msa-parsers 1.0.3

package/dist/msa/ClustalMSA.js

@@ -0,0 +1,53 @@
+import { parse } from 'clustal-js';
+export default class ClustalMSA {
+    MSA;
+    constructor(text) {
+        this.MSA = parse(text);
+    }
+    getMSA() {
+        return this.MSA;
+    }
+    getRow(name) {
+        return this.MSA.alns.find(aln => aln.id === name)?.seq || '';
+    }
+    getWidth() {
+        return this.MSA.alns[0].seq.length;
+    }
+    getRowData() {
+        return undefined;
+    }
+    getHeader() {
+        return this.MSA.header;
+    }
+    getNames() {
+        return this.MSA.alns.map(aln => aln.id);
+    }
+    getStructures() {
+        return {};
+    }
+    get alignmentNames() {
+        return [];
+    }
+    getTree() {
+        return {
+            id: 'root',
+            name: 'root',
+            noTree: true,
+            children: this.getNames().map(name => ({
+                id: name,
+                name,
+                children: [],
+            })),
+        };
+    }
+    get seqConsensus() {
+        return this.MSA.consensus;
+    }
+    get secondaryStructureConsensus() {
+        return undefined;
+    }
+    get tracks() {
+        return [];
+    }
+}
+//# sourceMappingURL=ClustalMSA.js.map

package/dist/msa/ClustalMSA.js.map

@@ -0,0 +1 @@
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package/dist/msa/EmfMSA.d.ts

@@ -0,0 +1,27 @@
+import type { NodeWithIds } from '../types';
+export default class EmfMSA {
+    private MSA;
+    constructor(text: string);
+    getMSA(): {
+        species: string;
+        protein: string;
+        chr: string;
+        start: number;
+        end: number;
+        strand: number;
+        geneId: string;
+        unknown: string;
+        seq: string;
+    }[];
+    getRow(name: string): string;
+    getWidth(): number;
+    getRowData(): undefined;
+    getHeader(): string;
+    getNames(): string[];
+    getStructures(): {};
+    get alignmentNames(): never[];
+    getTree(): NodeWithIds;
+    get seqConsensus(): undefined;
+    get secondaryStructureConsensus(): undefined;
+    get tracks(): never[];
+}

package/dist/msa/EmfMSA.js

@@ -0,0 +1,53 @@
+import { parseEmfAln } from 'emf-js';
+export default class EmfMSA {
+    MSA;
+    constructor(text) {
+        this.MSA = parseEmfAln(text);
+    }
+    getMSA() {
+        return this.MSA;
+    }
+    getRow(name) {
+        return this.MSA.find(aln => aln.protein === name)?.seq || '';
+    }
+    getWidth() {
+        return this.MSA[0].seq.length;
+    }
+    getRowData() {
+        return undefined;
+    }
+    getHeader() {
+        return '';
+    }
+    getNames() {
+        return this.MSA.map(aln => aln.protein);
+    }
+    getStructures() {
+        return {};
+    }
+    get alignmentNames() {
+        return [];
+    }
+    getTree() {
+        return {
+            id: 'root',
+            name: 'root',
+            noTree: true,
+            children: this.getNames().map(name => ({
+                id: name,
+                name,
+                children: [],
+            })),
+        };
+    }
+    get seqConsensus() {
+        return undefined;
+    }
+    get secondaryStructureConsensus() {
+        return undefined;
+    }
+    get tracks() {
+        return [];
+    }
+}
+//# sourceMappingURL=EmfMSA.js.map

package/dist/msa/EmfMSA.js.map

@@ -0,0 +1 @@
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package/dist/msa/FastaMSA.d.ts

@@ -0,0 +1,19 @@
+import type { NodeWithIds } from '../types';
+export default class FastaMSA {
+    private MSA;
+    constructor(text: string);
+    getMSA(): {
+        seqdata: Record<string, string>;
+    };
+    getRowData(): undefined;
+    getNames(): string[];
+    getRow(name: string): string;
+    getWidth(): number;
+    getStructures(): {};
+    get alignmentNames(): never[];
+    getHeader(): {};
+    getTree(): NodeWithIds;
+    get seqConsensus(): undefined;
+    get secondaryStructureConsensus(): undefined;
+    get tracks(): never[];
+}

