "S" + "cdsName": "S" }, { "codonRange": { "begin": 74, "end": 76 }, - "geneName": "E" + "cdsName": "E" }, { "codonRange": { "begin": 1, "end": 276 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 15, "end": 276 }, - 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"geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 9, - "geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 11, - "geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 13, - "geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 18, - "geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 28, - "geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 30, - "geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 32, - "geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 34, - "geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 38, - "geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 7, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 17, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 18, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 22, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 26, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 28, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 44, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 49, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 53, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 58, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 59, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 63, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 67, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 71, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 89, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 90, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 91, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 94, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 102, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 104, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 105, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 109, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 6, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codon": 19, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codon": 33, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codon": 64, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codon": 76, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codon": 85, - "geneName": "ORF9b" + "cdsName": "ORF9b" } ] } @@ -6702,7 +6702,7 @@ "end": 531 }, "description": "This column displays predicted neutralizing antibody escape relative to XBB for antibodies that neutralize XBB.\nThe remaining antibody fraction can be calculated as exp(-escape_score). An escape value of 0 means all binding is retained. A value of 1 means e^(-1)=0.4 of binding is retained. A value of 2 means ~17% of binding is retained etc.\nNote that the score does not distinguish between amino acids that are subsituted, so S:346T has the same score as S:346I.\nNote that only RBD mutations are considered, defined as mutations between S:330 and S:531. Mutations outside this range are ignored.\nThe score assumes that mutations do not interact. The underlying data looked at the impact of each mutation independently.\nThe score is calculated using the same logic as Bloom lab's antibody escape calculator (see https://doi.org/10.1093/ve/veac021) using data generated by Yunlong Cao's group (see https://doi.org/10.1101/2022.09.15.507787).", - "gene": "S", + "cds": "S", "ignore": { "clades": [ "outgroup" @@ -43173,7 +43173,7 @@ "end": 531 }, "description": "This column displays the predicted impact of RBD mutations on ACE2 binding, relative to an XBB baseline.\nA score is in log10 space. Hence a score of +1 should be interpreted as 10x higher affinity.\nThe score assumes that mutations do not interact. The underlying data looked at the impact of each mutation independently.\nThe score is calculated using the same data and logic as Bloom lab's ACE2 binding calculator (see https://doi.org/10.1101/2022.09.20.508745).", - "gene": "S", + "cds": "S", "ignore": { "clades": [ "outgroup" diff --git a/data/nextstrain/sars-cov-2/wuhan-hu-1/orfs/pathogen.json b/data/nextstrain/sars-cov-2/wuhan-hu-1/orfs/pathogen.json index 8ef2b991..21c7b362 100644 --- a/data/nextstrain/sars-cov-2/wuhan-hu-1/orfs/pathogen.json +++ b/data/nextstrain/sars-cov-2/wuhan-hu-1/orfs/pathogen.json @@ -59,2247 +59,2247 @@ "begin": 141, "end": 143 }, - "geneName": "S" + "cdsName": "S" }, { "codonRange": { "begin": 210, "end": 214 }, - "geneName": "S" + "cdsName": "S" }, { "codonRange": { "begin": 211, "end": 214 }, - "geneName": "S" + "cdsName": "S" }, { "codonRange": { "begin": 212, "end": 214 }, - "geneName": "S" + "cdsName": "S" }, { "codonRange": { "begin": 74, "end": 76 }, - "geneName": "E" + "cdsName": "E" }, { "codonRange": { "begin": 1, "end": 276 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 15, "end": 276 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 27, "end": 276 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 28, "end": 276 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 28, "end": 42 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 29, "end": 43 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 47, "end": 276 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 56, "end": 276 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 65, "end": 276 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 94, "end": 276 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 103, "end": 276 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 104, "end": 276 }, - 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"geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 76, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 77, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 78, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 79, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 80, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 81, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 82, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 83, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 84, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 85, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 86, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 87, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 88, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 89, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 90, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 91, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 92, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 93, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 94, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 95, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 96, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 97, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 98, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" } ] }, @@ -2331,359 +2331,359 @@ "ignoredStopCodons": [ { "codon": 417, - "geneName": "N" + "cdsName": "N" }, { "codon": 238, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codon": 240, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codon": 241, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codon": 244, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codon": 251, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codon": 253, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codon": 260, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codon": 263, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codon": 265, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codon": 7, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 12, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 22, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 26, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 30, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 42, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 45, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 48, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 50, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 53, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 54, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 55, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 58, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 20, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 34, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 37, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 39, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 40, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 43, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 52, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 61, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 71, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 74, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 75, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 76, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 79, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 80, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 82, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 84, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 88, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 89, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 90, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 91, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 93, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 94, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 96, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 112, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 116, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 117, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 120, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 2, - "geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 4, - "geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 9, - "geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 11, - "geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 13, - "geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 18, - "geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 28, - "geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 30, - "geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 32, - "geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 34, - "geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 38, - "geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 7, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 17, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 18, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 22, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 26, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 28, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 44, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 49, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 53, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 58, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 59, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 63, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 67, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 71, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 89, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 90, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 91, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 94, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 102, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 104, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 105, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 109, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 6, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codon": 19, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codon": 33, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codon": 64, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codon": 76, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codon": 85, - "geneName": "ORF9b" + "cdsName": "ORF9b" } ] } diff --git a/data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/pathogen.json b/data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/pathogen.json index a74a5aa1..a7a9f602 100644 --- a/data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/pathogen.json +++ b/data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/pathogen.json @@ -90,13 +90,13 @@ "nameShort": "Glyc.", "nameFriendly": "Glycosylation", "description": "N-linked glycosylation motifs (N-X-S/T with X any amino acid other than P)", - "includeGenes": [ + "includeCdses": [ { - "gene": "HA1", + "cds": "HA1", "ranges": [] }, { - "gene": "HA2", + "cds": "HA2", "ranges": [ { "begin": 0, diff --git a/data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/pathogen.json b/data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/pathogen.json index 08209501..3021ad5c 100644 --- a/data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/pathogen.json +++ b/data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/pathogen.json @@ -92,13 +92,13 @@ "nameShort": "Glyc.", "nameFriendly": "Glycosylation", "description": "N-linked glycosylation motifs (N-X-S/T with X any amino acid other than P)", - "includeGenes": [ + "includeCdses": [ { - "gene": "HA1", + "cds": "HA1", "ranges": [] }, { - "gene": "HA2", + "cds": "HA2", "ranges": [ { "begin": 0, diff --git a/data_output/nextstrain/flu/h1n1pdm/na/MW626056/unreleased/pathogen.json b/data_output/nextstrain/flu/h1n1pdm/na/MW626056/unreleased/pathogen.json index f70e8431..fdc9746d 100644 --- a/data_output/nextstrain/flu/h1n1pdm/na/MW626056/unreleased/pathogen.json +++ b/data_output/nextstrain/flu/h1n1pdm/na/MW626056/unreleased/pathogen.json @@ -90,9 +90,9 @@ "nameShort": "Glyc.", "nameFriendly": "Glycosylation", "description": "N-linked glycosylation motifs (N-X-S/T with X any amino acid other than P)", - "includeGenes": [ + "includeCdses": [ { - "gene": "NA", + "cds": "NA", "ranges": [ { "begin": 33, diff --git a/data_output/nextstrain/flu/h3n2/ha/CY163680/unreleased/pathogen.json b/data_output/nextstrain/flu/h3n2/ha/CY163680/unreleased/pathogen.json index af3b5f4d..a622f5e5 100644 --- a/data_output/nextstrain/flu/h3n2/ha/CY163680/unreleased/pathogen.json +++ b/data_output/nextstrain/flu/h3n2/ha/CY163680/unreleased/pathogen.json @@ -90,13 +90,13 @@ "nameShort": "Glyc.", "nameFriendly": "Glycosylation", "description": "N-linked glycosylation motifs (N-X-S/T with X any amino acid other than P)", - "includeGenes": [ + "includeCdses": [ { - "gene": "HA1", + "cds": "HA1", "ranges": [] }, { - "gene": "HA2", + "cds": "HA2", "ranges": [ { "begin": 0, diff --git a/data_output/nextstrain/flu/h3n2/ha/EPI1857216/unreleased/pathogen.json b/data_output/nextstrain/flu/h3n2/ha/EPI1857216/unreleased/pathogen.json index 25d0a30e..e60cf7fa 100644 --- a/data_output/nextstrain/flu/h3n2/ha/EPI1857216/unreleased/pathogen.json +++ b/data_output/nextstrain/flu/h3n2/ha/EPI1857216/unreleased/pathogen.json @@ -91,7 +91,7 @@ "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", + "cds": "HA1", "aaRange": { "begin": 100, "end": 200 @@ -138,13 +138,13 @@ "nameShort": "Glyc.", "nameFriendly": "Glycosylation", "description": "N-linked glycosylation motifs (N-X-S/T with X any amino acid other than P)", - "includeGenes": [ + "includeCdses": [ { - "gene": "HA1", + "cds": "HA1", "ranges": [] }, { - "gene": "HA2", + "cds": "HA2", "ranges": [ { "begin": 0, diff --git a/data_output/nextstrain/flu/h3n2/na/EPI1857215/unreleased/pathogen.json b/data_output/nextstrain/flu/h3n2/na/EPI1857215/unreleased/pathogen.json index 349aa973..20b76a9d 100644 --- a/data_output/nextstrain/flu/h3n2/na/EPI1857215/unreleased/pathogen.json +++ b/data_output/nextstrain/flu/h3n2/na/EPI1857215/unreleased/pathogen.json @@ -90,9 +90,9 @@ "nameShort": "Glyc.", "nameFriendly": "Glycosylation", "description": "N-linked glycosylation motifs (N-X-S/T with X any amino acid other than P)", - "includeGenes": [ + "includeCdses": [ { - "gene": "NA", + "cds": "NA", "ranges": [ { "begin": 33, diff --git a/data_output/nextstrain/flu/vic/ha/KX058884/unreleased/pathogen.json b/data_output/nextstrain/flu/vic/ha/KX058884/unreleased/pathogen.json index bf3170df..0690e4b4 100644 --- a/data_output/nextstrain/flu/vic/ha/KX058884/unreleased/pathogen.json +++ b/data_output/nextstrain/flu/vic/ha/KX058884/unreleased/pathogen.json @@ -92,13 +92,13 @@ "nameShort": "Glyc.", "nameFriendly": "Glycosylation", "description": "N-linked glycosylation motifs (N-X-S/T with X any amino acid other than P)", - "includeGenes": [ + "includeCdses": [ { - "gene": "HA1", + "cds": "HA1", "ranges": [] }, { - "gene": "HA2", + "cds": "HA2", "ranges": [ { "begin": 0, diff --git a/data_output/nextstrain/flu/vic/na/CY073894/unreleased/pathogen.json b/data_output/nextstrain/flu/vic/na/CY073894/unreleased/pathogen.json index 5cb7d0a7..35ea1fa2 100644 --- a/data_output/nextstrain/flu/vic/na/CY073894/unreleased/pathogen.json +++ b/data_output/nextstrain/flu/vic/na/CY073894/unreleased/pathogen.json @@ -90,9 +90,9 @@ "nameShort": "Glyc.", "nameFriendly": "Glycosylation", "description": "N-linked glycosylation motifs (N-X-S/T with X any amino acid other than P)", - "includeGenes": [ + "includeCdses": [ { - "gene": "NA", + "cds": "NA", "ranges": [ { "begin": 33, diff --git a/data_output/nextstrain/flu/yam/ha/JN993010/unreleased/pathogen.json b/data_output/nextstrain/flu/yam/ha/JN993010/unreleased/pathogen.json index 0d56d0a7..95c3975f 100644 --- a/data_output/nextstrain/flu/yam/ha/JN993010/unreleased/pathogen.json +++ b/data_output/nextstrain/flu/yam/ha/JN993010/unreleased/pathogen.json @@ -86,13 +86,13 @@ "nameShort": "Glyc.", "nameFriendly": "Glycosylation", "description": "N-linked glycosylation motifs (N-X-S/T with X any amino acid other than P)", - "includeGenes": [ + "includeCdses": [ { - "gene": "HA1", + "cds": "HA1", "ranges": [] }, { - "gene": "HA2", + "cds": "HA2", "ranges": [ { "begin": 0, diff --git a/data_output/nextstrain/mpox/all-clades/unreleased/pathogen.json b/data_output/nextstrain/mpox/all-clades/unreleased/pathogen.json index e3f51617..06a19bfd 100644 --- a/data_output/nextstrain/mpox/all-clades/unreleased/pathogen.json +++ b/data_output/nextstrain/mpox/all-clades/unreleased/pathogen.json @@ -38,119 +38,119 @@ "begin": 3, "end": 589 }, - "geneName": "OPG003" + "cdsName": "OPG003" }, { "codonRange": { "begin": 3, "end": 589 }, - "geneName": "OPG003_dup" + "cdsName": "OPG003_dup" }, { "codonRange": { "begin": 281, "end": 285 }, - "geneName": "OPG105" + "cdsName": "OPG105" }, { "codonRange": { "begin": 227, "end": 229 }, - "geneName": "OPG164" + "cdsName": "OPG164" }, { "codonRange": { "begin": 554, "end": 560 }, - "geneName": "OPG180" + "cdsName": "OPG180" }, { "codonRange": { "begin": 42, "end": 101 }, - "geneName": "OPG197" + "cdsName": "OPG197" }, { "codonRange": { "begin": 443, "end": 443 }, - "geneName": "OPG037" + "cdsName": "OPG037" }, { "codonRange": { "begin": 57, "end": 443 }, - "geneName": "OPG037" + "cdsName": "OPG037" }, { "codonRange": { "begin": 481, "end": 483 }, - "geneName": "OPG047" + "cdsName": "OPG047" }, { "codonRange": { "begin": 482, "end": 483 }, - "geneName": "OPG047" + "cdsName": "OPG047" }, { "codonRange": { "begin": 72, "end": 76 }, - "geneName": "OPG050" + "cdsName": "OPG050" }, { "codonRange": { "begin": 369, "end": 371 }, - "geneName": "OPG153" + "cdsName": "OPG153" }, { "codonRange": { "begin": 370, "end": 371 }, - "geneName": "OPG153" + "cdsName": "OPG153" }, { "codonRange": { "begin": 166, "end": 169 }, - "geneName": "OPG191" + "cdsName": "OPG191" }, { "codonRange": { "begin": 72, "end": 222 }, - "geneName": "OPG195" + "cdsName": "OPG195" }, { "codonRange": { "begin": 208, "end": 222 }, - "geneName": "OPG195" + "cdsName": "OPG195" }, { "codonRange": { "begin": 289, "end": 346 }, - "geneName": "OPG174" + "cdsName": "OPG174" } ], "scoreWeight": 20 @@ -183,23 +183,23 @@ "ignoredStopCodons": [ { "codon": 187, - "geneName": "OPG015_dup" + "cdsName": "OPG015_dup" }, { "codon": 187, - "geneName": "OPG015" + "cdsName": "OPG015" }, { "codon": 21, - "geneName": "OPG176" + "cdsName": "OPG176" }, { "codon": 299, - "geneName": "OPG187" + "cdsName": "OPG187" }, { "codon": 48, - "geneName": "OPG059" + "cdsName": "OPG059" } ], "scoreWeight": 20 diff --git a/data_output/nextstrain/mpox/clade-iib/unreleased/pathogen.json b/data_output/nextstrain/mpox/clade-iib/unreleased/pathogen.json index 934126a1..ee466470 100644 --- a/data_output/nextstrain/mpox/clade-iib/unreleased/pathogen.json +++ b/data_output/nextstrain/mpox/clade-iib/unreleased/pathogen.json @@ -38,7 +38,7 @@ "begin": 289, "end": 346 }, - "geneName": "OPG174" + "cdsName": "OPG174" } ], "scoreWeight": 20 @@ -71,15 +71,15 @@ "ignoredStopCodons": [ { "codon": 187, - "geneName": "OPG015_dup" + "cdsName": "OPG015_dup" }, { "codon": 187, - "geneName": "OPG015" + "cdsName": "OPG015" }, { "codon": 21, - "geneName": "OPG176" + "cdsName": "OPG176" } ], "scoreWeight": 40 diff --git a/data_output/nextstrain/mpox/lineage-b.1/unreleased/pathogen.json b/data_output/nextstrain/mpox/lineage-b.1/unreleased/pathogen.json index 6b453c98..5b40438e 100644 --- a/data_output/nextstrain/mpox/lineage-b.1/unreleased/pathogen.json +++ b/data_output/nextstrain/mpox/lineage-b.1/unreleased/pathogen.json @@ -267,11 +267,11 @@ "ignoredStopCodons": [ { "codon": 187, - "geneName": "OPG015_dup" + "cdsName": "OPG015_dup" }, { "codon": 187, - "geneName": "OPG015" + "cdsName": "OPG015" } ], "scoreWeight": 40 diff --git a/data_output/nextstrain/sars-cov-2/BA.2.86/unreleased/pathogen.json b/data_output/nextstrain/sars-cov-2/BA.2.86/unreleased/pathogen.json index c8d27170..2784af23 100644 --- a/data_output/nextstrain/sars-cov-2/BA.2.86/unreleased/pathogen.json +++ b/data_output/nextstrain/sars-cov-2/BA.2.86/unreleased/pathogen.json @@ -59,2247 +59,2247 @@ "begin": 141, "end": 143 }, - "geneName": "S" + "cdsName": "S" }, { "codonRange": { "begin": 210, "end": 214 }, - "geneName": "S" + "cdsName": "S" }, { "codonRange": { "begin": 211, "end": 214 }, - "geneName": "S" + "cdsName": "S" }, { "codonRange": { "begin": 212, "end": 214 }, - "geneName": "S" + "cdsName": "S" }, { "codonRange": { "begin": 74, "end": 76 }, - "geneName": "E" + "cdsName": "E" }, { "codonRange": { "begin": 1, "end": 276 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 15, "end": 276 }, - 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"geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 76, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 77, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 78, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 79, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 80, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 81, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 82, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 83, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 84, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 85, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 86, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 87, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 88, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 89, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 90, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 91, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 92, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 93, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 94, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 95, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 96, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 97, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 98, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" } ] }, @@ -2331,359 +2331,359 @@ "ignoredStopCodons": [ { "codon": 417, - "geneName": "N" + "cdsName": "N" }, { "codon": 238, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codon": 240, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codon": 241, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codon": 244, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codon": 251, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codon": 253, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codon": 260, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codon": 263, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codon": 265, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codon": 7, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 12, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 22, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 26, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 30, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 42, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 45, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 48, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 50, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 53, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 54, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 55, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 58, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 20, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 34, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 37, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 39, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 40, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 43, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 52, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 61, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 71, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 74, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 75, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 76, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 79, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 80, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 82, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 84, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 88, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 89, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 90, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 91, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 93, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 94, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 96, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 112, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 116, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 117, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 120, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 2, - "geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 4, - 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"geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 53, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 58, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 59, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 63, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 67, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 71, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 89, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 90, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 91, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 94, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 102, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 104, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 105, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 109, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 6, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codon": 19, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codon": 33, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codon": 64, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codon": 76, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codon": 85, - "geneName": "ORF9b" + "cdsName": "ORF9b" } ] } @@ -6768,7 +6768,7 @@ "end": 531 }, "description": "This column displays the predicted impact of RBD mutations on ACE2 binding, relative to a BA.2.86 baseline.\nA score is in log10 space. Hence a score of +1 should be interpreted as 10x higher affinity.\nThe score assumes that mutations do not interact. The underlying data looked at the impact of each mutation independently.\nThe score is calculated using the same data and logic as Bloom lab's ACE2 binding calculator (see https://doi.org/10.1101/2022.09.20.508745).", - "gene": "S", + "cds": "S", "ignore": { "clades": [ "outgroup" diff --git a/data_output/nextstrain/sars-cov-2/BA.2/unreleased/pathogen.json b/data_output/nextstrain/sars-cov-2/BA.2/unreleased/pathogen.json index 82ebb736..99d8b078 100644 --- a/data_output/nextstrain/sars-cov-2/BA.2/unreleased/pathogen.json +++ b/data_output/nextstrain/sars-cov-2/BA.2/unreleased/pathogen.json @@ -59,2247 +59,2247 @@ "begin": 141, "end": 143 }, - "geneName": "S" + "cdsName": "S" }, { "codonRange": { "begin": 210, "end": 214 }, - "geneName": "S" + "cdsName": "S" }, { "codonRange": { "begin": 211, "end": 214 }, - "geneName": "S" + "cdsName": "S" }, { "codonRange": { "begin": 212, "end": 214 }, - "geneName": "S" + "cdsName": "S" }, { "codonRange": { "begin": 74, "end": 76 }, - "geneName": "E" + "cdsName": "E" }, { "codonRange": { "begin": 1, "end": 276 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 15, "end": 276 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 27, "end": 276 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 28, "end": 276 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 28, "end": 42 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 29, "end": 43 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 47, "end": 276 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 56, "end": 276 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 65, "end": 276 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 94, "end": 276 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 103, "end": 276 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 104, "end": 276 }, - 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"geneName": "N" + "cdsName": "N" }, { "codon": 238, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codon": 240, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codon": 241, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codon": 244, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codon": 251, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codon": 253, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codon": 260, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codon": 263, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codon": 265, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codon": 7, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 12, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 22, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 26, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 30, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 42, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 45, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 48, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 50, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 53, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 54, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 55, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 58, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 20, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 34, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 37, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 39, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 40, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 43, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 52, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 61, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 71, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 74, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 75, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 76, - 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"geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 9, - "geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 11, - "geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 13, - "geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 18, - "geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 28, - "geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 30, - "geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 32, - "geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 34, - "geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 38, - "geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 7, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 17, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 18, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 22, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 26, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 28, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 44, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 49, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 53, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 58, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 59, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 63, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 67, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 71, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 89, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 90, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 91, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 94, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 102, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 104, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 105, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 109, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 6, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codon": 19, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codon": 33, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codon": 64, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codon": 76, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codon": 85, - "geneName": "ORF9b" + "cdsName": "ORF9b" } ] } @@ -6633,7 +6633,7 @@ "end": 531 }, "description": "This column displays predicted neutralizing antibody escape relative to BA.2.\nThe remaining antibody fraction can be calculated as exp(-escape_score). An escape value of 0 means all binding is retained. A value of 1 means e^(-1)=0.4 of binding is retained. A value of 2 means ~17% of binding is retained etc.\nNote that the score does not distinguish between amino acids that are subsituted, so S:346T has the same score as S:346I.\nNote that only RBD mutations are considered, defined as mutations between S:330 and S:531. Mutations outside this range are ignored.\nAll reversions are ignored as they are assumed to be artefacts.\nThe score assumes that mutations do not interact. The underlying data looked at the impact of each mutation independently.\nThe score is calculated using the same logic as Bloom lab's antibody escape calculator (see https://doi.org/10.1093/ve/veac021) using data generated by Yunlong Cao's group (see https://doi.org/10.1101/2022.09.15.507787).", - "gene": "S", + "cds": "S", "ignore": { "clades": [ "outgroup" @@ -218772,7 +218772,7 @@ "end": 531 }, "description": "This column displays the predicted impact of RBD mutations on ACE2 binding, relative to a BA.2 baseline.\nA score is in log10 space. Hence a score of +1 should be interpreted as 10x higher affinity.\nThe score assumes that mutations do not interact. The underlying data looked at the impact of each mutation independently.\nThe score is calculated using the same data and logic as Bloom lab's ACE2 binding calculator (see https://doi.org/10.1101/2022.09.20.508745).", - "gene": "S", + "cds": "S", "ignore": { "clades": [ "outgroup" diff --git a/data_output/nextstrain/sars-cov-2/XBB/unreleased/pathogen.json b/data_output/nextstrain/sars-cov-2/XBB/unreleased/pathogen.json index 5e989967..07760a4c 100644 --- a/data_output/nextstrain/sars-cov-2/XBB/unreleased/pathogen.json +++ b/data_output/nextstrain/sars-cov-2/XBB/unreleased/pathogen.json @@ -59,2247 +59,2247 @@ "begin": 141, "end": 143 }, - "geneName": "S" + "cdsName": "S" }, { "codonRange": { "begin": 210, "end": 214 }, - "geneName": "S" + "cdsName": "S" }, { "codonRange": { "begin": 211, "end": 214 }, - "geneName": "S" + "cdsName": "S" }, { "codonRange": { "begin": 212, "end": 214 }, - "geneName": "S" + "cdsName": "S" }, { "codonRange": { "begin": 74, "end": 76 }, - "geneName": "E" + "cdsName": "E" }, { "codonRange": { "begin": 1, "end": 276 }, - 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"geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 9, - "geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 11, - "geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 13, - "geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 18, - "geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 28, - "geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 30, - "geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 32, - "geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 34, - "geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 38, - "geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 7, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 17, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 18, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 22, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 26, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 28, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 44, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 49, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 53, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 58, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 59, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 63, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 67, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 71, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 89, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 90, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 91, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 94, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 102, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 104, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 105, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 109, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 6, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codon": 19, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codon": 33, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codon": 64, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codon": 76, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codon": 85, - "geneName": "ORF9b" + "cdsName": "ORF9b" } ] } @@ -6702,7 +6702,7 @@ "end": 531 }, "description": "This column displays predicted neutralizing antibody escape relative to XBB for antibodies that neutralize XBB.\nThe remaining antibody fraction can be calculated as exp(-escape_score). An escape value of 0 means all binding is retained. A value of 1 means e^(-1)=0.4 of binding is retained. A value of 2 means ~17% of binding is retained etc.\nNote that the score does not distinguish between amino acids that are subsituted, so S:346T has the same score as S:346I.