protvista-uniprot 2.11.1 → 2.11.3

package/dist/es/commonTypes.d.ts

@@ -0,0 +1,25 @@
+export declare type AlphafoldPayload = Array<{
+    entryId: string;
+    gene: string;
+    uniprotAccession: string;
+    uniprotId: string;
+    uniprotDescription: string;
+    taxId: number;
+    organismScientificName: string;
+    uniprotStart: number;
+    uniprotEnd: number;
+    uniprotSequence: string;
+    modelCreatedDate: string;
+    latestVersion: number;
+    allVersions: number[];
+    isReviewed: boolean;
+    isReferenceProteome: boolean;
+    cifUrl?: string;
+    bcifUrl?: string;
+    amAnnotationsUrl?: string;
+    amAnnotationsHg19Url?: string;
+    amAnnotationsHg38Url?: string;
+    pdbUrl: string;
+    paeImageUrl: string;
+    paeDocUrl: string;
+}>;

package/dist/es/commonTypes.js

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=commonTypes.js.map

package/dist/es/commonTypes.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"commonTypes.js","sourceRoot":"","sources":["../../src/commonTypes.ts"],"names":[],"mappings":""}

package/dist/es/config.json

@@ -284,6 +284,19 @@
                         }
                     ],
                     "tooltip": "Short conserved sequence motif of biological significance"
+                },
+                {
+                    "name": "zn_fing",
+                    "label": "Zinc finger",
+                    "filter": "ZN_FING",
+                    "trackType": "protvista-track",
+                    "data": [
+                        {
+                            "adapter": "protvista-feature-adapter",
+                            "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
+                        }
+                    ],
+                    "tooltip": "Small, functional, independently folded domain that coordinates one or more zinc ions"
                 }
             ]
         },
@@ -344,19 +357,6 @@
                     ],
                     "tooltip": "DNA-binding domains such as AP2/ERF domain, the ETS domain, the Fork-Head domain, the HMG box and the Myb domain"
                 },
-                {
-                    "name": "zn_fing",
-                    "label": "Zinc finger",
-                    "filter": "ZN_FING",
-                    "trackType": "protvista-track",
-                    "data": [
-                        {
-                            "adapter": "protvista-feature-adapter",
-                            "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
-                        }
-                    ],
-                    "tooltip": "Small, functional, independently folded domain that coordinates one or more zinc ions"
-                },
                 {
                     "name": "np_bind",
                     "label": "Nucleotide binding",
@@ -589,6 +589,18 @@
                     ],
                     "tooltip": ""
                 },
+                {
+                    "name": "hpp",
+                    "label": "Human proteome project",
+                    "trackType": "protvista-track",
+                    "data": [
+                        {
+                            "adapter": "protvista-proteomics-adapter",
+                            "url": "https://www.ebi.ac.uk/proteins/api/hpp/{accession}"
+                        }
+                    ],
+                    "tooltip": ""
+                },
                 {
                     "name": "proteomics-ptm",
                     "label": "PTM-containing peptide",
@@ -637,13 +649,41 @@
                     "data": [
                         {
                             "adapter": "protvista-alphafold-confidence-adapter",
-                            "url": "https://alphafold.ebi.ac.uk/api/prediction/{accession}"
+                            "url": [
+                                "https://alphafold.ebi.ac.uk/api/prediction/{accession}",
+                                "https://www.ebi.ac.uk/proteins/api/proteins/{accession}"
+                            ]
                         }
                     ],
                     "tooltip": "AlphaFold prediction confidence"
                 }
             ]
         },
+        {
+            "name": "ALPHAMISSENSE_PATHOGENICITY",
+            "label": "AlphaMissense",
+            "trackType": "protvista-coloured-sequence",
+            "scale": "P:100,A:50,B:0",
+            "color-range": "#9a131a:100,#a8a9ad:50,#3d5493:0",
+            "tracks": [
+                {
+                    "name": "alphamissense_pathogenicity",
+                    "label": "AlphaMissense Pathogenicity",
+                    "labelUrl": "https://alphafold.ebi.ac.uk/entry/{accession}",
+                    "trackType": "protvista-coloured-sequence",
+                    "data": [
+                        {
+                            "adapter": "protvista-alphamissense-pathogenicity-adapter",
+                            "url": [
+                                "https://alphafold.ebi.ac.uk/api/prediction/{accession}",
+                                "https://www.ebi.ac.uk/proteins/api/proteins/{accession}"
+                            ]
+                        }
+                    ],
+                    "tooltip": "AlphaMissense prediction pathogenicity"
+                }
+            ]
+        },
         {
             "name": "STRUCTURAL",
             "label": "Structural features",

