msa-parsers 5.0.7 → 5.0.13

package/dist/src/gff/parseGFF.test.js

@@ -1,92 +0,0 @@
-import { describe, expect, test } from 'vitest';
-import { parseGFF } from "./parseGFF.js";
-describe('parseGFF', () => {
-    test('parses empty string', () => {
-        expect(parseGFF('')).toEqual([]);
-        expect(parseGFF(undefined)).toEqual([]);
-    });
-    test('parses basic GFF3 line', () => {
-        const gff = 'seq1\tInterProScan\tprotein_match\t10\t50\t.\t+\t.\tName=PF00001';
-        const result = parseGFF(gff);
-        expect(result).toHaveLength(1);
-        expect(result[0]).toEqual({
-            seq_id: 'seq1',
-            source: 'InterProScan',
-            type: 'protein_match',
-            start: 10,
-            end: 50,
-            score: 0,
-            strand: '+',
-            phase: '.',
-            Name: 'PF00001',
-        });
-    });
-    test('parses multiple attributes', () => {
-        const gff = 'seq1\tPfam\tprotein_match\t10\t50\t1.5\t.\t.\tName=PF00001;signature_desc=7tm_1;description=GPCR';
-        const result = parseGFF(gff);
-        expect(result[0]).toMatchObject({
-            Name: 'PF00001',
-            signature_desc: '7tm_1',
-            description: 'GPCR',
-        });
-    });
-    test('handles URL-encoded attribute values', () => {
-        const gff = 'seq1\tSource\ttype\t1\t10\t.\t.\t.\tNote=Hello%20World%3B%3D';
-        const result = parseGFF(gff);
-        expect(result[0]?.Note).toBe('Hello World;=');
-    });
-    test('skips comment lines', () => {
-        const gff = `##gff-version 3
-# This is a comment
-seq1\tSource\ttype\t1\t10\t.\t.\t.\tName=test`;
-        const result = parseGFF(gff);
-        expect(result).toHaveLength(1);
-        expect(result[0]?.seq_id).toBe('seq1');
-    });
-    test('skips empty lines', () => {
-        const gff = `seq1\tSource\ttype\t1\t10\t.\t.\t.\tName=test1
-
-seq2\tSource\ttype\t20\t30\t.\t.\t.\tName=test2`;
-        const result = parseGFF(gff);
-        expect(result).toHaveLength(2);
-    });
-    test('handles missing attributes column', () => {
-        const gff = 'seq1\tSource\ttype\t1\t10\t.\t.\t.';
-        const result = parseGFF(gff);
-        expect(result).toHaveLength(1);
-        expect(result[0]?.seq_id).toBe('seq1');
-    });
-    test('handles partial GFF lines gracefully', () => {
-        const gff = 'seq1\tSource\ttype';
-        const result = parseGFF(gff);
-        expect(result).toHaveLength(1);
-        expect(result[0]).toMatchObject({
-            seq_id: 'seq1',
-            source: 'Source',
-            type: 'type',
-            start: 0,
-            end: 0,
-        });
-    });
-    test('parses numeric score', () => {
-        const gff = 'seq1\tSource\ttype\t1\t10\t45.6\t.\t.\tName=test';
-        const result = parseGFF(gff);
-        expect(result[0]?.score).toBe(45.6);
-    });
-    test('handles comma-separated values in attributes', () => {
-        const gff = 'seq1\tSource\ttype\t1\t10\t.\t.\t.\tOntology_term=GO:0001,GO:0002';
-        const result = parseGFF(gff);
-        expect(result[0]?.Ontology_term).toBe('GO:0001 GO:0002');
-    });
-    test('parses multiple lines', () => {
-        const gff = `seq1\tPfam\tprotein_match\t10\t50\t.\t.\t.\tName=PF00001
-seq1\tSMART\tprotein_match\t60\t100\t.\t.\t.\tName=SM00001
-seq2\tPfam\tprotein_match\t5\t40\t.\t.\t.\tName=PF00002`;
-        const result = parseGFF(gff);
-        expect(result).toHaveLength(3);
-        expect(result[0]?.seq_id).toBe('seq1');
-        expect(result[1]?.seq_id).toBe('seq1');
-        expect(result[2]?.seq_id).toBe('seq2');
-    });
-});
-//# sourceMappingURL=parseGFF.test.js.map

package/dist/src/gff/parseGFF.test.js.map

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package/dist/src/index.d.ts

@@ -1,5 +0,0 @@
-export * from './types.ts';
-export { generateNodeIds } from './util.ts';
-export { A3mMSA, ClustalMSA, EmfMSA, FastaMSA, StockholmMSA, getUngappedSequence, parseEmfTree, parseMSA, parseNewick, stockholmSniff, } from './msa/index.ts';
-export type { MSAParserType } from './msa/index.ts';
-export { gffToInterProResponse, gffToInterProResults, interProResponseToGFF, interProToGFF, parseGFF, } from './gff/index.ts';

package/dist/src/index.js

@@ -1,9 +0,0 @@
-// Types
-export * from "./types.js";
-// Utilities
-export { generateNodeIds } from "./util.js";
-// MSA parsers
-export { A3mMSA, ClustalMSA, EmfMSA, FastaMSA, StockholmMSA, getUngappedSequence, parseEmfTree, parseMSA, parseNewick, stockholmSniff, } from "./msa/index.js";
-// GFF parsing
-export { gffToInterProResponse, gffToInterProResults, interProResponseToGFF, interProToGFF, parseGFF, } from "./gff/index.js";
-//# sourceMappingURL=index.js.map

package/dist/src/index.js.map

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package/dist/src/msa/A3mMSA.d.ts

