msa-parsers 1.0.3

package/dist/gff/gffToInterPro.d.ts

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+import type { GFFRecord, InterProScanResponse, InterProScanResults } from '../types';
+/**
+ * Convert GFF records to InterProScan format
+ *
+ * InterProScan GFF3 output format:
+ * - seq_id: sequence identifier
+ * - source: database/signature (e.g., "Pfam", "SMART")
+ * - type: usually "protein_match"
+ * - start/end: domain positions (1-based)
+ * - Attributes: Name (accession), signature_desc (name), Dbxref, etc.
+ */
+export declare function gffToInterProResults(gffRecords: GFFRecord[]): Record<string, InterProScanResults>;
+/**
+ * Convert GFF string directly to InterProScan format
+ */
+export declare function parseGFFToInterPro(gffStr: string, parseGFFfn: (str: string) => GFFRecord[]): Record<string, InterProScanResults>;
+/**
+ * Create a full InterProScanResponse from GFF records
+ */
+export declare function gffToInterProResponse(gffRecords: GFFRecord[]): InterProScanResponse;

package/dist/gff/gffToInterPro.js

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+/**
+ * Convert GFF records to InterProScan format
+ *
+ * InterProScan GFF3 output format:
+ * - seq_id: sequence identifier
+ * - source: database/signature (e.g., "Pfam", "SMART")
+ * - type: usually "protein_match"
+ * - start/end: domain positions (1-based)
+ * - Attributes: Name (accession), signature_desc (name), Dbxref, etc.
+ */
+export function gffToInterProResults(gffRecords) {
+    const bySequence = new Map();
+    for (const record of gffRecords) {
+        const existing = bySequence.get(record.seq_id);
+        if (existing) {
+            existing.push(record);
+        }
+        else {
+            bySequence.set(record.seq_id, [record]);
+        }
+    }
+    const results = {};
+    for (const [seqId, records] of bySequence) {
+        const matchesByAccession = new Map();
+        const matchInfo = new Map();
+        for (const record of records) {
+            const accession = record.Name ||
+                record.ID ||
+                `${record.source}_${record.start}_${record.end}`;
+            const name = record.signature_desc ||
+                record.Name ||
+                accession;
+            const description = record.Ontology_term ||
+                record.description ||
+                record.Note ||
+                name;
+            if (!matchInfo.has(accession)) {
+                matchInfo.set(accession, { name, description, accession });
+            }
+            const locations = matchesByAccession.get(accession);
+            if (locations) {
+                locations.push({ start: record.start, end: record.end });
+            }
+            else {
+                matchesByAccession.set(accession, [
+                    { start: record.start, end: record.end },
+                ]);
+            }
+        }
+        const matches = [];
+        for (const [accession, locations] of matchesByAccession) {
+            const info = matchInfo.get(accession);
+            matches.push({
+                signature: {
+                    entry: info,
+                },
+                locations,
+            });
+        }
+        results[seqId] = {
+            matches,
+            xref: [{ id: seqId }],
+        };
+    }
+    return results;
+}
+/**
+ * Convert GFF string directly to InterProScan format
+ */
+export function parseGFFToInterPro(gffStr, parseGFFfn) {
+    const records = parseGFFfn(gffStr);
+    return gffToInterProResults(records);
+}
+/**
+ * Create a full InterProScanResponse from GFF records
+ */
+export function gffToInterProResponse(gffRecords) {
+    const resultsMap = gffToInterProResults(gffRecords);
+    return {
+        results: Object.values(resultsMap),
+    };
+}
+//# sourceMappingURL=gffToInterPro.js.map

package/dist/gff/gffToInterPro.js.map

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package/dist/gff/gffToInterPro.test.d.ts

