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Update variant.js
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Now using th eVRSified variant response for label, chromosome(s) etc.
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@mbaudis
mbaudis committed Aug 9, 2024
1 parent e636451 commit 5b396b5
Showing 1 changed file with 47 additions and 30 deletions.
77 changes: 47 additions & 30 deletions src/pages/variant.js
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Original file line number Diff line number Diff line change
Expand Up @@ -62,19 +62,36 @@ function VariantResponse({ response, id, datasetIds }) {
}

function Variant({ variant, id, datasetIds }) {
// TODO: derive variant parameters from location/adjacency etc.
var marker = variant.variantInternalId
var mParts = marker.split(':')
const chro = refseq2chro(mParts[0])
marker = marker + " (" + mParts[1] + ")"
// TODO: add variatrion type or sequence from VRS response

const v = variant.variation ? variant.variation : false
console.log(v)
var locations = []
if (variant.location) {
locations.push(variant.location)
} else if (variant.sequenceAdjecencies) {
locations.push(...variant.sequenceAdjecencies)
var chros = []
var markers = []
if (v.subject) {
locations.push(v.subject)
} else if (v.location) {
locations.push(v.location)
} else if (v.adjoinedSequences) {
locations.push(...v.adjoinedSequences)
}

console.log(locations)

locations.forEach(function (loc) {
if (loc.sequence_id) {
const chro = refseq2chro(loc.sequence_id)
chros.push(chro)
const i = loc.interval
const m = chro + ":" + i?.start?.value + "-" + i?.end.value
const l = "chr" + chro + " (" + i?.start?.value + "-" + i?.end.value + ")"
markers.push(m + ":" + l)
}
});

console.log(markers)

return (
<section className="content">
<h3>
Expand All @@ -83,20 +100,20 @@ function Variant({ variant, id, datasetIds }) {

<h5>Digest</h5>
<p>{variant.variantInternalId}</p>
{variant.variation?.molecularAttributes && (
{v?.molecularAttributes && (
<>
<h5>Molecular Attributes</h5>
<ul>
{variant.variation.molecularAttributes.geneIds && (
<li>Gene: <b>{variant.variation.molecularAttributes.geneIds[0]}</b></li>
{v.molecularAttributes.geneIds && (
<li>Gene: <b>{v.molecularAttributes.geneIds[0]}</b></li>
)}
{variant.variation.molecularAttributes?.molecularEffects && (
<li>Molecular effect: {variant.variation.molecularAttributes.molecularEffects[0].label}</li>
{v.molecularAttributes?.molecularEffects && (
<li>Molecular effect: {v.molecularAttributes.molecularEffects[0].label}</li>
)}
{variant.variation.molecularAttributes.aminoacidChanges && variant.variation.molecularAttributes.aminoacidChanges.length > 0 && variant.variation.molecularAttributes.aminoacidChanges[0] !== null && (
{v.molecularAttributes.aminoacidChanges && v.molecularAttributes.aminoacidChanges.length > 0 && variant.variation.molecularAttributes.aminoacidChanges[0] !== null && (
<li>Aminoacid changes:
<ul>
{variant.variation.molecularAttributes.aminoacidChanges.map((aa) => (
{v.molecularAttributes.aminoacidChanges.map((aa) => (
<li key={aa}>
{aa}
</li>
Expand All @@ -108,14 +125,14 @@ function Variant({ variant, id, datasetIds }) {
</>
)}

{variant.variation?.identifiers && (
{v?.identifiers && (
<>
<h5>Variant Identifiers</h5>
<ul>
{variant.variation.identifiers?.proteinHGVSIds && (
{v.identifiers?.proteinHGVSIds && (
<li>Protein HGVSids:
<ul>
{variant.variation.identifiers.proteinHGVSIds.map((ph) =>
{v.identifiers.proteinHGVSIds.map((ph) =>
<li key={ph}>
{ph}
</li>
Expand All @@ -124,7 +141,7 @@ function Variant({ variant, id, datasetIds }) {
</li>
)}

{variant.variation.identifiers?.genomicHGVSIds && (
{v.identifiers?.genomicHGVSIds && (
<li>Genomic HGVSids:
<ul>
{variant.variation.identifiers.genomicHGVSIds.map((gh) =>
Expand All @@ -136,13 +153,13 @@ function Variant({ variant, id, datasetIds }) {
</li>
)}

{variant.variation.identifiers?.clinvarIds && (
{v.identifiers?.clinvarIds && (
<li>ClinVar IDs:
<ul>
<li>
<ExternalLink
href={`http://www.ncbi.nlm.nih.gov/clinvar/variation/${variant.variation.identifiers.clinvarIds[0]}`}
label={variant.variation.identifiers.clinvarIds[1]}
label={v.identifiers.clinvarIds[1]}
/>
</li>
</ul>
Expand All @@ -153,11 +170,11 @@ function Variant({ variant, id, datasetIds }) {
</>
)}

{variant.variation?.variantAlternativeIds && (
{v?.variantAlternativeIds && (
<div>
<h5>Variant Alternative IDs</h5>
<ul>
{variant.variation.variantAlternativeIds.map((altid, key) => (
{v.variantAlternativeIds.map((altid, key) => (
<li key={key}>
{altid.id} - {altid.label}
</li>
Expand All @@ -166,18 +183,18 @@ function Variant({ variant, id, datasetIds }) {
</div>
)}

{variant.variation?.variantLevelData?.clinicalInterpretations && (
{v?.variantLevelData?.clinicalInterpretations && (
<>
{variant.variation.variantLevelData && variant.variation.variantLevelData.clinicalInterpretations.length > 0 && (
{v.variantLevelData && variant.variation.variantLevelData.clinicalInterpretations.length > 0 && (
<>
<h5>Clinical Interpretations</h5>
<p>Clinical Relevance: <b>{variant.variation.variantLevelData.clinicalInterpretations[0].clinicalRelevance}</b></p>
<p>Clinical Relevance: <b>{v.variantLevelData.clinicalInterpretations[0].clinicalRelevance}</b></p>
<table>
<tr>
<th>ID</th>
<th>Description</th>
</tr>
{variant.variation.variantLevelData.clinicalInterpretations?.map((clinicalInterpretations, key) => {
{v.variantLevelData.clinicalInterpretations?.map((clinicalInterpretations, key) => {
return (
<tr key={key}>
<td>
Expand Down Expand Up @@ -213,10 +230,10 @@ function Variant({ variant, id, datasetIds }) {

<ShowJSON data={variant} />

{variant.caseLevelData[0]?.biosampleId && marker && chro && (
{variant.caseLevelData[0]?.biosampleId && (
<>
<h5>Plot</h5>
<BiosamplePlot biosid={variant.caseLevelData[0].biosampleId} datasetIds={datasetIds} plotRegionLabels={marker} plotChros={chro} />
<BiosamplePlot biosid={variant.caseLevelData[0].biosampleId} datasetIds={datasetIds} plotRegionLabels={markers.join(",")} plotChros={chros.join(",")} />
</>
)}

Expand Down

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