@@ -1,33 +0,0 @@
-import type { NodeWithIds } from '../types.ts';
-export default class A3mMSA {
-    private MSA;
-    private orderedNames;
-    constructor(text: string);
-    /**
-     * Detect if text is likely A3M format
-     */
-    static sniff(text: string): boolean;
-    /**
-     * Expand A3M format to standard aligned format.
-     *
-     * In A3M, lowercase characters are insertions that implicitly introduce
-     * gaps in sequences that don't have an insert at that position.
-     * Gaps (-) following match columns in sequences without inserts align
-     * with lowercase inserts in other sequences.
-     */
-    private expandA3M;
-    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/src/msa/A3mMSA.js

@@ -1,282 +0,0 @@
-/**
- * A3M Format Parser
- *
- * The A3M format consists of aligned FASTA, in which alignments are shown with:
- * - Inserts as lowercase characters
- * - Matches as uppercase characters
- * - Deletions as '-'
- * - Gaps aligned to inserts as '.'
- *
- * Note that gaps aligned to inserts can be omitted in the A3M format.
- *
- * Example:
- * >query
- * ETESMKTVRIREKIKKFLGDRPRNTAEILEHINSTMRHGTTSQQLGNVLSKDKDIVKVGYIKRSGILSGGYDICEWATRNWVAEHCPEWTE
- * >seq1
- * ----MRTTRLRQKIKKFLNERGeANTTEILEHVNSTMRHGTTPQQLGNVLSKDKDILKVATTKRGGALSGRYEICVWTLRP-----------
- *
- * In the above, 'e' after 'G' in seq1 is a lowercase insert.
- *
- * @see https://yanglab.qd.sdu.edu.cn/trRosetta/msa_format.html
- */
-// Char code helpers for fast character classification
-const CODE_A = 65; // 'A'
-const CODE_Z = 90; // 'Z'
-const CODE_a = 97; // 'a'
-const CODE_z = 122; // 'z'
-const CODE_DASH = 45; // '-'
-const CODE_DOT = 46; // '.'
-function isLower(code) {
-    return code >= CODE_a && code <= CODE_z;
-}
-export default class A3mMSA {
-    MSA;
-    orderedNames;
-    constructor(text) {
-        const rawSeqs = [];
-        const names = [];
-        // First pass: parse sequences (like FASTA), preserving order
-        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) {
-                rawSeqs.push(entry.slice(newlineIdx + 1).replaceAll(/\s/g, ''));
-                names.push(id);
-            }
-        }
-        this.orderedNames = names;
-        this.MSA = { seqdata: this.expandA3M(rawSeqs, names) };
-    }
-    /**
-     * Detect if text is likely A3M format
-     */
-    static sniff(text) {
-        if (!text.startsWith('>')) {
-            return false;
-        }
-        const seqs = [];
-        for (const entry of text.split('>')) {
-            if (!/\S/.test(entry)) {
-                continue;
-            }
-            const newlineIdx = entry.indexOf('\n');
-            if (newlineIdx === -1) {
-                continue;
-            }
-            const seq = entry.slice(newlineIdx + 1).replaceAll(/\s/g, '');
-            if (seq) {
-                seqs.push(seq);
-            }
-        }
-        if (seqs.length < 2) {
-            return false;
-        }
-        // Check for lowercase and compute match column lengths in single pass per sequence
-        // In A3M, match columns = uppercase letters + dashes (deletions)
-        let hasLowercase = false;
-        let firstMatchLen = -1;
-        let sameMatchLength = true;
-        for (const seq of seqs) {
-            let matchLen = 0;
-            for (let i = 0; i < seq.length; i++) {
-                const code = seq.charCodeAt(i);
-                if (isLower(code)) {
-                    hasLowercase = true;
-                }
-                else if (code >= CODE_A && code <= CODE_Z || code === CODE_DASH) {
-                    // Uppercase letters and dashes are match columns
-                    matchLen++;
-                }
-            }
-            if (firstMatchLen === -1) {
-                firstMatchLen = matchLen;
-            }
-            else {
-                if (matchLen !== firstMatchLen) {
-                    sameMatchLength = false;
-                }
-            }
-        }
-        return hasLowercase && sameMatchLength;
-    }
-    /**
-     * Expand A3M format to standard aligned format.
-     *
-     * In A3M, lowercase characters are insertions that implicitly introduce
-     * gaps in sequences that don't have an insert at that position.
-     * Gaps (-) following match columns in sequences without inserts align
-     * with lowercase inserts in other sequences.
-     */
-    expandA3M(rawSeqs, names) {
-        const numSeqs = names.length;
-        if (numSeqs === 0) {
-            return {};
-        }
-        // Parse sequences: extract match chars (uppercase only) and insert content
-        // For each sequence, track: matchChars, insertContent (after each match)
-        const matchChars = [];
-        const insertContent = [];
-        for (let seqIdx = 0; seqIdx < numSeqs; seqIdx++) {
-            const seq = rawSeqs[seqIdx];
-            const matches = [];
-            const inserts = [];
-            let i = 0;
-            while (i < seq.length) {