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+export {};

package/dist/gff/gffToInterPro.test.js

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+import { describe, expect, test } from 'vitest';
+import { gffToInterProResponse, gffToInterProResults } from './gffToInterPro';
+describe('gffToInterProResults', () => {
+    test('converts empty array', () => {
+        expect(gffToInterProResults([])).toEqual({});
+    });
+    test('converts single GFF record', () => {
+        const records = [
+            {
+                seq_id: 'seq1',
+                source: 'Pfam',
+                type: 'protein_match',
+                start: 10,
+                end: 50,
+                score: 0,
+                strand: '.',
+                phase: '.',
+                Name: 'PF00001',
+                signature_desc: '7tm_1',
+                description: 'GPCR family',
+            },
+        ];
+        const result = gffToInterProResults(records);
+        expect(result).toHaveProperty('seq1');
+        expect(result.seq1?.matches).toHaveLength(1);
+        expect(result.seq1?.matches[0]?.signature.entry).toEqual({
+            accession: 'PF00001',
+            name: '7tm_1',
+            description: 'GPCR family',
+        });
+        expect(result.seq1?.matches[0]?.locations).toEqual([{ start: 10, end: 50 }]);
+        expect(result.seq1?.xref).toEqual([{ id: 'seq1' }]);
+    });
+    test('groups multiple records for same sequence', () => {
+        const records = [
+            {
+                seq_id: 'seq1',
+                source: 'Pfam',
+                type: 'protein_match',
+                start: 10,
+                end: 50,
+                score: 0,
+                strand: '.',
+                phase: '.',
+                Name: 'PF00001',
+            },
+            {
+                seq_id: 'seq1',
+                source: 'SMART',
+                type: 'protein_match',
+                start: 60,
+                end: 100,
+                score: 0,
+                strand: '.',
+                phase: '.',
+                Name: 'SM00001',
+            },
+        ];
+        const result = gffToInterProResults(records);
+        expect(Object.keys(result)).toHaveLength(1);
+        expect(result.seq1?.matches).toHaveLength(2);
+    });
+    test('handles multiple sequences', () => {
+        const records = [
+            {
+                seq_id: 'seq1',
+                source: 'Pfam',
+                type: 'protein_match',
+                start: 10,
+                end: 50,
+                score: 0,
+                strand: '.',
+                phase: '.',
+                Name: 'PF00001',
+            },
+            {
+                seq_id: 'seq2',
+                source: 'Pfam',
+                type: 'protein_match',
+                start: 5,
+                end: 40,
+                score: 0,
+                strand: '.',
+                phase: '.',
+                Name: 'PF00002',
+            },
+        ];
+        const result = gffToInterProResults(records);
+        expect(Object.keys(result)).toHaveLength(2);
+        expect(result).toHaveProperty('seq1');
+        expect(result).toHaveProperty('seq2');
+    });
+    test('combines locations for same accession', () => {
+        const records = [
+            {
+                seq_id: 'seq1',
+                source: 'Pfam',
+                type: 'protein_match',
+                start: 10,
+                end: 50,
+                score: 0,
+                strand: '.',
+                phase: '.',
+                Name: 'PF00001',
+            },
+            {
+                seq_id: 'seq1',
+                source: 'Pfam',
+                type: 'protein_match',
+                start: 100,
+                end: 150,
+                score: 0,
+                strand: '.',
+                phase: '.',
+                Name: 'PF00001',
+            },
+        ];
+        const result = gffToInterProResults(records);
+        expect(result.seq1?.matches).toHaveLength(1);
+        expect(result.seq1?.matches[0]?.locations).toHaveLength(2);
+        expect(result.seq1?.matches[0]?.locations).toEqual([
+            { start: 10, end: 50 },
+            { start: 100, end: 150 },
+        ]);
+    });
+    test('uses ID as fallback for Name', () => {
+        const records = [
+            {
+                seq_id: 'seq1',
+                source: 'Source',
+                type: 'protein_match',
+                start: 10,
+                end: 50,
+                score: 0,
+                strand: '.',
+                phase: '.',
+                ID: 'domain_123',
+            },
+        ];
+        const result = gffToInterProResults(records);
+        expect(result.seq1?.matches[0]?.signature.entry?.accession).toBe('domain_123');
+    });
+    test('generates fallback accession from source and positions', () => {
+        const records = [
+            {
+                seq_id: 'seq1',
+                source: 'CustomSource',
+                type: 'protein_match',
+                start: 10,
+                end: 50,
+                score: 0,
+                strand: '.',
+                phase: '.',
+            },
+        ];
+        const result = gffToInterProResults(records);
+        expect(result.seq1?.matches[0]?.signature.entry?.accession).toBe('CustomSource_10_50');
+    });
+});
+describe('gffToInterProResponse', () => {
+    test('wraps results in response format', () => {
+        const records = [
+            {
+                seq_id: 'seq1',
+                source: 'Pfam',
+                type: 'protein_match',
+                start: 10,
+                end: 50,
+                score: 0,
+                strand: '.',
+                phase: '.',
+                Name: 'PF00001',
+            },
+        ];
+        const response = gffToInterProResponse(records);
+        expect(response).toHaveProperty('results');
+        expect(response.results).toHaveLength(1);
+        expect(response.results[0]?.xref[0]?.id).toBe('seq1');
+    });
+});
+//# sourceMappingURL=gffToInterPro.test.js.map