package/dist/es/protvista-alphafold-confidence.d.ts

@@ -1,23 +1,9 @@
-declare type AlphafoldPayload = Array<{
-    entryId: string;
-    gene: string;
-    uniprotAccession: string;
-    uniprotId: string;
-    uniprotDescription: string;
-    taxId: number;
-    organismScientificName: string;
-    uniprotStart: number;
-    uniprotEnd: number;
-    uniprotSequence: string;
-    modelCreatedDate: string;
-    latestVersion: number;
-    allVersions: number[];
-    cifUrl: string;
-    bcifUrl: string;
-    pdbUrl: string;
-    paeImageUrl: string;
-    paeDocUrl: string;
-}>;
+import { AlphafoldPayload } from './commonTypes';
 export declare const getConfidenceURLFromPayload: (data: AlphafoldPayload) => string;
-export declare const transformData: (data: AlphafoldPayload) => Promise<string>;
+declare type PartialProtein = {
+    sequence: {
+        sequence: string;
+    };
+};
+export declare const transformData: (data: AlphafoldPayload, protein: PartialProtein) => Promise<string>;
 export {};

package/dist/es/protvista-alphafold-confidence.js

@@ -14,9 +14,10 @@ const loadConfidence = async (url) => {
         console.error('Could not load AlphaFold confidence', e);
     }
 };
-export const transformData = async (data) => {
+export const transformData = async (data, protein) => {
     const confidenceUrl = getConfidenceURLFromPayload(data);
-    if (confidenceUrl) {
+    const { uniprotSequence } = (data === null || data === void 0 ? void 0 : data[0]) || {};
+    if (confidenceUrl && uniprotSequence === protein.sequence.sequence) {
         const confidenceData = await loadConfidence(confidenceUrl);
         return confidenceData === null || confidenceData === void 0 ? void 0 : confidenceData.confidenceCategory.join('');
     }

package/dist/es/protvista-alphafold-confidence.js.map

@@ -1 +1 @@
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+{"version":3,"file":"protvista-alphafold-confidence.js","sourceRoot":"","sources":["../../src/protvista-alphafold-confidence.ts"],"names":[],"mappings":"AAQA,MAAM,CAAC,MAAM,2BAA2B,GAAG,CAAC,IAAsB,EAAE,EAAE;;IACpE,MAAM,MAAM,GAAG,MAAA,IAAI,aAAJ,IAAI,uBAAJ,IAAI,CAAG,CAAC,CAAC,0CAAE,MAAM,CAAC;IACjC,OAAO,CAAA,MAAM,aAAN,MAAM,uBAAN,MAAM,CAAE,MAAM;QACnB,CAAC,CAAC,MAAM,CAAC,OAAO,CAAC,QAAQ,EAAE,aAAa,CAAC,CAAC,OAAO,CAAC,MAAM,EAAE,OAAO,CAAC;QAClE,CAAC,CAAC,IAAI,CAAC;AACX,CAAC,CAAC;AAEF,MAAM,cAAc,GAAG,KAAK,EAC1B,GAAW,EAC0B,EAAE;IACvC,IAAI;QACF,MAAM,OAAO,GAAG,MAAM,KAAK,CAAC,GAAG,CAAC,CAAC;QACjC,OAAO,OAAO,CAAC,IAAI,EAAE,CAAC;KACvB;IAAC,OAAO,CAAC,EAAE;QACV,OAAO,CAAC,KAAK,CAAC,qCAAqC,EAAE,CAAC,CAAC,CAAC;KACzD;AACH,CAAC,CAAC;AAQF,MAAM,CAAC,MAAM,aAAa,GAAG,KAAK,EAChC,IAAsB,EACtB,OAAuB,EACvB,EAAE;IACF,MAAM,aAAa,GAAG,2BAA2B,CAAC,IAAI,CAAC,CAAC;IACxD,MAAM,EAAE,eAAe,EAAE,GAAG,CAAA,IAAI,aAAJ,IAAI,uBAAJ,IAAI,CAAG,CAAC,CAAC,KAAI,EAAE,CAAC;IAC5C,IAAI,aAAa,IAAI,eAAe,KAAK,OAAO,CAAC,QAAQ,CAAC,QAAQ,EAAE;QAClE,MAAM,cAAc,GAAG,MAAM,cAAc,CAAC,aAAa,CAAC,CAAC;QAC3D,OAAO,cAAc,aAAd,cAAc,uBAAd,cAAc,CAAE,kBAAkB,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;KACpD;AACH,CAAC,CAAC"}