package/dist/msa/FastaMSA.js

@@ -0,0 +1,69 @@
+export default class FastaMSA {
+    MSA;
+    constructor(text) {
+        const seqdata = {};
+        for (const entry of text.split('>')) {
+            if (!/\S/.test(entry)) {
+                continue;
+            }
+            const newlineIdx = entry.indexOf('\n');
+            if (newlineIdx === -1) {
+                continue;
+            }
+            const defLine = entry.slice(0, newlineIdx);
+            const spaceIdx = defLine.indexOf(' ');
+            const id = spaceIdx === -1 ? defLine : defLine.slice(0, spaceIdx);
+            if (id) {
+                seqdata[id] = entry.slice(newlineIdx + 1).replaceAll(/\s/g, '');
+            }
+        }
+        this.MSA = { seqdata };
+    }
+    getMSA() {
+        return this.MSA;
+    }
+    getRowData() {
+        return undefined;
+    }
+    getNames() {
+        return Object.keys(this.MSA.seqdata);
+    }
+    getRow(name) {
+        return this.MSA.seqdata[name] || '';
+    }
+    getWidth() {
+        const name = Object.keys(this.MSA.seqdata)[0];
+        return this.getRow(name).length;
+    }
+    getStructures() {
+        return {};
+    }
+    get alignmentNames() {
+        return [];
+    }
+    getHeader() {
+        return {};
+    }
+    getTree() {
+        return {
+            id: 'root',
+            name: 'root',
+            noTree: true,
+            children: this.getNames().map(name => ({
+                id: name,
+                children: [],
+                name,
+            })),
+        };
+    }
+    get seqConsensus() {
+        return undefined;
+    }
+    get secondaryStructureConsensus() {
+        return undefined;
+    }
+    get tracks() {
+        return [];
+    }
+}
+//# sourceMappingURL=FastaMSA.js.map

package/dist/msa/FastaMSA.js.map

@@ -0,0 +1 @@
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package/dist/msa/StockholmMSA.d.ts

@@ -0,0 +1,54 @@
+import type { NodeWithIds } from '../types';
+import type { StockholmData } from './stockholmParser';
+export default class StockholmMSA {
+    private data;
+    private MSA;
+    constructor(text: string, currentAlignment: number);
+    getMSA(): StockholmData;
+    getRow(name: string): string;
+    getWidth(): number;
+    get alignmentNames(): string[];
+    getHeader(): {
+        General: Record<string, string[]>;
+        Accessions: {
+            [k: string]: string | undefined;
+        };
+        Dbxref: {
+            [k: string]: string;
+        };
+    };
+    getRowData(rowName: string): {
+        name: string;
+        accession: string | undefined;
+        dbxref: string | undefined;
+    };
+    getNames(): string[];
+    getSeqCoords(): void;
+    getStructures(): Record<string, {
+        pdb: string;
+        chain: string;
+        startPos: number;
+        endPos: number;
+    }[]>;
+    getTree(): NodeWithIds;
+    get seqConsensus(): string | undefined;
+    get secondaryStructureConsensus(): string | undefined;
+    get tracks(): ({
+        id: string;
+        name: string;
+        data: string | undefined;
+        customColorScheme: {
+            '>'?: undefined;
+            '<'?: undefined;
+        };
+    } | {
+        id: string;
+        name: string;
+        data: string | undefined;
+        customColorScheme: {
+            '>': string;
+            '<': string;
+        };
+    })[];
+}
+export { sniff as stockholmSniff } from './stockholmParser';

