Merge pull request #1376 from nextstrain/feat/rename-gene-to-cds

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;

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 (
-        <Tr key={`${gene}-${position}`}>
+        <Tr key={`${cds}-${position}`}>
           <TdNormal>
             <GeneText $background={bg} $color={fg}>
-              {gene}
+              {cds}
             </GeneText>
           </TdNormal>
           <TdNormal className="text-center">{position + 1}</TdNormal>

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) => (
-      <Alert key={`${warning.geneName}: ${warning.warning}`} color="warning" fade={false} className="px-2 py-1 my-1">
+      <Alert key={`${warning.cdsName}: ${warning.warning}`} color="warning" fade={false} className="px-2 py-1 my-1">
         <WarningIcon />
         {warning.warning}
       </Alert>

packages_rs/nextclade-web/src/components/Results/ListOfFrameShifts.tsx

@@ -12,7 +12,7 @@ export function FrameShiftRows({ frameShifts }: FrameShiftRowsProps) {
   return (
     <ul>
       {frameShifts.map((fs) => (
-        <li key={`${fs.geneName}_${fs.codon.begin}`}>{formatFrameShift(fs)}</li>
+        <li key={`${fs.cdsName}_${fs.codon.begin}`}>{formatFrameShift(fs)}</li>
       ))}
     </ul>
   )

packages_rs/nextclade-web/src/components/Results/ListOfInsertions.tsx

@@ -177,17 +177,17 @@ export function ListOfInsertionsAa({ insertions }: ListOfInsertionsAaProps) {
   const { thead, tbody } = useMemo(() => {
     const thead = (
       <tr>
-        <ThNormal className="text-center">{t('Gene.')}</ThNormal>
+        <ThNormal className="text-center">{t('CDS')}</ThNormal>
         <ThNormal className="text-center">{t('After ref pos.')}</ThNormal>
         <ThNormal className="text-center">{t('Length')}</ThNormal>
         <ThFragment className="text-center">{t('Inserted fragment')}</ThFragment>
       </tr>
     )
 
     const insertionsTruncated = insertions.slice(0, 20)
-    const tbody = insertionsTruncated.map(({ pos, ins, gene }) => (
+    const tbody = insertionsTruncated.map(({ pos, ins, cds }) => (
       <tr key={pos}>
-        <TdNormal className="text-center">{gene}</TdNormal>
+        <TdNormal className="text-center">{cds}</TdNormal>
         <TdNormal className="text-center">{pos + 1}</TdNormal>
         <TdNormal className="text-center">{ins.length}</TdNormal>
         <TdFragment className="text-left">

packages_rs/nextclade-web/src/components/Results/ListOfStopCodons.tsx

@@ -12,7 +12,7 @@ export function StopCodonsItems({ stopCodons }: StopCodonsRowsProps) {
   return (
     <ul>
       {stopCodons.map((sc) => (
-        <li key={`${sc.geneName}_${sc.codon}`}>{formatStopCodon(sc)}</li>
+        <li key={`${sc.cdsName}_${sc.codon}`}>{formatStopCodon(sc)}</li>
       ))}
     </ul>
   )

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({
               </tr>
 
               <tr>
-                <td>{t('Gene')}</td>
-                <td>{geneName}</td>
+                <td>{t('CDS')}</td>
+                <td>{cdsName}</td>
               </tr>
 
               <tr>

packages_rs/nextclade-web/src/components/SequenceView/PeptideView.tsx

@@ -50,7 +50,7 @@ export function PeptideViewMissing({ geneName, reasons }: PeptideViewMissingProp
       <Tooltip wide fullWidth target={id} isOpen={showTooltip} onMouseEnter={onMouseEnter} onMouseLeave={onMouseLeave}>
         <p>{t('This gene is missing due to the following errors during analysis: ')}</p>
         {reasons.map((warn) => (
-          <Alert key={warn.geneName} color="warning" fade={false} className="px-2 py-1 my-1">
+          <Alert key={warn.cdsName} color="warning" fade={false} className="px-2 py-1 my-1">
             <WarningIcon />
             {warn.warning}
           </Alert>
@@ -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 (
       <SequenceViewWrapper>
@@ -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 (
         <PeptideMarkerInsertion

packages_rs/nextclade-web/src/components/SequenceView/SequenceMarkerFrameShift.tsx