package/dist/gff/gffToInterPro.test.js.map

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

@@ -0,0 +1,3 @@
+export { parseGFF } from './parseGFF';
+export { gffToInterProResponse, gffToInterProResults } from './gffToInterPro';
+export { interProResponseToGFF, interProToGFF } from './interProToGFF';

package/dist/gff/index.js

@@ -0,0 +1,4 @@
+export { parseGFF } from './parseGFF';
+export { gffToInterProResponse, gffToInterProResults } from './gffToInterPro';
+export { interProResponseToGFF, interProToGFF } from './interProToGFF';
+//# sourceMappingURL=index.js.map

package/dist/gff/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/gff/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,qBAAqB,EAAE,oBAAoB,EAAE,MAAM,iBAAiB,CAAA;AAC7E,OAAO,EAAE,qBAAqB,EAAE,aAAa,EAAE,MAAM,iBAAiB,CAAA"}

package/dist/gff/interProToGFF.d.ts

@@ -0,0 +1,9 @@
+import type { InterProScanResults } from '../types';
+/**
+ * Convert InterProScan results to GFF3 format
+ */
+export declare function interProToGFF(results: Record<string, InterProScanResults>): string;
+/**
+ * Convert InterProScan JSON response to GFF3 format
+ */
+export declare function interProResponseToGFF(results: InterProScanResults[]): string;

package/dist/gff/interProToGFF.js

@@ -0,0 +1,48 @@
+/**
+ * Convert InterProScan results to GFF3 format
+ */
+export function interProToGFF(results) {
+    const lines = ['##gff-version 3'];
+    for (const [seqId, data] of Object.entries(results)) {
+        for (const match of data.matches) {
+            const entry = match.signature.entry;
+            if (!entry) {
+                continue;
+            }
+            for (const location of match.locations) {
+                const attributes = [
+                    `Name=${encodeURIComponent(entry.accession)}`,
+                    `signature_desc=${encodeURIComponent(entry.name)}`,
+                    `description=${encodeURIComponent(entry.description)}`,
+                ].join(';');
+                const line = [
+                    seqId,
+                    'InterProScan',
+                    'protein_match',
+                    location.start,
+                    location.end,
+                    '.',
+                    '.',
+                    '.',
+                    attributes,
+                ].join('\t');
+                lines.push(line);
+            }
+        }
+    }
+    return lines.join('\n');
+}
+/**
+ * Convert InterProScan JSON response to GFF3 format
+ */
+export function interProResponseToGFF(results) {
+    const resultsMap = {};
+    for (const result of results) {
+        const seqId = result.xref[0]?.id;
+        if (seqId) {
+            resultsMap[seqId] = result;
+        }
+    }
+    return interProToGFF(resultsMap);
+}
+//# sourceMappingURL=interProToGFF.js.map

package/dist/gff/interProToGFF.js.map

@@ -0,0 +1 @@
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package/dist/gff/interProToGFF.test.d.ts