package/dist/es/protvista-alphamissense-pathogenicity.d.ts

@@ -0,0 +1,8 @@
+import { AlphafoldPayload } from './commonTypes';
+declare type PartialProtein = {
+    sequence: {
+        sequence: string;
+    };
+};
+export declare const transformData: (data: AlphafoldPayload, protein: PartialProtein) => Promise<string>;
+export {};

package/dist/es/protvista-alphamissense-pathogenicity.js

@@ -0,0 +1,67 @@
+// from example data
+// benign: [0.0448,0.3397]: x < 0.34
+// ambiguous: [0.34,0.564]: 0.34 <= x <= 0.564
+// pathogenic: [0.5646,0.9999]: 0.564 < x
+const benign = 0.34;
+const pathogenic = 0.564;
+const rowSplitter = /\s*\n\s*/;
+const cellSplitter = /^(.)(\d+)(.),(.+),(\w+)$/;
+const parseCSV = (rawText) => {
+    const positions = [];
+    for (const [i, row] of rawText.split(rowSplitter).entries()) {
+        if (i === 0 || !row) {
+            continue;
+        }
+        const [, wildType, positionString, mutated, pathogenicityScore, pathogenicityLabel,] = row.match(cellSplitter);
+        const position = +positionString;
+        const index = position - 1;
+        if (!positions[index]) {
+            positions[index] = [];
+        }
+        positions[index].push({
+            wildType,
+            position,
+            mutated,
+            pathogenicityScore: +pathogenicityScore,
+            pathogenicityLabel,
+        });
+    }
+    const out = [];
+    for (const position of positions) {
+        let letter = 'A';
+        // maximum
+        // const value = Math.max(
+        //   ...position.map((variation) => variation.pathogenicityScore)
+        // );
+        // average
+        const value = position.reduce((acc, variation) => acc + +variation.pathogenicityScore, 0) / position.length;
+        if (value > pathogenic) {
+            letter = 'P';
+        }
+        else if (value < benign) {
+            letter = 'B';
+        }
+        out.push(letter);
+    }
+    return out.join('');
+};
+// Load and parse
+const loadAndParseAnnotations = async (url) => {
+    try {
+        const payload = await fetch(url);
+        const rawCSV = await payload.text();
+        return parseCSV(rawCSV);
+    }
+    catch (e) {
+        console.error('Could not load AlphaMissense pathogenicity', e);
+    }
+};
+export const transformData = async (data, protein) => {
+    const { amAnnotationsUrl, uniprotSequence } = (data === null || data === void 0 ? void 0 : data[0]) || {};
+    if (amAnnotationsUrl && uniprotSequence === protein.sequence.sequence) {
+        const variationData = await loadAndParseAnnotations(amAnnotationsUrl);
+        // return confidenceData?.confidenceCategory.join('');
+        return variationData;
+    }
+};
+//# sourceMappingURL=protvista-alphamissense-pathogenicity.js.map

package/dist/es/protvista-alphamissense-pathogenicity.js.map

@@ -0,0 +1 @@
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package/dist/es/protvista-uniprot.d.ts

@@ -56,26 +56,16 @@ export declare const transformDataProteomicsPTMApdapter: (data: {
     tooltipContent: string;
     color: any;
 }[];
-export declare const transformDataAlphaFoldConfidenceAdapter: (data: {
-    entryId: string;
-    gene: string;
-    uniprotAccession: string;
-    uniprotId: string;
-    uniprotDescription: string;
-    taxId: number;
-    organismScientificName: string;
-    uniprotStart: number;
-    uniprotEnd: number;
-    uniprotSequence: string;
-    modelCreatedDate: string;
-    latestVersion: number;
-    allVersions: number[];
-    cifUrl: string;
-    bcifUrl: string;
-    pdbUrl: string;
-    paeImageUrl: string;
-    paeDocUrl: string;
-}[]) => Promise<string>;
+export declare const transformDataAlphaFoldConfidenceAdapter: (data: import("./commonTypes").AlphafoldPayload, protein: {
+    sequence: {
+        sequence: string;
+    };
+}) => Promise<string>;
+export declare const transformDataAlphaMissensePathogenicityAdapter: (data: import("./commonTypes").AlphafoldPayload, protein: {
+    sequence: {
+        sequence: string;
+    };
+}) => Promise<string>;
 export declare const filterConfig: {
     name: string;
     type: {
@@ -101,7 +91,7 @@ declare type ProtvistaTrackConfig = {
     filter: string;
     trackType: TrackType;
     data: {
-        url: string;
+        url: string | string[];
         adapter?: 'protvista-feature-adapter' | 'protvista-structure-adapter' | 'protvista-proteomics-adapter' | 'protvista-variation-adapter' | 'protvista-interpro-adapter';
     }[];
     tooltip: string;