package/dist/msa/StockholmMSA.js

@@ -0,0 +1,113 @@
+import parseNewick from './parseNewick';
+import { parseAll } from './stockholmParser';
+import { generateNodeIds } from '../util';
+export default class StockholmMSA {
+    data;
+    MSA;
+    constructor(text, currentAlignment) {
+        const res = parseAll(text);
+        this.data = res;
+        this.MSA = res[currentAlignment];
+    }
+    getMSA() {
+        return this.MSA;
+    }
+    getRow(name) {
+        return this.MSA.seqdata[name] || '';
+    }
+    getWidth() {
+        const name = Object.keys(this.MSA.seqdata)[0];
+        return this.getRow(name).length;
+    }
+    get alignmentNames() {
+        return this.data.map((aln, idx) => aln.gf.DE?.[0] ?? `Alignment ${idx + 1}`);
+    }
+    getHeader() {
+        const acEntries = this.MSA.gs.AC ?? {};
+        const drEntries = this.MSA.gs.DR ?? {};
+        return {
+            General: this.MSA.gf,
+            Accessions: Object.fromEntries(Object.entries(acEntries).map(([k, v]) => [k, v[0]])),
+            Dbxref: Object.fromEntries(Object.entries(drEntries).map(([k, v]) => [k, v.join('; ')])),
+        };
+    }
+    getRowData(rowName) {
+        return {
+            name: rowName,
+            accession: this.MSA.gs.AC?.[rowName]?.[0],
+            dbxref: this.MSA.gs.DR?.[rowName]?.join('; '),
+        };
+    }
+    getNames() {
+        return Object.keys(this.MSA.seqdata);
+    }
+    getSeqCoords() { }
+    getStructures() {
+        const pdbRegex = /PDB; +(\S+) +(\S); ([0-9]+)-([0-9]+)/;
+        const drEntries = this.MSA.gs.DR ?? {};
+        const args = Object.entries(drEntries)
+            .flatMap(([id, drList]) => drList.map(dr => {
+            const match = pdbRegex.exec(dr);
+            return match ? { id, match } : null;
+        }))
+            .filter((item) => !!item)
+            .map(({ id, match }) => ({
+            id,
+            pdb: match[1].toLowerCase(),
+            chain: match[2],
+            startPos: +match[3],
+            endPos: +match[4],
+        }));
+        const ret = {};
+        for (const entry of args) {
+            const { id, ...rest } = entry;
+            if (!ret[id]) {
+                ret[id] = [];
+            }
+            ret[id].push(rest);
+        }
+        return ret;
+    }
+    getTree() {
+        const tree = this.MSA.gf.NH?.[0];
+        return tree
+            ? generateNodeIds(parseNewick(tree))
+            : {
+                id: 'root',
+                name: 'root',
+                noTree: true,
+                children: this.getNames().map(name => ({
+                    id: name,
+                    children: [],
+                    name,
+                })),
+            };
+    }
+    get seqConsensus() {
+        return this.MSA.gc.seq_cons;
+    }
+    get secondaryStructureConsensus() {
+        return this.MSA.gc.SS_cons;
+    }
+    get tracks() {
+        return [
+            {
+                id: 'seqConsensus',
+                name: 'Sequence consensus',
+                data: this.seqConsensus,
+                customColorScheme: {},
+            },
+            {
+                id: 'secondaryStruct',
+                name: 'Secondary-structure',
+                data: this.secondaryStructureConsensus,
+                customColorScheme: {
+                    '>': 'pink',
+                    '<': 'lightblue',
+                },
+            },
+        ];
+    }
+}
+export { sniff as stockholmSniff } from './stockholmParser';
+//# sourceMappingURL=StockholmMSA.js.map

package/dist/msa/StockholmMSA.js.map

@@ -0,0 +1 @@
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package/dist/msa/index.d.ts

@@ -0,0 +1,18 @@
+import A3mMSA from './A3mMSA';
+import ClustalMSA from './ClustalMSA';
+import EmfMSA from './EmfMSA';
+import FastaMSA from './FastaMSA';
+import StockholmMSA from './StockholmMSA';
+export { parseEmfTree } from 'emf-js';
+export { default as parseNewick } from './parseNewick';
+export type MSAParserType = StockholmMSA | A3mMSA | FastaMSA | EmfMSA | ClustalMSA;
+export declare function parseMSA(text: string, currentAlignment?: number): MSAParserType;
+/**
+ * Get ungapped sequence from an aligned row
+ */
+export declare function getUngappedSequence(alignedSeq: string): string;
+export { default as A3mMSA } from './A3mMSA';
+export { default as ClustalMSA } from './ClustalMSA';
+export { default as EmfMSA } from './EmfMSA';
+export { default as FastaMSA } from './FastaMSA';
+export { default as StockholmMSA, stockholmSniff } from './StockholmMSA';

package/dist/msa/index.js

@@ -0,0 +1,34 @@
+import A3mMSA from './A3mMSA';
+import ClustalMSA from './ClustalMSA';
+import EmfMSA from './EmfMSA';
+import FastaMSA from './FastaMSA';
+import StockholmMSA, { stockholmSniff } from './StockholmMSA';
+export { parseEmfTree } from 'emf-js';
+export { default as parseNewick } from './parseNewick';
+export function parseMSA(text, currentAlignment = 0) {
+    if (stockholmSniff(text)) {
+        return new StockholmMSA(text, currentAlignment);
+    }
+    if (A3mMSA.sniff(text)) {
+        return new A3mMSA(text);
+    }
+    if (text.startsWith('>')) {
+        return new FastaMSA(text);
+    }
+    if (text.startsWith('SEQ')) {
+        return new EmfMSA(text);
+    }
+    return new ClustalMSA(text);
+}
+/**
+ * Get ungapped sequence from an aligned row
+ */
+export function getUngappedSequence(alignedSeq) {
+    return alignedSeq.replaceAll(/[.-]/g, '');
+}
+export { default as A3mMSA } from './A3mMSA';
+export { default as ClustalMSA } from './ClustalMSA';
+export { default as EmfMSA } from './EmfMSA';
+export { default as FastaMSA } from './FastaMSA';
+export { default as StockholmMSA, stockholmSniff } from './StockholmMSA';
+//# sourceMappingURL=index.js.map

package/dist/msa/index.js.map

@@ -0,0 +1 @@
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package/dist/msa/index.test.d.ts