@@ -23,7 +23,7 @@ export interface FrameShiftMarkerProps extends SVGProps<SVGRectElement> {
 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

packages_rs/nextclade-web/src/components/SequenceView/SequenceView.tsx

@@ -132,7 +132,7 @@ export function SequenceViewUnsized({ sequence, width }: SequenceViewProps) {
 
   const frameShiftMarkers = frameShifts.map((frameShift) => (
     <SequenceMarkerFrameShift
-      key={`${frameShift.geneName}_${frameShift.nucAbs.map((na) => na.begin).join('-')}`}
+      key={`${frameShift.cdsName}_${frameShift.nucAbs.map((na) => na.begin).join('-')}`}
       index={index}
       seqName={seqName}
       frameShift={frameShift}

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)}`
 }

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}`
 }

packages_rs/nextclade-web/src/helpers/formatQCStopCodons.ts

@@ -13,7 +13,7 @@ export function formatQCStopCodons<TFunction extends TFunctionInterface>(
 
   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}}',

packages_rs/nextclade/src/align/insertions_strip.rs

@@ -105,7 +105,7 @@ pub fn insertions_strip<T: Letter<T>>(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<AaIns> {
     .iter_cdses()
     .flat_map(|(cds_name, cds_tr)| {
       cds_tr.insertions.iter().map(|Insertion::<Aa> { pos, ins }| AaIns {
-        gene: cds_name.clone(),
+        cds: cds_name.clone(),
         pos: *pos,
         ins: ins.clone(),
       })

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};
@@ -53,16 +53,16 @@ fn process_one_aa_motifs_desc(
   let AaMotifsDesc {
     name,
     motifs,
-    include_genes,
+    include_cdses: include_genes,
     ..
   } = aa_motifs_desc;
 
   // If no genes specified, process all genes
   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()
     })

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<AaMotif
 
   Ok(AaMotifMutation {
     name: motif.name.clone(),
-    gene: motif.cds.clone(),
+    cds: motif.cds.clone(),
     position: motif.position,
     ref_seq,
     qry_seq: motif.seq.clone(),
@@ -149,7 +149,7 @@ fn add_qry_seq(motif: &AaMotif, qry_translation: &Translation) -> Option<AaMotif
         let qry_seq = from_aa_seq(&tr.seq[sequenced_motif_range.to_std()]);
         Some(AaMotifMutation {
           name: motif.name.clone(),
-          gene: motif.cds.clone(),
+          cds: motif.cds.clone(),
           position: motif.position,
           ref_seq: motif.seq.clone(),
           qry_seq,

packages_rs/nextclade/src/analyze/find_private_aa_mutations.rs

@@ -3,7 +3,7 @@ use crate::alphabet::letter::Letter;
 use crate::analyze::aa_del::AaDel;
 use crate::analyze::aa_sub::AaSub;
 use crate::analyze::is_sequenced::is_aa_sequenced;
-use crate::analyze::letter_ranges::GeneAaRange;
+use crate::analyze::letter_ranges::CdsAaRange;
 use crate::coord::position::{AaRefPosition, PositionLike};
 use crate::coord::range::AaRefRange;
 use crate::gene::cds::Cds;
@@ -33,7 +33,7 @@ pub fn find_private_aa_mutations(
   node: &AuspiceGraphNodePayload,
   aa_substitutions: &[AaSub],
   aa_deletions: &[AaDel],
-  aa_unknowns: &[GeneAaRange],
+  aa_unknowns: &[CdsAaRange],
   aa_unsequenced_ranges: &BTreeMap<String, Vec<AaRefRange>>,
   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<AaRefPosition, Aa>,
   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<AaRefPosition, Aa>,
-  aa_unknowns: &[&GeneAaRange],
+  aa_unknowns: &[&CdsAaRange],
   aa_unsequenced_ranges: &[AaRefRange],
   ref_peptide: &[Aa],
   seq_positions_mutated_or_deleted: &mut BTreeSet<AaRefPosition>,

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()