msa-parsers 1.0.3

package/dist/gff/parseGFF.test.js

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+import { describe, expect, test } from 'vitest';
+import { parseGFF } from './parseGFF';
+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/gff/parseGFF.test.js.map

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package/dist/index.d.ts

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

package/dist/index.js

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

package/dist/index.js.map

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package/dist/msa/A3mMSA.d.ts

@@ -0,0 +1,33 @@
+import type { NodeWithIds } from '../types';
+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/msa/A3mMSA.js

@@ -0,0 +1,280 @@
+/**
+ * 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 lengths in single pass per sequence
+        // In A3M, only uppercase letters are match columns (not gaps)
+        let hasLowercase = false;
+        let firstUppercaseLen = -1;
+        let sameUppercaseLength = true;
+        for (const seq of seqs) {
+            let uppercaseLen = 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) {
+                    uppercaseLen++;
+                }
+            }
+            if (firstUppercaseLen === -1) {
+                firstUppercaseLen = uppercaseLen;
+            }
+            else {
+                if (uppercaseLen !== firstUppercaseLen) {
+                    sameUppercaseLength = false;
+                }
+            }
+        }
+        return hasLowercase && sameUppercaseLength;
+    }
+    /**
+     * 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) {
+                    // Uppercase letter - match column
+                    matches.push(seq[i]);
+                    // Collect following lowercase/gap characters as insert content
+                    let ins = '';
+                    let j = i + 1;
+                    while (j < seq.length) {
+                        const c = seq.charCodeAt(j);
+                        if (isLower(c) || c === CODE_DASH || c === CODE_DOT) {
+                            ins += seq[j];
+                            j++;
+                        }
+                        else {
+                            break;
+                        }
+                    }
+                    inserts.push(ins);
+                    i = j;
+                }
+                else if (code === CODE_DASH || code === CODE_DOT) {
+                    // Leading gap before first match - 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/msa/A3mMSA.js.map

