msa-parsers 1.0.3

package/dist/msa/parseNewick.js

@@ -0,0 +1,95 @@
+/**
+ * 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) {
+    const ancestors = [];
+    let tree = {};
+    const tokens = s.split(/\s*(;|\(|\)|,|:)\s*/);
+    for (let i = 0; i < tokens.length; i++) {
+        const token = tokens[i];
+        const subtree = {};
+        switch (token) {
+            case '(': // new children
+                tree.children = [subtree];
+                ancestors.push(tree);
+                tree = subtree;
+                break;
+            case ',': // another branch
+                ancestors.at(-1)?.children.push(subtree);
+                tree = subtree;
+                break;
+            case ')': // optional name next
+                tree = ancestors.pop();
+                break;
+            case ':': // optional length next
+                break;
+            default: {
+                const x = tokens[i - 1];
+                if (x === ')' || x === '(' || x === ',') {
+                    tree.name = token;
+                }
+                else if (x === ':') {
+                    tree.length = Number.parseFloat(token);
+                }
+            }
+        }
+    }
+    return tree;
+}
+//# sourceMappingURL=parseNewick.js.map

package/dist/msa/parseNewick.js.map

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

@@ -0,0 +1,22 @@
+/**
+ * Stockholm format parser
+ * Based on stockholm-js by Ian Holmes
+ * Rewritten in TypeScript
+ */
+export interface StockholmData {
+    gf: Record<string, string[]>;
+    gc: Record<string, string>;
+    gs: Record<string, Record<string, string[]>>;
+    gr: Record<string, Record<string, string>>;
+    seqname: string[];
+    seqdata: Record<string, string>;
+}
+export declare function sniff(text: string): boolean;
+export declare function parseAll(text: string, opts?: {
+    strict?: boolean;
+    quiet?: boolean;
+}): StockholmData[];
+export declare function parse(text: string, opts?: {
+    strict?: boolean;
+    quiet?: boolean;
+}): StockholmData;

package/dist/msa/stockholmParser.js

@@ -0,0 +1,141 @@
+/**
+ * Stockholm format parser
+ * Based on stockholm-js by Ian Holmes
+ * Rewritten in TypeScript
+ */
+function createStockholm() {
+    return {
+        gf: {},
+        gc: {},
+        gs: {},
+        gr: {},
+        seqname: [],
+        seqdata: {},
+    };
+}
+const formatStartRegex = /^# STOCKHOLM 1.0/;
+const formatEndRegex = /^\/\/\s*$/;
+const gfRegex = /^#=GF\s+(\S+)\s+(.*?)\s*$/;
+const gcRegex = /^#=GC\s+(\S+)\s+(.*?)\s*$/;
+const gsRegex = /^#=GS\s+(\S+)\s+(\S+)\s+(.*?)\s*$/;
+const grRegex = /^#=GR\s+(\S+)\s+(\S+)\s+(.*?)\s*$/;
+const lineRegex = /^\s*(\S+)\s+(\S+)\s*$/;
+const nonwhiteRegex = /\S/;
+export function sniff(text) {
+    return formatStartRegex.test(text);
+}
+export function parseAll(text, opts) {
+    const options = opts ?? {};
+    const db = [];
+    let stock = null;
+    const lines = text.split('\n');
+    for (const line of lines) {
+        let match;
+        if (formatStartRegex.test(line)) {
+            stock = createStockholm();
+        }
+        else if (formatEndRegex.test(line)) {
+            if (stock) {
+                db.push(stock);
+            }
+            stock = null;
+        }
+        else if ((match = gfRegex.exec(line))) {
+            if (!stock) {
+                if (options.strict) {
+                    throw new Error('No format header: # STOCKHOLM 1.0');
+                }
+                stock = createStockholm();
+            }
+            const tag = match[1];
+            if (!stock.gf[tag]) {
+                stock.gf[tag] = [];
+            }
+            stock.gf[tag].push(match[2]);
+        }
+        else if ((match = gcRegex.exec(line))) {
+            if (!stock) {
+                if (options.strict) {
+                    throw new Error('No format header: # STOCKHOLM 1.0');
+                }
+                stock = createStockholm();
+            }
+            const tag = match[1];
+            if (!stock.gc[tag]) {
+                stock.gc[tag] = '';
+            }
+            stock.gc[tag] += match[2];
+        }
+        else if ((match = gsRegex.exec(line))) {
+            if (!stock) {
+                if (options.strict) {
+                    throw new Error('No format header: # STOCKHOLM 1.0');
+                }
+                stock = createStockholm();
+            }
+            const seqname = match[1];
+            const tag = match[2];
+            const value = match[3];
+            if (!stock.gs[tag]) {
+                stock.gs[tag] = {};
+            }
+            if (!stock.gs[tag][seqname]) {
+                stock.gs[tag][seqname] = [];
+            }
+            stock.gs[tag][seqname].push(value);
+        }
+        else if ((match = grRegex.exec(line))) {
+            if (!stock) {
+                if (options.strict) {
+                    throw new Error('No format header: # STOCKHOLM 1.0');
+                }
+                stock = createStockholm();
+            }
+            const seqname = match[1];
+            const tag = match[2];
+            const value = match[3];
+            if (!stock.gr[tag]) {
+                stock.gr[tag] = {};
+            }
+            if (!stock.gr[tag][seqname]) {
+                stock.gr[tag][seqname] = '';
+            }
+            stock.gr[tag][seqname] += value;
+        }
+        else if ((match = lineRegex.exec(line))) {
+            if (!stock) {
+                if (options.strict) {
+                    throw new Error('No format header: # STOCKHOLM 1.0');
+                }
+                stock = createStockholm();
+            }
+            const seqname = match[1];
+            const seqdata = match[2];
+            if (!stock.seqdata[seqname]) {
+                stock.seqdata[seqname] = '';
+                stock.seqname.push(seqname);
+            }
+            stock.seqdata[seqname] += seqdata;
+        }
+        else if (nonwhiteRegex.test(line)) {
+            if (options.strict) {
+                throw new Error('Malformed line');
+            }
+        }
+    }
+    if (stock) {
+        db.push(stock);
+    }
+    return db;
+}
+export function parse(text, opts) {
+    const db = parseAll(text, opts);
+    if (db.length === 0) {
+        throw new Error('No alignments found');
+    }
+    if (db.length > 1) {
+        throw new Error('More than one alignment found');
+    }
+    return db[0];
+}
+//# sourceMappingURL=stockholmParser.js.map

