From 3539f582aedf4e74014fcd3256f95cc931834a50 Mon Sep 17 00:00:00 2001 From: ivan-aksamentov Date: Tue, 9 Jan 2024 01:01:43 +0100 Subject: [PATCH 1/2] feat: rename 'gene' to 'cds' in code and public interfaces As well as `geneName` to `cdsName` --- .../src/components/Results/ColumnAaMotifs.tsx | 8 ++++---- .../components/Results/ColumnNameTooltip.tsx | 2 +- .../components/Results/ListOfFrameShifts.tsx | 2 +- .../components/Results/ListOfInsertions.tsx | 6 +++--- .../components/Results/ListOfStopCodons.tsx | 2 +- .../SequenceView/PeptideMarkerFrameShift.tsx | 8 ++++---- .../components/SequenceView/PeptideView.tsx | 10 +++++----- .../SequenceView/SequenceMarkerFrameShift.tsx | 6 +++--- .../components/SequenceView/SequenceView.tsx | 2 +- .../src/helpers/formatFrameShift.ts | 4 ++-- .../src/helpers/formatMutation.ts | 4 ++-- .../src/helpers/formatQCStopCodons.ts | 2 +- .../nextclade/src/align/insertions_strip.rs | 6 +++--- .../nextclade/src/analyze/find_aa_motifs.rs | 12 ++++++------ .../src/analyze/find_aa_motifs_changes.rs | 8 ++++---- .../src/analyze/find_private_aa_mutations.rs | 10 +++++----- .../nextclade/src/analyze/is_sequenced.rs | 4 ++-- .../nextclade/src/analyze/letter_ranges.rs | 12 ++++++------ packages_rs/nextclade/src/analyze/phenotype.rs | 2 +- .../nextclade/src/analyze/virus_properties.rs | 8 ++++---- packages_rs/nextclade/src/gene/gene_map.rs | 6 +++--- packages_rs/nextclade/src/io/nextclade_csv.rs | 18 +++++++++--------- packages_rs/nextclade/src/qc/qc_config.rs | 4 ++-- .../nextclade/src/qc/qc_rule_frame_shifts.rs | 2 +- .../nextclade/src/qc/qc_rule_stop_codons.rs | 2 +- .../nextclade/src/run/nextclade_run_one.rs | 10 +++++----- .../src/translate/frame_shifts_translate.rs | 4 ++-- .../nextclade/src/translate/translate_genes.rs | 2 +- packages_rs/nextclade/src/tree/split_muts2.rs | 12 ++++++------ packages_rs/nextclade/src/tree/tree_builder.rs | 8 ++++---- .../nextclade/src/tree/tree_preprocess.rs | 14 +++++++------- packages_rs/nextclade/src/types/outputs.rs | 8 ++++---- 32 files changed, 104 insertions(+), 104 deletions(-) diff --git a/packages_rs/nextclade-web/src/components/Results/ColumnAaMotifs.tsx b/packages_rs/nextclade-web/src/components/Results/ColumnAaMotifs.tsx index 4c5f1e688..004f1e3f1 100644 --- a/packages_rs/nextclade-web/src/components/Results/ColumnAaMotifs.tsx +++ b/packages_rs/nextclade-web/src/components/Results/ColumnAaMotifs.tsx @@ -244,15 +244,15 @@ export function ListOfAaMotifMutations({ motifs }: ListOfAaMotifMutationsProps) const aaMotifsTruncated = motifs.slice(0, 20) - const tbody = aaMotifsTruncated.map(({ gene, position, refSeq, qrySeq }) => { - const cdsObj = cdses.find((cds) => cds.name === gene) + const tbody = aaMotifsTruncated.map(({ cds, position, refSeq, qrySeq }) => { + const cdsObj = cdses.find((cds1) => cds1.name === cds) const bg = cdsObj?.color ?? theme.gray400 const fg = theme.gray200 return ( - + - {gene} + {cds} {position + 1} diff --git a/packages_rs/nextclade-web/src/components/Results/ColumnNameTooltip.tsx b/packages_rs/nextclade-web/src/components/Results/ColumnNameTooltip.tsx index 868ac0395..2b67523b3 100644 --- a/packages_rs/nextclade-web/src/components/Results/ColumnNameTooltip.tsx +++ b/packages_rs/nextclade-web/src/components/Results/ColumnNameTooltip.tsx @@ -68,7 +68,7 @@ export function ColumnNameTooltip({ index }: ColumnNameTooltipProps) { const warningComponents = useMemo(() => { return (result?.analysisResult?.warnings ?? []).map((warning) => ( - + {warning.warning} diff --git a/packages_rs/nextclade-web/src/components/Results/ListOfFrameShifts.tsx b/packages_rs/nextclade-web/src/components/Results/ListOfFrameShifts.tsx index 718b5e555..61e16c376 100644 --- a/packages_rs/nextclade-web/src/components/Results/ListOfFrameShifts.tsx +++ b/packages_rs/nextclade-web/src/components/Results/ListOfFrameShifts.tsx @@ -12,7 +12,7 @@ export function FrameShiftRows({ frameShifts }: FrameShiftRowsProps) { return ( ) diff --git a/packages_rs/nextclade-web/src/components/Results/ListOfInsertions.tsx b/packages_rs/nextclade-web/src/components/Results/ListOfInsertions.tsx index ef2093600..7cd1e41e7 100644 --- a/packages_rs/nextclade-web/src/components/Results/ListOfInsertions.tsx +++ b/packages_rs/nextclade-web/src/components/Results/ListOfInsertions.tsx @@ -177,7 +177,7 @@ export function ListOfInsertionsAa({ insertions }: ListOfInsertionsAaProps) { const { thead, tbody } = useMemo(() => { const thead = ( - {t('Gene.')} + {t('CDS')} {t('After ref pos.')} {t('Length')} {t('Inserted fragment')} @@ -185,9 +185,9 @@ export function ListOfInsertionsAa({ insertions }: ListOfInsertionsAaProps) { ) const insertionsTruncated = insertions.slice(0, 20) - const tbody = insertionsTruncated.map(({ pos, ins, gene }) => ( + const tbody = insertionsTruncated.map(({ pos, ins, cds }) => ( - {gene} + {cds} {pos + 1} {ins.length} diff --git a/packages_rs/nextclade-web/src/components/Results/ListOfStopCodons.tsx b/packages_rs/nextclade-web/src/components/Results/ListOfStopCodons.tsx index 1832f385f..45091f00a 100644 --- a/packages_rs/nextclade-web/src/components/Results/ListOfStopCodons.tsx +++ b/packages_rs/nextclade-web/src/components/Results/ListOfStopCodons.tsx @@ -12,7 +12,7 @@ export function StopCodonsItems({ stopCodons }: StopCodonsRowsProps) { return (