package/dist/es/protvista-uniprot.js

@@ -21,6 +21,7 @@ import { transformData as _transformDataVariationAdapter } from 'protvista-varia
 import { transformData as _transformDataInterproAdapter } from 'protvista-interpro-adapter';
 import { transformData as _transformDataProteomicsPTMApdapter } from './protvista-ptm-exchange';
 import { transformData as _transformDataAlphaFoldConfidenceAdapter } from './protvista-alphafold-confidence';
+import { transformData as _transformDataAlphaMissensePathogenicityAdapter } from './protvista-alphamissense-pathogenicity';
 import defaultConfig from './config.json';
 import _ProtvistaUniprotStructure from './protvista-uniprot-structure';
 import _DownloadPanel from './download-panel';
@@ -36,6 +37,7 @@ export const transformDataVariationAdapter = _transformDataVariationAdapter;
 export const transformDataInterproAdapter = _transformDataInterproAdapter;
 export const transformDataProteomicsPTMApdapter = _transformDataProteomicsPTMApdapter;
 export const transformDataAlphaFoldConfidenceAdapter = _transformDataAlphaFoldConfidenceAdapter;
+export const transformDataAlphaMissensePathogenicityAdapter = _transformDataAlphaMissensePathogenicityAdapter;
 export const filterConfig = _filterConfig;
 export const colorConfig = _colorConfig;
 export const ProtvistaUniprotStructure = _ProtvistaUniprotStructure;
@@ -48,6 +50,7 @@ const adapters = {
     'protvista-variation-adapter': transformDataVariationAdapter,
     'protvista-proteomics-ptm-adapter': transformDataProteomicsPTMApdapter,
     'protvista-alphafold-confidence-adapter': transformDataAlphaFoldConfidenceAdapter,
+    'protvista-alphamissense-pathogenicity-adapter': transformDataAlphaMissensePathogenicityAdapter,
 };
 class ProtvistaUniprot extends LitElement {
     constructor() {
@@ -101,9 +104,7 @@ class ProtvistaUniprot extends LitElement {
         const accession = this.accession;
         if (accession && this.config) {
             // Get the list of unique urls
-            const urls = this.config.categories
-                .map(({ tracks }) => tracks.map(({ data }) => data[0].url))
-                .flat();
+            const urls = this.config.categories.flatMap(({ tracks }) => tracks.flatMap(({ data }) => data[0].url));
             const uniqueUrls = [...new Set(urls)];
             // Get the data for all urls and store it
             await Promise.all(uniqueUrls.map((url) => load(url.replace('{accession}', accession))
@@ -126,23 +127,23 @@ class ProtvistaUniprot extends LitElement {
                 .categories) {
                 const categoryData = await Promise.all(tracks.map(async ({ data: dataConfig, name: trackName, filter }) => {
                     const { url, adapter } = dataConfig[0]; // TODO handle array
-                    const trackData = this.rawData[url] || [];
+                    const trackData = (Array.isArray(url) ? url : [url]).map((url) => this.rawData[url] || []);
                     if (!trackData ||
                         (adapter === 'protvista-variation-adapter' &&
-                            trackData.length === 0)) {
+                            trackData[0].length === 0)) {
                         return;
                     }
                     // 1. Convert data
                     let transformedData = adapter
-                        ? await adapters[adapter](trackData)
+                        ? await adapters[adapter](...trackData)
                         : trackData;
                     if (adapter === 'protvista-interpro-adapter') {
                         const representativeDomains = [];
-                        transformedData === null || transformedData === void 0 ? void 0 : transformedData.forEach(feature => {
+                        transformedData === null || transformedData === void 0 ? void 0 : transformedData.forEach((feature) => {
                             var _a;
-                            (_a = feature.locations) === null || _a === void 0 ? void 0 : _a.forEach(location => {
+                            (_a = feature.locations) === null || _a === void 0 ? void 0 : _a.forEach((location) => {
                                 var _a;
-                                (_a = location.fragments) === null || _a === void 0 ? void 0 : _a.forEach(fragment => {
+                                (_a = location.fragments) === null || _a === void 0 ? void 0 : _a.forEach((fragment) => {
                                     if (fragment.representative) {
                                         representativeDomains.push({
                                             ...feature,

package/dist/es/protvista-uniprot.js.map

@@ -1 +1 @@
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