package/dist/msa/stockholmParser.js.map

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

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

package/dist/msa/stockholmParser.test.js

@@ -0,0 +1,111 @@
+import { describe, expect, test } from 'vitest';
+import { parse, parseAll, sniff } from './stockholmParser';
+describe('stockholmParser', () => {
+    describe('sniff', () => {
+        test('returns true for Stockholm format', () => {
+            expect(sniff('# STOCKHOLM 1.0\n')).toBe(true);
+        });
+        test('returns false for non-Stockholm format', () => {
+            expect(sniff('>seq1\nACDEF')).toBe(false);
+            expect(sniff('CLUSTAL W')).toBe(false);
+        });
+    });
+    describe('parseAll', () => {
+        test('parses simple Stockholm file', () => {
+            const stockholm = `# STOCKHOLM 1.0
+seq1  ACDEFGHIKL
+seq2  ACDEFGHIKL
+//`;
+            const result = parseAll(stockholm);
+            expect(result).toHaveLength(1);
+            expect(result[0]?.seqdata).toEqual({
+                seq1: 'ACDEFGHIKL',
+                seq2: 'ACDEFGHIKL',
+            });
+            expect(result[0]?.seqname).toEqual(['seq1', 'seq2']);
+        });
+        test('parses GF lines', () => {
+            const stockholm = `# STOCKHOLM 1.0
+#=GF DE Description of the alignment
+#=GF NH (A:0.1,B:0.2);
+seq1  ACDEF
+//`;
+            const result = parseAll(stockholm);
+            expect(result[0]?.gf.DE).toEqual(['Description of the alignment']);
+            expect(result[0]?.gf.NH).toEqual(['(A:0.1,B:0.2);']);
+        });
+        test('parses GC lines', () => {
+            const stockholm = `# STOCKHOLM 1.0
+seq1          ACDEF
+#=GC seq_cons *****
+#=GC SS_cons  <<>>>
+//`;
+            const result = parseAll(stockholm);
+            expect(result[0]?.gc.seq_cons).toBe('*****');
+            expect(result[0]?.gc.SS_cons).toBe('<<>>>');
+        });
+        test('parses GS lines', () => {
+            const stockholm = `# STOCKHOLM 1.0
+#=GS seq1 AC P12345
+#=GS seq1 DR PDB; 1ABC A; 1-100
+seq1  ACDEF
+//`;
+            const result = parseAll(stockholm);
+            expect(result[0]?.gs.AC?.seq1).toEqual(['P12345']);
+            expect(result[0]?.gs.DR?.seq1).toEqual(['PDB; 1ABC A; 1-100']);
+        });
+        test('parses multiple alignments', () => {
+            const stockholm = `# STOCKHOLM 1.0
+seq1  ACDEF
+//
+# STOCKHOLM 1.0
+seq2  GHIKL
+//`;
+            const result = parseAll(stockholm);
+            expect(result).toHaveLength(2);
+            expect(result[0]?.seqdata.seq1).toBe('ACDEF');
+            expect(result[1]?.seqdata.seq2).toBe('GHIKL');
+        });
+        test('concatenates interleaved sequence blocks', () => {
+            const stockholm = `# STOCKHOLM 1.0
+seq1  ACDEF
+seq2  GHIKL
+
+seq1  MNOPQ
+seq2  RSTUV
+//`;
+            const result = parseAll(stockholm);
+            expect(result[0]?.seqdata.seq1).toBe('ACDEFMNOPQ');
+            expect(result[0]?.seqdata.seq2).toBe('GHIKLRSTUV');
+        });
+        test('handles file without trailing //', () => {
+            const stockholm = `# STOCKHOLM 1.0
+seq1  ACDEF`;
+            const result = parseAll(stockholm);
+            expect(result).toHaveLength(1);
+            expect(result[0]?.seqdata.seq1).toBe('ACDEF');
+        });
+    });
+    describe('parse', () => {
+        test('returns single alignment', () => {
+            const stockholm = `# STOCKHOLM 1.0
+seq1  ACDEF
+//`;
+            const result = parse(stockholm);
+            expect(result.seqdata.seq1).toBe('ACDEF');
+        });
+        test('throws on empty input', () => {
+            expect(() => parse('')).toThrow('No alignments found');
+        });
+        test('throws on multiple alignments', () => {
+            const stockholm = `# STOCKHOLM 1.0
+seq1  ACDEF
+//
+# STOCKHOLM 1.0
+seq2  GHIKL
+//`;
+            expect(() => parse(stockholm)).toThrow('More than one alignment found');
+        });
+    });
+});
+//# sourceMappingURL=stockholmParser.test.js.map