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

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

package/dist/msa/A3mMSA.test.js

@@ -0,0 +1,155 @@
+import { describe, expect, test } from 'vitest';
+import A3mMSA from './A3mMSA';
+describe('A3mMSA', () => {
+    describe('sniff', () => {
+        test('returns false for non-FASTA text', () => {
+            expect(A3mMSA.sniff('not fasta')).toBe(false);
+            expect(A3mMSA.sniff('CLUSTAL W')).toBe(false);
+        });
+        test('returns false for regular FASTA', () => {
+            const fasta = `>seq1
+ACDEFGHIKLMNPQRSTVWY
+>seq2
+ACDEFGHIKLMNPQRSTVWY`;
+            expect(A3mMSA.sniff(fasta)).toBe(false);
+        });
+        test('returns true for A3M format', () => {
+            const a3m = `>seq1
+ACDEFghiKLMNPQ
+>seq2
+ACDEF---KLMNPQ`;
+            expect(A3mMSA.sniff(a3m)).toBe(true);
+        });
+        test('returns false for single sequence', () => {
+            const a3m = `>seq1
+ACDEFghiKLMNPQ`;
+            expect(A3mMSA.sniff(a3m)).toBe(false);
+        });
+    });
+    describe('parsing', () => {
+        test('parses simple A3M', () => {
+            const a3m = `>seq1
+ACDEFghiKLMNPQ
+>seq2
+ACDEF---KLMNPQ`;
+            const msa = new A3mMSA(a3m);
+            expect(msa.getNames()).toEqual(['seq1', 'seq2']);
+            const seq1 = msa.getRow('seq1');
+            const seq2 = msa.getRow('seq2');
+            expect(seq1.length).toBe(seq2.length);
+            expect(seq1).toContain('GHI');
+        });
+        test('expands lowercase insertions', () => {
+            const a3m = `>seq1
+ACabc
+>seq2
+AC---`;
+            const msa = new A3mMSA(a3m);
+            const seq1 = msa.getRow('seq1');
+            const seq2 = msa.getRow('seq2');
+            expect(seq1).toBe('ACABC');
+            expect(seq2).toBe('AC...');
+        });
+        test('handles multiple insertions', () => {
+            const a3m = `>seq1
+AabcDdefG
+>seq2
+A---D---G`;
+            const msa = new A3mMSA(a3m);
+            const seq1 = msa.getRow('seq1');
+            const seq2 = msa.getRow('seq2');
+            expect(seq1.length).toBe(seq2.length);
+        });
+        test('getWidth returns correct width', () => {
+            const a3m = `>seq1
+ACDEF
+>seq2
+ACDEF`;
+            const msa = new A3mMSA(a3m);
+            expect(msa.getWidth()).toBe(5);
+        });
+        test('getMSA returns seqdata', () => {
+            const a3m = `>seq1
+ACDEF
+>seq2
+GHIKL`;
+            const msa = new A3mMSA(a3m);
+            const data = msa.getMSA();
+            expect(data.seqdata).toHaveProperty('seq1');
+            expect(data.seqdata).toHaveProperty('seq2');
+        });
+        test('getTree returns noTree structure', () => {
+            const a3m = `>seq1
+ACDEF
+>seq2
+GHIKL`;
+            const msa = new A3mMSA(a3m);
+            const tree = msa.getTree();
+            expect(tree.noTree).toBe(true);
+            expect(tree.children).toHaveLength(2);
+        });
+        test('handles empty sequences', () => {
+            const a3m = `>seq1
+ACDEF`;
+            const msa = new A3mMSA(a3m);
+            expect(msa.getNames()).toEqual(['seq1']);
+        });
+        test('handles sequences with only ID on defline', () => {
+            const a3m = `>seq1 description here
+ACDEF
+>seq2 another description
+GHIKL`;
+            const msa = new A3mMSA(a3m);
+            expect(msa.getNames()).toEqual(['seq1', 'seq2']);
+        });
+        test('preserves sequence order', () => {
+            const a3m = `>z_seq
+AAAAA
+>a_seq
+CCCCC
+>m_seq
+DDDDD`;
+            const msa = new A3mMSA(a3m);
+            expect(msa.getNames()).toEqual(['z_seq', 'a_seq', 'm_seq']);
+        });
+    });
+    describe('properties', () => {
+        test('alignmentNames is empty array', () => {
+            const a3m = `>seq1
+ACDEF`;
+            const msa = new A3mMSA(a3m);
+            expect(msa.alignmentNames).toEqual([]);
+        });
+        test('seqConsensus is undefined', () => {
+            const a3m = `>seq1
+ACDEF`;
+            const msa = new A3mMSA(a3m);
+            expect(msa.seqConsensus).toBeUndefined();
+        });
+        test('secondaryStructureConsensus is undefined', () => {
+            const a3m = `>seq1
+ACDEF`;
+            const msa = new A3mMSA(a3m);
+            expect(msa.secondaryStructureConsensus).toBeUndefined();
+        });
+        test('tracks is empty array', () => {
+            const a3m = `>seq1
+ACDEF`;
+            const msa = new A3mMSA(a3m);
+            expect(msa.tracks).toEqual([]);
+        });
+        test('getStructures returns empty object', () => {
+            const a3m = `>seq1
+ACDEF`;
+            const msa = new A3mMSA(a3m);
+            expect(msa.getStructures()).toEqual({});
+        });
+        test('getHeader returns empty object', () => {
+            const a3m = `>seq1
+ACDEF`;
+            const msa = new A3mMSA(a3m);
+            expect(msa.getHeader()).toEqual({});
+        });
+    });
+});
+//# sourceMappingURL=A3mMSA.test.js.map

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

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

@@ -0,0 +1,30 @@
+import type { NodeWithIds } from '../types';
+export default class ClustalMSA {
+    private MSA;
+    constructor(text: string);
+    getMSA(): {
+        consensus: string;
+        alns: {
+            id: string;
+            seq: string;
+        }[];
+        header: {
+            info: string;
+            version: string | undefined;
+        };
+    };
+    getRow(name: string): string;
+    getWidth(): number;
+    getRowData(): undefined;
+    getHeader(): {
+        info: string;
+        version: string | undefined;
+    };
+    getNames(): string[];
+    getStructures(): {};
+    get alignmentNames(): never[];
+    getTree(): NodeWithIds;
+    get seqConsensus(): string;
+    get secondaryStructureConsensus(): undefined;
+    get tracks(): never[];
+}