@@ -0,0 +1 @@
+export {};

package/dist/msa/index.test.js

@@ -0,0 +1,60 @@
+import { describe, expect, test } from 'vitest';
+import A3mMSA from './A3mMSA';
+import ClustalMSA from './ClustalMSA';
+import FastaMSA from './FastaMSA';
+import { getUngappedSequence, parseMSA } from './index';
+describe('parseMSA', () => {
+    test('parses FASTA format', () => {
+        const fasta = `>seq1
+ACDEF
+>seq2
+GHIKL`;
+        const msa = parseMSA(fasta);
+        expect(msa).toBeInstanceOf(FastaMSA);
+        expect(msa.getNames()).toEqual(['seq1', 'seq2']);
+    });
+    test('parses A3M format', () => {
+        const a3m = `>seq1
+ACDEFghiKLMNPQ
+>seq2
+ACDEF---KLMNPQ`;
+        const msa = parseMSA(a3m);
+        expect(msa).toBeInstanceOf(A3mMSA);
+    });
+    test('parses Clustal format', () => {
+        const clustal = `CLUSTAL W (1.83) multiple sequence alignment
+
+seq1      ACDEFGHIKL
+seq2      ACDEFGHIKL
+          **********`;
+        const msa = parseMSA(clustal);
+        expect(msa).toBeInstanceOf(ClustalMSA);
+    });
+    test('defaults to Clustal for unknown format', () => {
+        const unknown = `some unknown format
+that doesn't match anything`;
+        const msa = parseMSA(unknown);
+        expect(msa).toBeInstanceOf(ClustalMSA);
+    });
+});
+describe('getUngappedSequence', () => {
+    test('removes dashes', () => {
+        expect(getUngappedSequence('AC--DEF')).toBe('ACDEF');
+    });
+    test('removes dots', () => {
+        expect(getUngappedSequence('AC..DEF')).toBe('ACDEF');
+    });
+    test('removes mixed gaps', () => {
+        expect(getUngappedSequence('A-C.D--E..F')).toBe('ACDEF');
+    });
+    test('handles empty string', () => {
+        expect(getUngappedSequence('')).toBe('');
+    });
+    test('handles string with only gaps', () => {
+        expect(getUngappedSequence('---...')).toBe('');
+    });
+    test('handles string with no gaps', () => {
+        expect(getUngappedSequence('ACDEF')).toBe('ACDEF');
+    });
+});
+//# sourceMappingURL=index.test.js.map

package/dist/msa/index.test.js.map

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package/dist/msa/parseNewick.d.ts

@@ -0,0 +1,60 @@
+/**
+ * Newick format parser in JavaScript.
+ *
+ * Copyright (c) Jason Davies 2010.
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in
+ * all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ * THE SOFTWARE.
+ *
+ * Example tree (from http://en.wikipedia.org/wiki/Newick_format):
+ *
+ * +--0.1--A
+ * F-----0.2-----B            +-------0.3----C
+ * +------------------0.5-----E
+ *                            +---------0.4------D
+ *
+ * Newick format:
+ * (A:0.1,B:0.2,(C:0.3,D:0.4)E:0.5)F;
+ *
+ * Converted to JSON:
+ * {
+ *   name: "F",
+ *   children: [
+ *     {name: "A", length: 0.1},
+ *     {name: "B", length: 0.2},
+ *     {
+ *       name: "E",
+ *       length: 0.5,
+ *       children: [
+ *         {name: "C", length: 0.3},
+ *         {name: "D", length: 0.4}
+ *       ]
+ *     }
+ *   ]
+ * }
+ *
+ * Converted to JSON, but with no names or lengths:
+ * {
+ *   children: [
+ *     {}, {}, {
+ *       children: [{}, {}]
+ *     }
+ *   ]
+ * }
+ */
+export default function parse(s: string): Record<string, any>;