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

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package/dist/types.d.ts

@@ -0,0 +1,66 @@
+export interface Node {
+    children?: Node[];
+    name?: string;
+    length?: number;
+}
+export interface NodeWithIds {
+    id: string;
+    name: string;
+    children: NodeWithIds[];
+    length?: number;
+    noTree?: boolean;
+}
+export interface NodeWithIdsAndLength {
+    id: string;
+    name: string;
+    children: NodeWithIdsAndLength[];
+    noTree?: boolean;
+    length: number;
+}
+export interface GFFRecord {
+    seq_id: string;
+    source: string;
+    type: string;
+    start: number;
+    end: number;
+    score: number;
+    strand: string;
+    phase: string;
+    [key: string]: string | number;
+}
+export interface InterProScanMatch {
+    signature: {
+        entry?: {
+            name: string;
+            description: string;
+            accession: string;
+        };
+    };
+    locations: {
+        start: number;
+        end: number;
+    }[];
+}
+export interface InterProScanResults {
+    matches: InterProScanMatch[];
+    xref: {
+        id: string;
+    }[];
+}
+export interface InterProScanResponse {
+    results: InterProScanResults[];
+}
+export interface MSAParser {
+    getMSA(): unknown;
+    getRow(name: string): string;
+    getWidth(): number;
+    getNames(): string[];
+    getTree(): NodeWithIds;
+    getHeader(): unknown;
+    getRowData(name: string): unknown;
+    getStructures(): Record<string, unknown>;
+    alignmentNames: string[];
+    seqConsensus: string | undefined;
+    secondaryStructureConsensus: string | undefined;
+    tracks: unknown[];
+}

package/dist/types.js

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

package/dist/types.js.map

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

package/dist/util.d.ts

@@ -0,0 +1,2 @@
+import type { Node, NodeWithIds } from './types';
+export declare function generateNodeIds(tree: Node, parent?: string, depth?: number): NodeWithIds;

package/dist/util.js

@@ -0,0 +1,10 @@
+export function generateNodeIds(tree, parent = 'node', depth = 0) {
+    const id = `${parent}-${depth}`;
+    return {
+        ...tree,
+        id,
+        name: tree.name || id,
+        children: tree.children?.map((b, i) => generateNodeIds(b, `${id}-${i}`, depth + 1)) || [],
+    };
+}
+//# sourceMappingURL=util.js.map

package/dist/util.js.map

@@ -0,0 +1 @@
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package/package.json

@@ -0,0 +1,25 @@
+{
+  "name": "msa-parsers",
+  "version": "1.0.3",
+  "license": "MIT",
+  "main": "dist/index.js",
+  "module": "dist/index.js",
+  "types": "dist/index.d.ts",
+  "files": [
+    "dist",
+    "src"
+  ],
+  "scripts": {
+    "clean": "rimraf dist",
+    "build": "tsc",
+    "watch": "tsc --watch",
+    "test": "vitest"
+  },
+  "dependencies": {
+    "clustal-js": "^2.0.13",
+    "emf-js": "^2.0.0"
+  },
+  "publishConfig": {
+    "access": "public"
+  }
+}