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

package/dist/gff/interProToGFF.test.js

@@ -0,0 +1,189 @@
+import { describe, expect, test } from 'vitest';
+import { interProResponseToGFF, interProToGFF } from './interProToGFF';
+describe('interProToGFF', () => {
+    test('converts empty results', () => {
+        const gff = interProToGFF({});
+        expect(gff).toBe('##gff-version 3');
+    });
+    test('converts single result', () => {
+        const results = {
+            seq1: {
+                matches: [
+                    {
+                        signature: {
+                            entry: {
+                                accession: 'PF00001',
+                                name: '7tm_1',
+                                description: 'GPCR family',
+                            },
+                        },
+                        locations: [{ start: 10, end: 50 }],
+                    },
+                ],
+                xref: [{ id: 'seq1' }],
+            },
+        };
+        const gff = interProToGFF(results);
+        const lines = gff.split('\n');
+        expect(lines[0]).toBe('##gff-version 3');
+        expect(lines[1]).toContain('seq1');
+        expect(lines[1]).toContain('InterProScan');
+        expect(lines[1]).toContain('protein_match');
+        expect(lines[1]).toContain('10');
+        expect(lines[1]).toContain('50');
+        expect(lines[1]).toContain('Name=PF00001');
+        expect(lines[1]).toContain('signature_desc=7tm_1');
+        expect(lines[1]).toContain('description=GPCR%20family');
+    });
+    test('handles multiple locations', () => {
+        const results = {
+            seq1: {
+                matches: [
+                    {
+                        signature: {
+                            entry: {
+                                accession: 'PF00001',
+                                name: 'domain',
+                                description: 'test',
+                            },
+                        },
+                        locations: [
+                            { start: 10, end: 50 },
+                            { start: 100, end: 150 },
+                        ],
+                    },
+                ],
+                xref: [{ id: 'seq1' }],
+            },
+        };
+        const gff = interProToGFF(results);
+        const lines = gff.split('\n');
+        expect(lines).toHaveLength(3);
+        expect(lines[1]).toContain('10\t50');
+        expect(lines[2]).toContain('100\t150');
+    });
+    test('handles multiple sequences', () => {
+        const results = {
+            seq1: {
+                matches: [
+                    {
+                        signature: {
+                            entry: {
+                                accession: 'PF00001',
+                                name: 'domain1',
+                                description: 'test1',
+                            },
+                        },
+                        locations: [{ start: 10, end: 50 }],
+                    },
+                ],
+                xref: [{ id: 'seq1' }],
+            },
+            seq2: {
+                matches: [
+                    {
+                        signature: {
+                            entry: {
+                                accession: 'PF00002',
+                                name: 'domain2',
+                                description: 'test2',
+                            },
+                        },
+                        locations: [{ start: 5, end: 40 }],
+                    },
+                ],
+                xref: [{ id: 'seq2' }],
+            },
+        };
+        const gff = interProToGFF(results);
+        const lines = gff.split('\n');
+        expect(lines).toHaveLength(3);
+        expect(lines.some(l => l.includes('seq1'))).toBe(true);
+        expect(lines.some(l => l.includes('seq2'))).toBe(true);
+    });
+    test('skips matches without entry', () => {
+        const results = {
+            seq1: {
+                matches: [
+                    {
+                        signature: {},
+                        locations: [{ start: 10, end: 50 }],
+                    },
+                ],
+                xref: [{ id: 'seq1' }],
+            },
+        };
+        const gff = interProToGFF(results);
+        const lines = gff.split('\n');
+        expect(lines).toHaveLength(1);
+        expect(lines[0]).toBe('##gff-version 3');
+    });
+    test('URL-encodes special characters in attributes', () => {
+        const results = {
+            seq1: {
+                matches: [
+                    {
+                        signature: {
+                            entry: {
+                                accession: 'PF00001',
+                                name: 'test;name=value',
+                                description: 'description with spaces',
+                            },
+                        },
+                        locations: [{ start: 10, end: 50 }],
+                    },
+                ],
+                xref: [{ id: 'seq1' }],
+            },
+        };
+        const gff = interProToGFF(results);
+        expect(gff).toContain('signature_desc=test%3Bname%3Dvalue');
+        expect(gff).toContain('description=description%20with%20spaces');
+    });
+});
+describe('interProResponseToGFF', () => {
+    test('converts array of results', () => {
+        const results = [
+            {
+                matches: [
+                    {
+                        signature: {
+                            entry: {
+                                accession: 'PF00001',
+                                name: 'domain',
+                                description: 'test',
+                            },
+                        },
+                        locations: [{ start: 10, end: 50 }],
+                    },
+                ],
+                xref: [{ id: 'seq1' }],
+            },
+        ];
+        const gff = interProResponseToGFF(results);
+        expect(gff).toContain('##gff-version 3');
+        expect(gff).toContain('seq1');
+    });
+    test('handles results without xref', () => {
+        const results = [
+            {
+                matches: [
+                    {
+                        signature: {
+                            entry: {
+                                accession: 'PF00001',
+                                name: 'domain',
+                                description: 'test',
+                            },
+                        },
+                        locations: [{ start: 10, end: 50 }],
+                    },
+                ],
+                xref: [],
+            },
+        ];
+        const gff = interProResponseToGFF(results);
+        expect(gff).toBe('##gff-version 3');
+    });
+});
+//# sourceMappingURL=interProToGFF.test.js.map