    {stopCodons.map((sc) => ( -
  • {formatStopCodon(sc)}
    • +
  • {formatStopCodon(sc)}
    • ))}
) diff --git a/packages_rs/nextclade-web/src/components/SequenceView/PeptideMarkerFrameShift.tsx b/packages_rs/nextclade-web/src/components/SequenceView/PeptideMarkerFrameShift.tsx index 6a1eda6cb..05016ac12 100644 --- a/packages_rs/nextclade-web/src/components/SequenceView/PeptideMarkerFrameShift.tsx +++ b/packages_rs/nextclade-web/src/components/SequenceView/PeptideMarkerFrameShift.tsx @@ -34,10 +34,10 @@ function PeptideMarkerFrameShiftUnmemoed({ const onMouseEnter = useCallback(() => setShowTooltip(true), []) const onMouseLeave = useCallback(() => setShowTooltip(false), []) - const { geneName, nucAbs, codon, gapsLeading, gapsTrailing } = frameShift + const { cdsName, nucAbs, codon, gapsLeading, gapsTrailing } = frameShift const id = getSafeId('frame-shift-aa-marker', { index, seqName, ...frameShift }) - const cds = useRecoilValue(cdsAtom(geneName)) + const cds = useRecoilValue(cdsAtom(cdsName)) if (!cds) { return null } @@ -92,8 +92,8 @@ function PeptideMarkerFrameShiftUnmemoed({ - {t('Gene')} - {geneName} + {t('CDS')} + {cdsName} diff --git a/packages_rs/nextclade-web/src/components/SequenceView/PeptideView.tsx b/packages_rs/nextclade-web/src/components/SequenceView/PeptideView.tsx index e754f241c..ca57e9af3 100644 --- a/packages_rs/nextclade-web/src/components/SequenceView/PeptideView.tsx +++ b/packages_rs/nextclade-web/src/components/SequenceView/PeptideView.tsx @@ -50,7 +50,7 @@ export function PeptideViewMissing({ geneName, reasons }: PeptideViewMissingProp

{t('This gene is missing due to the following errors during analysis: ')}

{reasons.map((warn) => ( - + {warn.warning} @@ -87,7 +87,7 @@ export function PeptideViewUnsized({ width, sequence, warnings, viewedGene }: Pe ) } - const warningsForThisGene = (warnings ?? []).filter((warn) => warn.geneName === viewedGene) + const warningsForThisGene = (warnings ?? []).filter((warn) => warn.cdsName === viewedGene) if (warningsForThisGene.length > 0) { return ( @@ -101,11 +101,11 @@ export function PeptideViewUnsized({ width, sequence, warnings, viewedGene }: Pe const pixelsPerAa = width / Math.round(cdsLength) const groups = aaChangesGroups.filter((group) => group.name === viewedGene) - const unknownAaRangesForGene = unknownAaRanges.find((range) => range.geneName === viewedGene) + const unknownAaRangesForGene = unknownAaRanges.find((range) => range.cdsName === viewedGene) const unsequencedRanges = aaUnsequencedRanges[viewedGene] ?? [] const frameShiftMarkers = frameShifts - .filter((frameShift) => frameShift.geneName === cds.name) + .filter((frameShift) => frameShift.cdsName === cds.name) .map((frameShift) => { const id = getSafeId('frame-shift-aa-marker', { ...frameShift }) return ( @@ -120,7 +120,7 @@ export function PeptideViewUnsized({ width, sequence, warnings, viewedGene }: Pe }) const insertionMarkers = aaInsertions - .filter((ins) => ins.gene === viewedGene) + .filter((ins) => ins.cds === viewedGene) .map((insertion) => { return ( { export const SequenceMarkerFrameShift = React.memo(SequenceMarkerFrameShiftUnmemoed) function SequenceMarkerFrameShiftUnmemoed({ index, seqName, frameShift, pixelsPerBase }: FrameShiftMarkerProps) { - const { geneName, nucAbs, codon, gapsTrailing, gapsLeading } = frameShift + const { cdsName, nucAbs, codon, gapsTrailing, gapsLeading } = frameShift const frameShiftSegments = useMemo( () => @@ -43,7 +43,7 @@ function SequenceMarkerFrameShiftUnmemoed({ index, seqName, frameShift, pixelsPe key={id} identifier={id} index={index} - geneName={geneName} + geneName={cdsName} codon={codon} nucAbs={nucAbs} gapsTrailing={gapsTrailing} @@ -52,7 +52,7 @@ function SequenceMarkerFrameShiftUnmemoed({ index, seqName, frameShift, pixelsPe /> ) }), - [codon, gapsLeading, gapsTrailing, geneName, index, nucAbs, pixelsPerBase, seqName], + [codon, gapsLeading, gapsTrailing, cdsName, index, nucAbs, pixelsPerBase, seqName], ) // eslint-disable-next-line react/jsx-no-useless-fragment diff --git a/packages_rs/nextclade-web/src/components/SequenceView/SequenceView.tsx b/packages_rs/nextclade-web/src/components/SequenceView/SequenceView.tsx index bdde32a8d..af16a5667 100644 --- a/packages_rs/nextclade-web/src/components/SequenceView/SequenceView.tsx +++ b/packages_rs/nextclade-web/src/components/SequenceView/SequenceView.tsx @@ -132,7 +132,7 @@ export function SequenceViewUnsized({ sequence, width }: SequenceViewProps) { const frameShiftMarkers = frameShifts.map((frameShift) => ( na.begin).join('-')}`} + key={`${frameShift.cdsName}_${frameShift.nucAbs.map((na) => na.begin).join('-')}`} index={index} seqName={seqName} frameShift={frameShift} diff --git a/packages_rs/nextclade-web/src/helpers/formatFrameShift.ts b/packages_rs/nextclade-web/src/helpers/formatFrameShift.ts index fbd3da2c3..50112de0c 100644 --- a/packages_rs/nextclade-web/src/helpers/formatFrameShift.ts +++ b/packages_rs/nextclade-web/src/helpers/formatFrameShift.ts @@ -1,6 +1,6 @@ import type { FrameShift } from 'src/types' import { formatRange } from 'src/helpers/formatRange' -export function formatFrameShift({ geneName, codon }: FrameShift) { - return `${geneName}:${formatRange(codon)}` +export function formatFrameShift({ cdsName, codon }: FrameShift) { + return `${cdsName}:${formatRange(codon)}` } diff --git a/packages_rs/nextclade-web/src/helpers/formatMutation.ts b/packages_rs/nextclade-web/src/helpers/formatMutation.ts index 18be9a7c8..533ea8162 100644 --- a/packages_rs/nextclade-web/src/helpers/formatMutation.ts +++ b/packages_rs/nextclade-web/src/helpers/formatMutation.ts @@ -24,8 +24,8 @@ export function formatAADeletion({ cdsName, refAa, pos }: AaDel) { return `${cdsName}:${notation}` } -export function formatStopCodon({ geneName, codon }: StopCodonLocation) { +export function formatStopCodon({ cdsName, codon }: StopCodonLocation) { // NOTE: by convention, codons are numbered starting from 1, however our arrays are 0-based const codonOneBased = codon + 1 - return `${geneName}:${codonOneBased}` + return `${cdsName}:${codonOneBased}` } diff --git a/packages_rs/nextclade-web/src/helpers/formatQCStopCodons.ts b/packages_rs/nextclade-web/src/helpers/formatQCStopCodons.ts index 513193191..799ce6509 100644 --- a/packages_rs/nextclade-web/src/helpers/formatQCStopCodons.ts +++ b/packages_rs/nextclade-web/src/helpers/formatQCStopCodons.ts @@ -13,7 +13,7 @@ export function formatQCStopCodons( const { score, stopCodons, totalStopCodons } = qcStopCodons - const geneList = uniq(stopCodons.map((sc) => sc.geneName)).join(', ') + const geneList = uniq(stopCodons.map((sc) => sc.cdsName)).join(', ') return t( '{{totalStopCodons}} misplaced stop codon(s) detected. Affected gene(s): {{geneList}}. QC score: {{score}}', diff --git a/packages_rs/nextclade/src/align/insertions_strip.rs b/packages_rs/nextclade/src/align/insertions_strip.rs index 77feea87b..509d70ce9 100644 --- a/packages_rs/nextclade/src/align/insertions_strip.rs +++ b/packages_rs/nextclade/src/align/insertions_strip.rs @@ -105,7 +105,7 @@ pub fn insertions_strip>(qry_seq: &[T], ref_seq: &[T]) -> StripInse #[derive(Clone, Debug, Eq, PartialEq, Serialize, Deserialize, schemars::JsonSchema)] #[serde(rename_all = "camelCase")] pub struct AaIns { - pub gene: String, + pub cds: String, pub pos: i32, #[schemars(with = "String")] @@ -117,7 +117,7 @@ pub struct AaIns { /// Order amino acid insertions by gene, position, then length impl Ord for AaIns { fn cmp(&self, other: &Self) -> Ordering { - (&self.gene, self.pos, self.ins.len()).cmp(&(&other.gene, other.pos, other.ins.len())) + (&self.cds, self.pos, self.ins.len()).cmp(&(&other.cds, other.pos, other.ins.len())) } } @@ -132,7 +132,7 @@ pub fn get_aa_insertions(translation: &Translation) -> Vec { .iter_cdses() .flat_map(|(cds_name, cds_tr)| { cds_tr.insertions.iter().map(|Insertion:: { pos, ins }| AaIns { - gene: cds_name.clone(), + cds: cds_name.clone(), pos: *pos, ins: ins.clone(), }) diff --git a/packages_rs/nextclade/src/analyze/find_aa_motifs.rs b/packages_rs/nextclade/src/analyze/find_aa_motifs.rs index 057222fd1..3fc300027 100644 --- a/packages_rs/nextclade/src/analyze/find_aa_motifs.rs +++ b/packages_rs/nextclade/src/analyze/find_aa_motifs.rs @@ -1,6 +1,6 @@ use crate::alphabet::aa::from_aa_seq; use crate::analyze::find_aa_motifs_changes::AaMotifsMap; -use crate::analyze::virus_properties::{AaMotifsDesc, CountAaMotifsGeneDesc}; +use crate::analyze::virus_properties::{AaMotifsDesc, CountAaMotifsCdsDesc}; use crate::coord::position::AaRefPosition; use crate::coord::range::{intersect_or_none, AaRefRange}; use crate::translate::translate_genes::{CdsTranslation, Translation}; @@ -53,7 +53,7 @@ fn process_one_aa_motifs_desc( let AaMotifsDesc { name, motifs, - include_genes, + include_cdses: include_genes, .. } = aa_motifs_desc; @@ -61,8 +61,8 @@ fn process_one_aa_motifs_desc( let include_genes = if include_genes.is_empty() { translation .cdses() - .map(|translation| CountAaMotifsGeneDesc { - gene: translation.name.clone(), + .map(|translation| CountAaMotifsCdsDesc { + cds: translation.name.clone(), ranges: vec![], }) .collect_vec() @@ -72,10 +72,10 @@ fn process_one_aa_motifs_desc( include_genes .iter() - .flat_map(|CountAaMotifsGeneDesc { gene, ranges }| { + .flat_map(|CountAaMotifsCdsDesc { cds, ranges }| { translation .cdses() - .filter(|CdsTranslation { name, .. }| name == gene) + .filter(|CdsTranslation { name, .. }| name == cds) .flat_map(|translation| process_one_translation(translation, name, motifs, ranges)) .collect_vec() }) diff --git a/packages_rs/nextclade/src/analyze/find_aa_motifs_changes.rs b/packages_rs/nextclade/src/analyze/find_aa_motifs_changes.rs index f7fdf674e..9f4b5b6e6 100644 --- a/packages_rs/nextclade/src/analyze/find_aa_motifs_changes.rs +++ b/packages_rs/nextclade/src/analyze/find_aa_motifs_changes.rs @@ -27,7 +27,7 @@ pub struct AaMotifChanges { #[serde(rename_all = "camelCase")] pub struct AaMotifMutation { pub name: String, - pub gene: String, + pub cds: String, pub position: AaRefPosition, pub ref_seq: String, pub qry_seq: String, @@ -99,7 +99,7 @@ fn find_aa_motifs_changes_one( Zip::from((kept_ref, kept_qry)) .map(|(motif_ref, motif_qry)| AaMotifMutation { name: motif_ref.name, - gene: motif_ref.cds, + cds: motif_ref.cds, position: motif_ref.position, ref_seq: motif_ref.seq, qry_seq: motif_qry.seq, @@ -129,7 +129,7 @@ fn add_ref_seq(motif: &AaMotif, ref_translation: &Translation) -> Result Option>, ref_peptides: &Translation, gene_map: &GeneMap, @@ -56,7 +56,7 @@ pub fn find_private_aa_mutations( let aa_deletions = aa_deletions.iter().filter(|del| del.cds_name == cds.name).collect_vec(); - let aa_unknowns = aa_unknowns.iter().filter(|unk| unk.gene_name == cds.name).collect_vec(); + let aa_unknowns = aa_unknowns.iter().filter(|unk| unk.cds_name == cds.name).collect_vec(); let private_aa_mutations = find_private_aa_mutations_for_one_gene( cds, @@ -79,7 +79,7 @@ pub fn find_private_aa_mutations_for_one_gene( node_mut_map: &BTreeMap, aa_substitutions: &[&AaSub], aa_deletions: &[&AaDel], - aa_unknowns: &[&GeneAaRange], + aa_unknowns: &[&CdsAaRange], aa_unsequenced_ranges: &[AaRefRange], ref_peptide: &[Aa], ) -> PrivateAaMutations { @@ -246,7 +246,7 @@ fn process_seq_deletions( fn find_reversions( cds: &Cds, node_mut_map: &BTreeMap, - aa_unknowns: &[&GeneAaRange], + aa_unknowns: &[&CdsAaRange], aa_unsequenced_ranges: &[AaRefRange], ref_peptide: &[Aa], seq_positions_mutated_or_deleted: &mut BTreeSet, diff --git a/packages_rs/nextclade/src/analyze/is_sequenced.rs b/packages_rs/nextclade/src/analyze/is_sequenced.rs index 50cfbe6ea..d31dd06d9 100644 --- a/packages_rs/nextclade/src/analyze/is_sequenced.rs +++ b/packages_rs/nextclade/src/analyze/is_sequenced.rs @@ -1,5 +1,5 @@ use crate::alphabet::letter::Letter; -use crate::analyze::letter_ranges::{GeneAaRange, NucRange}; +use crate::analyze::letter_ranges::{CdsAaRange, NucRange}; use crate::coord::position::{AaRefPosition, NucRefGlobalPosition}; use crate::coord::range::{AaRefRange, NucRefGlobalRange}; use itertools::Itertools; @@ -22,7 +22,7 @@ pub fn is_nuc_non_acgtn(pos: NucRefGlobalPosition, non_acgtns: &[NucRange]) -> b /// Decides whether a given position in peptide is considered "sequenced". /// The position is considered sequenced if it is not contained in any of the unknown of unsequenced regions -pub fn is_aa_sequenced(pos: AaRefPosition, aa_unknowns: &[&GeneAaRange], aa_unsequenced_ranges: &[AaRefRange]) -> bool { +pub fn is_aa_sequenced(pos: AaRefPosition, aa_unknowns: &[&CdsAaRange], aa_unsequenced_ranges: &[AaRefRange]) -> bool { let is_missing = aa_unknowns.iter().any(|missing| missing.contains_pos(pos)); let is_unsequenced = aa_unsequenced_ranges .iter() diff --git a/packages_rs/nextclade/src/analyze/letter_ranges.rs b/packages_rs/nextclade/src/analyze/letter_ranges.rs index ee4d4f9ef..3504c86e5 100644 --- a/packages_rs/nextclade/src/analyze/letter_ranges.rs +++ b/packages_rs/nextclade/src/analyze/letter_ranges.rs @@ -99,29 +99,29 @@ pub fn find_letter_ranges, P: PositionLike>(qry_aln: &[L], letter: #[derive(Clone, Debug, Serialize, Deserialize, schemars::JsonSchema)] #[serde(rename_all = "camelCase")] -pub struct GeneAaRange { - pub gene_name: String, +pub struct CdsAaRange { + pub cds_name: String, #[serde(rename = "character")] pub letter: Aa, pub ranges: Vec, pub length: usize, } -impl GeneAaRange { +impl CdsAaRange { pub fn contains_pos(&self, pos: AaRefPosition) -> bool { self.ranges.iter().any(|range| range.contains_pos(pos)) } } /// Finds contiguous ranges (segments) consisting of a given amino acid in the sequence. -pub fn find_aa_letter_ranges(translation: &Translation, letter: Aa) -> Vec { +pub fn find_aa_letter_ranges(translation: &Translation, letter: Aa) -> Vec { translation .cdses() .filter_map(|CdsTranslation { name, seq, .. }| { let ranges = find_letter_ranges_by(seq, |candidate| candidate == letter); let length = ranges.iter().map(LetterRange::len).sum(); - (length > 0).then(|| GeneAaRange { - gene_name: name.clone(), + (length > 0).then(|| CdsAaRange { + cds_name: name.clone(), letter, ranges, length, diff --git a/packages_rs/nextclade/src/analyze/phenotype.rs b/packages_rs/nextclade/src/analyze/phenotype.rs index ceddafff0..06a7ce8ed 100644 --- a/packages_rs/nextclade/src/analyze/phenotype.rs +++ b/packages_rs/nextclade/src/analyze/phenotype.rs @@ -6,7 +6,7 @@ use num_traits::real::Real; pub fn calculate_phenotype(phenotype_data: &PhenotypeData, aa_substitutions: &[AaSub]) -> f64 { let aa_substitutions = aa_substitutions .iter() - .filter_map(|sub| (sub.cds_name == phenotype_data.gene && phenotype_data.aa_range.contains(sub.pos)).then_some(sub)) + .filter_map(|sub| (sub.cds_name == phenotype_data.cds && phenotype_data.aa_range.contains(sub.pos)).then_some(sub)) .collect_vec(); let phenotype: f64 = phenotype_data diff --git a/packages_rs/nextclade/src/analyze/virus_properties.rs b/packages_rs/nextclade/src/analyze/virus_properties.rs index 4b277bd9c..034fefc27 100644 --- a/packages_rs/nextclade/src/analyze/virus_properties.rs +++ b/packages_rs/nextclade/src/analyze/virus_properties.rs @@ -141,7 +141,7 @@ pub struct PhenotypeData { pub name: String, pub name_friendly: String, pub description: String, - pub gene: String, + pub cds: String, pub aa_range: AaRefRange, #[serde(default)] pub ignore: PhenotypeDataIgnore, @@ -166,13 +166,13 @@ pub struct AaMotifsDesc { pub motifs: Vec, #[serde(default, skip_serializing_if = "Vec::is_empty")] - pub include_genes: Vec, + pub include_cdses: Vec, } #[derive(Debug, Clone, Serialize, Deserialize, schemars::JsonSchema, Validate)] #[serde(rename_all = "camelCase")] -pub struct CountAaMotifsGeneDesc { - pub gene: String, +pub struct CountAaMotifsCdsDesc { + pub cds: String, #[serde(default, skip_serializing_if = "Vec::is_empty")] pub ranges: Vec, diff --git a/packages_rs/nextclade/src/gene/gene_map.rs b/packages_rs/nextclade/src/gene/gene_map.rs index 0189d2292..cc549d29e 100644 --- a/packages_rs/nextclade/src/gene/gene_map.rs +++ b/packages_rs/nextclade/src/gene/gene_map.rs @@ -86,8 +86,8 @@ impl GeneMap { } #[must_use] - pub fn contains(&self, gene_name: &str) -> bool { - self.genes.iter().any(|gene| gene.name == gene_name) + pub fn contains(&self, name: &str) -> bool { + self.genes.iter().any(|gene| gene.name == name) } pub fn get(&self, gene_name: &str) -> Result<&Gene, Report> { @@ -95,7 +95,7 @@ impl GeneMap { .genes .iter() .find(|gene| gene.name == gene_name) - .ok_or_else(|| make_internal_report!("Gene is expected to be present, but not found: '{gene_name}'")) + .ok_or_else(|| make_internal_report!("Gene '{gene_name}' is expected to be present, but not found")) } pub fn get_cds>(&self, cds_name: S) -> Result<&Cds, Report> { diff --git a/packages_rs/nextclade/src/io/nextclade_csv.rs b/packages_rs/nextclade/src/io/nextclade_csv.rs index b01cba894..9c8a21035 100644 --- a/packages_rs/nextclade/src/io/nextclade_csv.rs +++ b/packages_rs/nextclade/src/io/nextclade_csv.rs @@ -4,7 +4,7 @@ use crate::alphabet::nuc::{from_nuc, from_nuc_seq, Nuc}; use crate::analyze::aa_del::AaDel; use crate::analyze::aa_sub::AaSub; use crate::analyze::find_aa_motifs::AaMotif; -use crate::analyze::letter_ranges::{GeneAaRange, NucRange}; +use crate::analyze::letter_ranges::{CdsAaRange, NucRange}; use crate::analyze::nuc_del::NucDelRange; use crate::analyze::nuc_sub::{NucSub, NucSubLabeled}; use crate::analyze::pcr_primer_changes::PcrPrimerChange; @@ -718,22 +718,22 @@ pub fn format_aa_deletions(aa_dels: &[AaDel], delimiter: &str) -> String { pub fn format_aa_insertions(insertions: &[AaIns], delimiter: &str) -> String { insertions .iter() - .map(|AaIns { gene, ins, pos }: &AaIns| { + .map(|AaIns { cds, ins, pos }: &AaIns| { let ins_str = from_aa_seq(ins); let pos_one_based = pos + 1; - format!("{gene}:{pos_one_based}:{ins_str}") + format!("{cds}:{pos_one_based}:{ins_str}") }) .join(delimiter) } #[inline] -pub fn format_unknown_aa_ranges(unknown_aa_ranges: &[GeneAaRange], delimiter: &str) -> String { +pub fn format_unknown_aa_ranges(unknown_aa_ranges: &[CdsAaRange], delimiter: &str) -> String { unknown_aa_ranges .iter() - .flat_map(|GeneAaRange { gene_name, ranges, .. }: &GeneAaRange| { + .flat_map(|CdsAaRange { cds_name, ranges, .. }: &CdsAaRange| { ranges.iter().map(move |range| { let range_str = range.range().to_string(); - format!("{gene_name}:{range_str}") + format!("{cds_name}:{range_str}") }) }) .join(delimiter) @@ -744,9 +744,9 @@ pub fn format_frame_shifts(frame_shifts: &[FrameShift], delimiter: &str) -> Stri frame_shifts .iter() .map(|frame_shift| { - let gene_name = &frame_shift.gene_name; + let cds_name = &frame_shift.cds_name; let range = &frame_shift.codon.to_string(); - format!("{gene_name}:{range}") + format!("{cds_name}:{range}") }) .join(delimiter) } @@ -767,7 +767,7 @@ pub fn format_clustered_snps(snps: &[ClusteredSnp], delimiter: &str) -> String { pub fn format_stop_codons(stop_codons: &[StopCodonLocation], delimiter: &str) -> String { stop_codons .iter() - .map(|StopCodonLocation { gene_name, codon }| format!("{gene_name}:{codon}")) + .map(|StopCodonLocation { cds_name, codon }| format!("{cds_name}:{codon}")) .join(delimiter) } diff --git a/packages_rs/nextclade/src/qc/qc_config.rs b/packages_rs/nextclade/src/qc/qc_config.rs index 208541fa9..b30b7727a 100644 --- a/packages_rs/nextclade/src/qc/qc_config.rs +++ b/packages_rs/nextclade/src/qc/qc_config.rs @@ -70,7 +70,7 @@ pub struct QcRulesConfigSnpClusters { #[serde(rename_all = "camelCase")] #[serde(default)] pub struct FrameShiftLocation { - pub gene_name: String, + pub cds_name: String, pub codon_range: AaRefRange, } @@ -97,7 +97,7 @@ impl Default for QcRulesConfigFrameShifts { #[derive(Debug, Default, Clone, Eq, PartialEq, Serialize, Deserialize, schemars::JsonSchema, Validate)] #[serde(rename_all = "camelCase")] pub struct StopCodonLocation { - pub gene_name: String, + pub cds_name: String, pub codon: usize, } diff --git a/packages_rs/nextclade/src/qc/qc_rule_frame_shifts.rs b/packages_rs/nextclade/src/qc/qc_rule_frame_shifts.rs index e6497d2bc..b89c4ac5b 100644 --- a/packages_rs/nextclade/src/qc/qc_rule_frame_shifts.rs +++ b/packages_rs/nextclade/src/qc/qc_rule_frame_shifts.rs @@ -9,7 +9,7 @@ pub fn is_frame_shift_ignored(frame_shift: &FrameShift, config: &QcRulesConfigFr config .ignored_frame_shifts .iter() - .any(|ignored| ignored.gene_name == frame_shift.gene_name && ignored.codon_range == frame_shift.codon) + .any(|ignored| ignored.cds_name == frame_shift.cds_name && ignored.codon_range == frame_shift.codon) } #[derive(Clone, Debug, Default, Serialize, Deserialize, schemars::JsonSchema)] diff --git a/packages_rs/nextclade/src/qc/qc_rule_stop_codons.rs b/packages_rs/nextclade/src/qc/qc_rule_stop_codons.rs index a7eb2cc09..0299596c4 100644 --- a/packages_rs/nextclade/src/qc/qc_rule_stop_codons.rs +++ b/packages_rs/nextclade/src/qc/qc_rule_stop_codons.rs @@ -34,7 +34,7 @@ pub fn rule_stop_codons(translation: &Translation, config: &QcRulesConfigStopCod for (codon, aa) in peptide.iter().enumerate().take(len_minus_one) { if aa.is_stop() { let stop_codon = StopCodonLocation { - gene_name: name.clone(), + cds_name: name.clone(), codon, }; diff --git a/packages_rs/nextclade/src/run/nextclade_run_one.rs b/packages_rs/nextclade/src/run/nextclade_run_one.rs index 044c4ee43..8c2fe2b45 100644 --- a/packages_rs/nextclade/src/run/nextclade_run_one.rs +++ b/packages_rs/nextclade/src/run/nextclade_run_one.rs @@ -13,7 +13,7 @@ use crate::analyze::find_private_aa_mutations::{find_private_aa_mutations, Priva use crate::analyze::find_private_nuc_mutations::{find_private_nuc_mutations, PrivateNucMutations}; use crate::analyze::letter_composition::get_letter_composition; use crate::analyze::letter_ranges::{ - find_aa_letter_ranges, find_letter_ranges, find_letter_ranges_by, GeneAaRange, NucRange, + find_aa_letter_ranges, find_letter_ranges, find_letter_ranges_by, CdsAaRange, NucRange, }; use crate::analyze::nuc_changes::{find_nuc_changes, FindNucChangesOutput}; use crate::analyze::nuc_del::NucDelRange; @@ -51,7 +51,7 @@ struct NextcladeResultWithAa { aa_insertions: Vec, frame_shifts: Vec, total_frame_shifts: usize, - unknown_aa_ranges: Vec, + unknown_aa_ranges: Vec, total_unknown_aa: usize, aa_alignment_ranges: BTreeMap>, aa_unsequenced_ranges: BTreeMap>, @@ -181,7 +181,7 @@ pub fn nextclade_run_one( if alignment.is_reverse_complement { warnings.push(PeptideWarning { - gene_name: "nuc".to_owned(), + cds_name: "nuc".to_owned(), warning: format!("When processing sequence #{index} '{seq_name}': Sequence is reverse-complemented: Seed matching failed for the original sequence, but succeeded for its reverse complement. Outputs will be derived from the reverse complement and 'reverse complement' suffix will be added to sequence ID.") }); } @@ -307,14 +307,14 @@ pub fn nextclade_run_one( phenotype_data .iter() .filter_map(|phenotype_data| { - let PhenotypeData { name, gene, ignore, .. } = phenotype_data; + let PhenotypeData { name, cds, ignore, .. } = phenotype_data; if ignore.clades.contains(&clade) { return None; } let phenotype = calculate_phenotype(phenotype_data, &aa_substitutions); Some(PhenotypeValue { name: name.clone(), - gene: gene.clone(), + cds: cds.clone(), value: phenotype, }) }) diff --git a/packages_rs/nextclade/src/translate/frame_shifts_translate.rs b/packages_rs/nextclade/src/translate/frame_shifts_translate.rs index 97a859713..7d7fecf51 100644 --- a/packages_rs/nextclade/src/translate/frame_shifts_translate.rs +++ b/packages_rs/nextclade/src/translate/frame_shifts_translate.rs @@ -60,7 +60,7 @@ pub fn find_codon_mask_range( #[derive(Clone, Debug, Serialize, Deserialize, schemars::JsonSchema)] #[serde(rename_all = "camelCase")] pub struct FrameShift { - pub gene_name: String, + pub cds_name: String, pub nuc_rel: NucAlnLocalRange, pub nuc_abs: Vec, pub codon: AaRefRange, @@ -90,7 +90,7 @@ pub fn frame_shift_transform( let gaps_trailing = Range::new(codon.end, codon_mask.end); Ok(FrameShift { - gene_name: cds.name.clone(), + cds_name: cds.name.clone(), nuc_abs: nuc_ref_global, codon, nuc_rel: nuc_aln_local.clone(), diff --git a/packages_rs/nextclade/src/translate/translate_genes.rs b/packages_rs/nextclade/src/translate/translate_genes.rs index bb419290b..185a1c2c7 100644 --- a/packages_rs/nextclade/src/translate/translate_genes.rs +++ b/packages_rs/nextclade/src/translate/translate_genes.rs @@ -329,7 +329,7 @@ pub fn translate_genes( ) { Ok(translation) => Either::Left((cds.name.clone(), translation)), Err(report) => Either::Right(PeptideWarning { - gene_name: cds.name.clone(), + cds_name: cds.name.clone(), warning: report_to_string(&report), }), } diff --git a/packages_rs/nextclade/src/tree/split_muts2.rs b/packages_rs/nextclade/src/tree/split_muts2.rs index 5fe4ab0f0..20c46585e 100644 --- a/packages_rs/nextclade/src/tree/split_muts2.rs +++ b/packages_rs/nextclade/src/tree/split_muts2.rs @@ -64,9 +64,9 @@ pub fn split_muts2(left: &BranchMutations, right: &BranchMutations) -> SplitMuts let mut shared_keys = keys_mut_left.intersection(&keys_mut_right).collect_vec(); shared_keys.sort(); - for gene_name in shared_keys.clone() { - let aa_muts_left = &left.aa_muts[gene_name]; - let aa_muts_right = &right.aa_muts[gene_name]; + for cds_name in shared_keys.clone() { + let aa_muts_left = &left.aa_muts[cds_name]; + let aa_muts_right = &right.aa_muts[cds_name]; let mut aa_subs_for_gene_shared = Vec::::new(); let mut aa_subs_for_gene_left = Vec::::new(); let mut aa_subs_for_gene_right = Vec::::new(); @@ -99,9 +99,9 @@ pub fn split_muts2(left: &BranchMutations, right: &BranchMutations) -> SplitMuts aa_subs_for_gene_right.push(aa_muts_right[j].clone()); j += 