-                const code = seq.charCodeAt(i);
-                if (code >= CODE_A && code <= CODE_Z || code === CODE_DASH) {
-                    // Uppercase letter or dash - match column (dash = deletion)
-                    matches.push(seq[i]);
-                    // Collect following lowercase/dot characters as insert content
-                    // Note: dash is NOT insert content, it's a match column
-                    let ins = '';
-                    let j = i + 1;
-                    while (j < seq.length) {
-                        const c = seq.charCodeAt(j);
-                        if (isLower(c) || c === CODE_DOT) {
-                            ins += seq[j];
-                            j++;
-                        }
-                        else {
-                            break;
-                        }
-                    }
-                    inserts.push(ins);
-                    i = j;
-                }
-                else if (code === CODE_DOT) {
-                    // Leading dot (gap aligned to insert) - skip
-                    i++;
-                }
-                else if (isLower(code)) {
-                    // Leading insert before first match
-                    let ins = '';
-                    while (i < seq.length && isLower(seq.charCodeAt(i))) {
-                        ins += seq[i];
-                        i++;
-                    }
-                    // Add empty match with this insert
-                    matches.push('');
-                    inserts.push(ins);
-                }
-                else {
-                    i++;
-                }
-            }
-            matchChars.push(matches);
-            insertContent.push(inserts);
-        }
-        // Find number of match positions (should be same for all valid A3M)
-        const numPositions = Math.max(...matchChars.map(m => m.length), 0);
-        // Find max insert length at each position (only count lowercase, not gaps)
-        const maxInserts = new Array(numPositions).fill(0);
-        for (let seqIdx = 0; seqIdx < numSeqs; seqIdx++) {
-            const inserts = insertContent[seqIdx];
-            for (let pos = 0; pos < inserts.length; pos++) {
-                // Count only lowercase characters as actual inserts
-                let lcCount = 0;
-                for (const c of inserts[pos]) {
-                    if (isLower(c.charCodeAt(0))) {
-                        lcCount++;
-                    }
-                }
-                if (lcCount > maxInserts[pos]) {
-                    maxInserts[pos] = lcCount;
-                }
-            }
-        }
-        // Build expanded sequences
-        const expanded = {};
-        for (let seqIdx = 0; seqIdx < numSeqs; seqIdx++) {
-            const matches = matchChars[seqIdx];
-            const inserts = insertContent[seqIdx];
-            const result = [];
-            for (let pos = 0; pos < numPositions; pos++) {
-                const maxIns = maxInserts[pos];
-                if (pos < matches.length) {
-                    const matchChar = matches[pos];
-                    const insContent = inserts[pos] || '';
-                    // Add match character (or gap if empty)
-                    result.push(matchChar || '-');
-                    // Process insert content
-                    let lcContent = '';
-                    for (const c of insContent) {
-                        if (isLower(c.charCodeAt(0))) {
-                            lcContent += c.toUpperCase();
-                        }
-                    }
-                    // Add the insert content (uppercased)
-                    result.push(lcContent);
-                    // Pad with gaps to match max insert length
-                    const padding = maxIns - lcContent.length;
-                    if (padding > 0) {
-                        result.push('.'.repeat(padding));
-                    }
-                }
-                else {
-                    // This sequence is shorter - add gaps
-                    result.push('-');
-                    if (maxIns > 0) {
-                        result.push('.'.repeat(maxIns));
-                    }
-                }
-            }
-            expanded[names[seqIdx]] = result.join('');
-        }
-        return expanded;
-    }
-    getMSA() {
-        return this.MSA;
-    }
-    getRowData() {
-        return undefined;
-    }
-    getNames() {
-        return this.orderedNames;
-    }
-    getRow(name) {
-        return this.MSA.seqdata[name] || '';
-    }
-    getWidth() {
-        const name = Object.keys(this.MSA.seqdata)[0];
-        return name ? this.getRow(name).length : 0;
-    }
-    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=A3mMSA.js.map

package/dist/src/msa/A3mMSA.js.map

@@ -1 +0,0 @@
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package/dist/src/msa/A3mMSA.test.d.ts

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