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feat: rename 'gene' to 'cds' in code and public interfaces #125

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merged 3 commits into from
Jan 9, 2024
Merged

feat: rename 'gene' to 'cds' in code and public interfaces #125

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317ebee
feat: rename 'gene' to 'cds' in code and public interfaces
ivan-aksamentov Jan 9, 2024
777f7bd
feat: apply "rename 'gene' to 'cds' in code and public interfaces"
ivan-aksamentov Jan 9, 2024
a81f0ed
refactor: remove commented code
ivan-aksamentov Jan 9, 2024
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6 changes: 3 additions & 3 deletions data/nextstrain/flu/h1n1pdm/ha/CY121680/pathogen.json
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Original file line number Diff line number Diff line change
Expand Up @@ -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,
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6 changes: 3 additions & 3 deletions data/nextstrain/flu/h1n1pdm/ha/MW626062/pathogen.json
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Original file line number Diff line number Diff line change
Expand Up @@ -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,
Expand Down
4 changes: 2 additions & 2 deletions data/nextstrain/flu/h1n1pdm/na/MW626056/pathogen.json
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Original file line number Diff line number Diff line change
Expand Up @@ -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,
Expand Down
6 changes: 3 additions & 3 deletions data/nextstrain/flu/h3n2/ha/CY163680/pathogen.json
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Original file line number Diff line number Diff line change
Expand Up @@ -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,
Expand Down
8 changes: 4 additions & 4 deletions data/nextstrain/flu/h3n2/ha/EPI1857216/pathogen.json
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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,
Expand Down
4 changes: 2 additions & 2 deletions data/nextstrain/flu/h3n2/na/EPI1857215/pathogen.json
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Original file line number Diff line number Diff line change
Expand Up @@ -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,
Expand Down
6 changes: 3 additions & 3 deletions data/nextstrain/flu/vic/ha/KX058884/pathogen.json
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Original file line number Diff line number Diff line change
Expand Up @@ -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,
Expand Down
4 changes: 2 additions & 2 deletions data/nextstrain/flu/vic/na/CY073894/pathogen.json
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Original file line number Diff line number Diff line change
Expand Up @@ -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,
Expand Down
6 changes: 3 additions & 3 deletions data/nextstrain/flu/yam/ha/JN993010/pathogen.json
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Original file line number Diff line number Diff line change
Expand Up @@ -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,
Expand Down
44 changes: 22 additions & 22 deletions data/nextstrain/mpox/all-clades/pathogen.json
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down
8 changes: 4 additions & 4 deletions data/nextstrain/mpox/clade-iib/pathogen.json
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Original file line number Diff line number Diff line change
Expand Up @@ -38,7 +38,7 @@
"begin": 289,
"end": 346
},
"geneName": "OPG174"
"cdsName": "OPG174"
}
],
"scoreWeight": 20
Expand Down Expand Up @@ -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
Expand Down
4 changes: 2 additions & 2 deletions data/nextstrain/mpox/lineage-b.1/pathogen.json
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Original file line number Diff line number Diff line change
Expand Up @@ -267,11 +267,11 @@
"ignoredStopCodons": [
{
"codon": 187,
"geneName": "OPG015_dup"
"cdsName": "OPG015_dup"
},
{
"codon": 187,
"geneName": "OPG015"
"cdsName": "OPG015"
}
],
"scoreWeight": 40
Expand Down
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