1; } - aa_subs_shared.insert(gene_name.to_string(), aa_subs_for_gene_shared); - aa_subs_left.insert(gene_name.to_string(), aa_subs_for_gene_left); - aa_subs_right.insert(gene_name.to_string(), aa_subs_for_gene_right); + aa_subs_shared.insert(cds_name.to_string(), aa_subs_for_gene_shared); + aa_subs_left.insert(cds_name.to_string(), aa_subs_for_gene_left); + aa_subs_right.insert(cds_name.to_string(), aa_subs_for_gene_right); } for (k, v) in &left.aa_muts { if !shared_keys.contains(&k) { diff --git a/packages_rs/nextclade/src/tree/tree_builder.rs b/packages_rs/nextclade/src/tree/tree_builder.rs index 4b638ad04..6ef0cbda9 100644 --- a/packages_rs/nextclade/src/tree/tree_builder.rs +++ b/packages_rs/nextclade/src/tree/tree_builder.rs @@ -258,10 +258,10 @@ pub fn convert_private_mutations_to_node_branch_attrs(mutations: &BranchMutation let nuc_muts = mutations.nuc_muts.iter().sorted().map(NucSub::to_string).collect_vec(); branch_attrs.insert("nuc".to_owned(), nuc_muts); - for (gene_name, aa_muts) in &mutations.aa_muts { + for (cds_name, aa_muts) in &mutations.aa_muts { if !aa_muts.is_empty() { let aa_muts = aa_muts.iter().sorted().map(AaSub::to_string_without_gene).collect_vec(); - branch_attrs.insert(gene_name.clone(), aa_muts); + branch_attrs.insert(cds_name.clone(), aa_muts); } } @@ -272,9 +272,9 @@ pub fn convert_private_mutations_to_node_branch_attrs_aa_labels(aa_muts: &BTreeM aa_muts .iter() .filter(|(_, aa_muts)| !aa_muts.is_empty()) - .map(|(gene_name, aa_muts)| { + .map(|(cds_name, aa_muts)| { let aa_muts = aa_muts.iter().sorted().map(AaSub::to_string_without_gene).join(", "); - format!("{gene_name}: {aa_muts}") + format!("{cds_name}: {aa_muts}") }) .join("; ") } diff --git a/packages_rs/nextclade/src/tree/tree_preprocess.rs b/packages_rs/nextclade/src/tree/tree_preprocess.rs index ef4a1afb6..bab55747c 100644 --- a/packages_rs/nextclade/src/tree/tree_preprocess.rs +++ b/packages_rs/nextclade/src/tree/tree_preprocess.rs @@ -176,7 +176,7 @@ fn map_aa_muts( let aa_muts = parent_aa_muts.get(&ref_cds_tr.name).unwrap_or(&empty); ( ref_cds_tr.name.clone(), - map_aa_muts_for_one_gene(&ref_cds_tr.name, node, &ref_cds_tr.seq, aa_muts), + map_aa_muts_for_one_cds(&ref_cds_tr.name, node, &ref_cds_tr.seq, aa_muts), ) }) .map(|(name, muts)| -> Result<_, Report> { @@ -185,27 +185,27 @@ fn map_aa_muts( .collect() } -fn map_aa_muts_for_one_gene( - gene_name: &str, +fn map_aa_muts_for_one_cds( + cds_name: &str, node: &AuspiceGraphNodePayload, ref_peptide: &[Aa], parent_aa_muts: &BTreeMap, ) -> Result, Report> { let mut aa_muts = parent_aa_muts.clone(); - match node.branch_attrs.mutations.get(gene_name) { + match node.branch_attrs.mutations.get(cds_name) { None => Ok(aa_muts), Some(mutations) => { for mutation_str in mutations { - let mutation = AaSub::from_str_and_gene(mutation_str, gene_name)?; + let mutation = AaSub::from_str_and_gene(mutation_str, cds_name)?; if ref_peptide.len() < mutation.pos.as_usize() { return make_error!( "When preprocessing reference tree node {}: amino acid mutation {}:{} is outside of the peptide {} (length {}). This is likely an inconsistency between reference tree, reference sequence, and genome annotation in the Nextclade dataset", node.name, - gene_name, + cds_name, mutation.to_string_without_gene(), - gene_name, + cds_name, ref_peptide.len(), ); } diff --git a/packages_rs/nextclade/src/types/outputs.rs b/packages_rs/nextclade/src/types/outputs.rs index 16b0da96d..5200c6dfb 100644 --- a/packages_rs/nextclade/src/types/outputs.rs +++ b/packages_rs/nextclade/src/types/outputs.rs @@ -6,7 +6,7 @@ use crate::analyze::aa_sub::AaSub; use crate::analyze::find_aa_motifs_changes::{AaMotifsChangesMap, AaMotifsMap}; use crate::analyze::find_private_aa_mutations::PrivateAaMutations; use crate::analyze::find_private_nuc_mutations::PrivateNucMutations; -use crate::analyze::letter_ranges::{GeneAaRange, NucRange}; +use crate::analyze::letter_ranges::{CdsAaRange, NucRange}; use crate::analyze::nuc_del::NucDelRange; use crate::analyze::nuc_sub::NucSub; use crate::analyze::pcr_primer_changes::PcrPrimerChange; @@ -22,7 +22,7 @@ use std::collections::BTreeMap; #[derive(Debug, Clone, Serialize, Deserialize, schemars::JsonSchema)] #[serde(rename_all = "camelCase")] pub struct PeptideWarning { - pub gene_name: String, + pub cds_name: String, pub warning: String, } @@ -30,7 +30,7 @@ pub struct PeptideWarning { #[serde(rename_all = "camelCase")] pub struct PhenotypeValue { pub name: String, - pub gene: String, + pub cds: String, pub value: f64, } @@ -60,7 +60,7 @@ pub struct NextcladeOutputs { pub total_aminoacid_deletions: usize, pub aa_insertions: Vec, pub total_aminoacid_insertions: usize, - pub unknown_aa_ranges: Vec, + pub unknown_aa_ranges: Vec, pub total_unknown_aa: usize, pub aa_changes_groups: Vec, pub nuc_to_aa_muts: BTreeMap>, From 66d3f2173c8dd30186efe9babad78093d819539b Mon Sep 17 00:00:00 2001 From: ivan-aksamentov Date: Tue, 9 Jan 2024 16:29:09 +0100 Subject: [PATCH 2/2] feat: rename 'gene' to 'cds' in output files --- .../nextclade-cli/src/cli/nextclade_ordered_writer.rs | 3 --- packages_rs/nextclade/src/io/nextclade_csv.rs | 10 +++++----- packages_rs/nextclade/src/run/nextclade_run_one.rs | 2 +- packages_rs/nextclade/src/tree/tree.rs | 2 +- .../nextclade/src/tree/tree_attach_new_nodes.rs | 4 ++-- .../nextclade/src/tree/tree_find_nearest_node.rs | 2 +- packages_rs/nextclade/src/types/outputs.rs | 2 +- 7 files changed, 11 insertions(+), 14 deletions(-) diff --git a/packages_rs/nextclade-cli/src/cli/nextclade_ordered_writer.rs b/packages_rs/nextclade-cli/src/cli/nextclade_ordered_writer.rs index 6a145b3d0..f2845cc1c 100644 --- a/packages_rs/nextclade-cli/src/cli/nextclade_ordered_writer.rs +++ b/packages_rs/nextclade-cli/src/cli/nextclade_ordered_writer.rs @@ -133,9 +133,6 @@ impl NextcladeOrderedWriter { }) => { let NextcladeOutputs { warnings, - insertions, - aa_insertions, - missing_genes, is_reverse_complement, .. } = &analysis_result; diff --git a/packages_rs/nextclade/src/io/nextclade_csv.rs b/packages_rs/nextclade/src/io/nextclade_csv.rs index 9c8a21035..2d34e663d 100644 --- a/packages_rs/nextclade/src/io/nextclade_csv.rs +++ b/packages_rs/nextclade/src/io/nextclade_csv.rs @@ -203,7 +203,7 @@ lazy_static! { o!("pcrPrimerChanges") => true, }, CsvColumnCategory::ErrsWarns => indexmap! { - o!("failedGenes") => true, + o!("failedCdses") => true, o!("warnings") => true, o!("errors") => true, } @@ -323,7 +323,7 @@ impl NextcladeResultsCsvWriter { clade, private_nuc_mutations, // private_aa_mutations, - missing_genes, + missing_cdses, // divergence, coverage, phenotype_values, @@ -546,7 +546,7 @@ impl NextcladeResultsCsvWriter { qc.stop_codons.as_ref().map(|sc| sc.status.to_string()), )?; self.add_entry("isReverseComplement", &is_reverse_complement.to_string())?; - self.add_entry("failedGenes", &format_failed_genes(missing_genes, ARRAY_ITEM_DELIMITER))?; + self.add_entry("failedCdses", &format_failed_cdses(missing_cdses, ARRAY_ITEM_DELIMITER))?; self.add_entry( "warnings", &warnings.iter().map(|PeptideWarning { warning, .. }| warning).join(";"), @@ -772,8 +772,8 @@ pub fn format_stop_codons(stop_codons: &[StopCodonLocation], delimiter: &str) -> } #[inline] -pub fn format_failed_genes(failed_genes: &[String], delimiter: &str) -> String { - failed_genes.join(delimiter) +pub fn format_failed_cdses(failed_cdses: &[String], delimiter: &str) -> String { + failed_cdses.join(delimiter) } #[inline] diff --git a/packages_rs/nextclade/src/run/nextclade_run_one.rs b/packages_rs/nextclade/src/run/nextclade_run_one.rs index 8c2fe2b45..c79e6922e 100644 --- a/packages_rs/nextclade/src/run/nextclade_run_one.rs +++ b/packages_rs/nextclade/src/run/nextclade_run_one.rs @@ -391,7 +391,7 @@ pub fn nextclade_run_one( pcr_primer_changes, total_pcr_primer_changes, warnings, - missing_genes, + missing_cdses: missing_genes, coverage, aa_motifs, aa_motifs_changes, diff --git a/packages_rs/nextclade/src/tree/tree.rs b/packages_rs/nextclade/src/tree/tree.rs index 0ddedf9ef..f61ab4d5e 100644 --- a/packages_rs/nextclade/src/tree/tree.rs +++ b/packages_rs/nextclade/src/tree/tree.rs @@ -185,7 +185,7 @@ pub struct TreeNodeAttrs { #[serde(skip_serializing_if = "Option::is_none")] #[serde(rename = "Missing genes")] - pub missing_genes: Option, + pub missing_cdses: Option, #[serde(flatten)] pub other: serde_json::Value, diff --git a/packages_rs/nextclade/src/tree/tree_attach_new_nodes.rs b/packages_rs/nextclade/src/tree/tree_attach_new_nodes.rs index 23202cfe5..dd15b943e 100644 --- a/packages_rs/nextclade/src/tree/tree_attach_new_nodes.rs +++ b/packages_rs/nextclade/src/tree/tree_attach_new_nodes.rs @@ -1,6 +1,6 @@ use crate::analyze::find_private_nuc_mutations::BranchMutations; use crate::io::nextclade_csv::{ - format_failed_genes, format_missings, format_non_acgtns, format_nuc_deletions, format_pcr_primer_changes, + format_failed_cdses, format_missings, format_non_acgtns, format_nuc_deletions, format_pcr_primer_changes, }; use crate::tree::tree::{ AuspiceGraphNodePayload, TreeBranchAttrs, TreeBranchAttrsLabels, TreeNodeAttr, TreeNodeAttrs, TreeNodeTempData, @@ -81,7 +81,7 @@ pub fn create_new_auspice_node( has_pcr_primer_changes, pcr_primer_changes, qc_status: Some(TreeNodeAttr::new(&result.qc.overall_status.to_string())), - missing_genes: Some(TreeNodeAttr::new(&format_failed_genes(&result.missing_genes, ", "))), + missing_cdses: Some(TreeNodeAttr::new(&format_failed_cdses(&result.missing_cdses, ", "))), other, }, tmp: TreeNodeTempData::default(), diff --git a/packages_rs/nextclade/src/tree/tree_find_nearest_node.rs b/packages_rs/nextclade/src/tree/tree_find_nearest_node.rs index 4fbe0e3f9..a4bdf6593 100644 --- a/packages_rs/nextclade/src/tree/tree_find_nearest_node.rs +++ b/packages_rs/nextclade/src/tree/tree_find_nearest_node.rs @@ -164,7 +164,7 @@ mod tests { has_pcr_primer_changes: None, pcr_primer_changes: None, qc_status: None, - missing_genes: None, + missing_cdses: None, other: serde_json::Value::default(), }, diff --git a/packages_rs/nextclade/src/types/outputs.rs b/packages_rs/nextclade/src/types/outputs.rs index 5200c6dfb..e9863922a 100644 --- a/packages_rs/nextclade/src/types/outputs.rs +++ b/packages_rs/nextclade/src/types/outputs.rs @@ -74,7 +74,7 @@ pub struct NextcladeOutputs { pub private_nuc_mutations: PrivateNucMutations, pub private_aa_mutations: BTreeMap, pub warnings: Vec, - pub missing_genes: Vec, + pub missing_cdses: Vec, pub divergence: f64, pub coverage: f64, pub qc: QcResult,