\nNote that only RBD mutations are considered, defined as mutations between S:330 and S:531. Mutations outside this range are ignored.\nThe score assumes that mutations do not interact. The underlying data looked at the impact of each mutation independently.\nThe score is calculated using the same logic as Bloom lab's antibody escape calculator (see https://doi.org/10.1093/ve/veac021) using data generated by Yunlong Cao's group (see https://doi.org/10.1101/2022.09.15.507787).", - "gene": "S", + "cds": "S", "ignore": { "clades": [ "outgroup" @@ -43173,7 +43173,7 @@ "end": 531 }, "description": "This column displays the predicted impact of RBD mutations on ACE2 binding, relative to an XBB baseline.\nA score is in log10 space. Hence a score of +1 should be interpreted as 10x higher affinity.\nThe score assumes that mutations do not interact. The underlying data looked at the impact of each mutation independently.\nThe score is calculated using the same data and logic as Bloom lab's ACE2 binding calculator (see https://doi.org/10.1101/2022.09.20.508745).", - "gene": "S", + "cds": "S", "ignore": { "clades": [ "outgroup" diff --git a/data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/unreleased/pathogen.json b/data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/unreleased/pathogen.json index 8ef2b991..21c7b362 100644 --- a/data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/unreleased/pathogen.json +++ b/data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/unreleased/pathogen.json @@ -59,2247 +59,2247 @@ "begin": 141, "end": 143 }, - "geneName": "S" + "cdsName": "S" }, { "codonRange": { "begin": 210, "end": 214 }, - "geneName": "S" + "cdsName": "S" }, { "codonRange": { "begin": 211, "end": 214 }, - "geneName": "S" + "cdsName": "S" }, { "codonRange": { "begin": 212, "end": 214 }, - "geneName": "S" + "cdsName": "S" }, { "codonRange": { "begin": 74, "end": 76 }, - "geneName": "E" + "cdsName": "E" }, { "codonRange": { "begin": 1, "end": 276 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 15, "end": 276 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 27, "end": 276 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 28, "end": 276 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 28, "end": 42 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 29, "end": 43 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 47, "end": 276 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 56, "end": 276 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 65, "end": 276 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 94, "end": 276 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 103, "end": 276 }, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codonRange": { "begin": 104, "end": 276 }, - 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"geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 40, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 41, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 42, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 43, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 44, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 45, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 46, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 47, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 48, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 49, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 50, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 51, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 52, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 53, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 54, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 55, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 56, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 57, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 58, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 59, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 60, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 61, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 62, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 63, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 64, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 65, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 66, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 67, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 68, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 69, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 70, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 71, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 72, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 73, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 74, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 75, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 76, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 77, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 78, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 79, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 80, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 81, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 82, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 83, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 84, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 85, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 86, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 87, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 88, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 89, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 90, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 91, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 92, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 93, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 94, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 95, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 96, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 97, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codonRange": { "begin": 98, "end": 98 }, - "geneName": "ORF9b" + "cdsName": "ORF9b" } ] }, @@ -2331,359 +2331,359 @@ "ignoredStopCodons": [ { "codon": 417, - "geneName": "N" + "cdsName": "N" }, { "codon": 238, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codon": 240, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codon": 241, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codon": 244, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codon": 251, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codon": 253, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codon": 260, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codon": 263, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codon": 265, - "geneName": "ORF3a" + "cdsName": "ORF3a" }, { "codon": 7, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 12, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 22, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 26, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 30, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 42, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 45, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 48, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 50, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 53, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 54, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 55, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 58, - "geneName": "ORF6" + "cdsName": "ORF6" }, { "codon": 20, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 34, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 37, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 39, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 40, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 43, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 52, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 61, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 71, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 74, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 75, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 76, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 79, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 80, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 82, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 84, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 88, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 89, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 90, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 91, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 93, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 94, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 96, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 112, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 116, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 117, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 120, - "geneName": "ORF7a" + "cdsName": "ORF7a" }, { "codon": 2, - "geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 4, - "geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 9, - "geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 11, - "geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 13, - "geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 18, - "geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 28, - "geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 30, - "geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 32, - "geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 34, - "geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 38, - "geneName": "ORF7b" + "cdsName": "ORF7b" }, { "codon": 7, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 17, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 18, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 22, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 26, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 28, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 44, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 49, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 53, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 58, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 59, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 63, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 67, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 71, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 89, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 90, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 91, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 94, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 102, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 104, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 105, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 109, - "geneName": "ORF8" + "cdsName": "ORF8" }, { "codon": 6, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codon": 19, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codon": 33, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codon": 64, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codon": 76, - "geneName": "ORF9b" + "cdsName": "ORF9b" }, { "codon": 85, - "geneName": "ORF9b" + "cdsName": "ORF9b" } ] } diff --git a/scripts/migrate_003_gene_to_cds.py b/scripts/migrate_003_gene_to_cds.py new file mode 100644 index 00000000..0b8637d8 --- /dev/null +++ b/scripts/migrate_003_gene_to_cds.py @@ -0,0 +1,49 @@ +from lib.container import dict_rename_many, dict_get +from lib.fs import find_files, json_read, json_write + + +def rename_gene_to_cds(pathogen): + motifs = dict_get(pathogen, ["aaMotifs"]) + if motifs: + for i, motif in enumerate(motifs): + motifs[i] = dict_rename_many(motifs[i], {"includeGenes": "includeCdses"}) + + for i, motif in enumerate(motifs): + includes = dict_get(motif, ["includeCdses"]) + if includes: + for j, include in enumerate(includes): + motifs[i]["includeCdses"][j] = dict_rename_many(motifs[i]["includeCdses"][j], {"gene": "cds"}) + + phenotype_data = dict_get(pathogen, ["phenotypeData"]) + if phenotype_data: + for i, phenotype_datum in enumerate(phenotype_data): + phenotype_data[i] = dict_rename_many(phenotype_datum, {"gene": "cds"}) + + qc = dict_get(pathogen, ["qc"]) + if qc: + frame_shifts = dict_get(qc, ["frameShifts"]) + if frame_shifts: + ignoreds = dict_get(frame_shifts, ["ignoredFrameShifts"]) + if ignoreds: + for i, ignored in enumerate(ignoreds): + ignoreds[i] = dict_rename_many(ignoreds[i], {"geneName": "cdsName"}) + + stop_codons = dict_get(qc, ["stopCodons"]) + if stop_codons: + ignoreds = dict_get(stop_codons, ["ignoredStopCodons"]) + if ignoreds: + for i, ignored in enumerate(ignoreds): + ignoreds[i] = dict_rename_many(ignoreds[i], {"geneName": "cdsName"}) + + return pathogen + + +def main(): + for file in find_files("pathogen.json", here="data/"): + pathogen = json_read(file) + pathogen = rename_gene_to_cds(pathogen) + json_write(pathogen, file, no_sort_keys=True) + + +if __name__ == '__main__': + main()