package/dist/gff/interProToGFF.test.js.map

@@ -0,0 +1 @@
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package/dist/gff/parseGFF.d.ts

@@ -0,0 +1,2 @@
+import type { GFFRecord } from '../types';
+export declare function parseGFF(str?: string): GFFRecord[];

package/dist/gff/parseGFF.js

@@ -0,0 +1,41 @@
+function parseAttributes(col9) {
+    if (!col9) {
+        return {};
+    }
+    return Object.fromEntries(col9
+        .split(';')
+        .map(f => f.trim())
+        .filter(f => !!f)
+        .map(f => f.split('='))
+        .map(([key, val]) => [
+        key?.trim() ?? '',
+        val ? decodeURIComponent(val).trim().split(',').join(' ') : undefined,
+    ])
+        .filter(([key]) => key !== ''));
+}
+export function parseGFF(str) {
+    if (!str) {
+        return [];
+    }
+    return str
+        .split('\n')
+        .map(f => f.trim())
+        .filter(f => !!f && !f.startsWith('#'))
+        .map(f => {
+        const parts = f.split('\t');
+        const [seq_id, source, type, start, end, score, strand, phase] = parts;
+        const col9 = parts[8];
+        return {
+            seq_id: seq_id ?? '',
+            source: source ?? '',
+            type: type ?? '',
+            start: Number(start) || 0,
+            end: Number(end) || 0,
+            score: Number(score) || 0,
+            strand: strand ?? '.',
+            phase: phase ?? '.',
+            ...parseAttributes(col9),
+        };
+    });
+}
+//# sourceMappingURL=parseGFF.js.map

package/dist/gff/parseGFF.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"parseGFF.js","sourceRoot":"","sources":["../../src/gff/parseGFF.ts"],"names":[],"mappings":"AAEA,SAAS,eAAe,CAAC,IAAa;IACpC,IAAI,CAAC,IAAI,EAAE,CAAC;QACV,OAAO,EAAE,CAAA;IACX,CAAC;IACD,OAAO,MAAM,CAAC,WAAW,CACvB,IAAI;SACD,KAAK,CAAC,GAAG,CAAC;SACV,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;SAClB,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;SAChB,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC;SACtB,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,GAAG,CAAC,EAAE,EAAE,CAAC;QACnB,GAAG,EAAE,IAAI,EAAE,IAAI,EAAE;QACjB,GAAG,CAAC,CAAC,CAAC,kBAAkB,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,SAAS;KACtE,CAAC;SACD,MAAM,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,GAAG,KAAK,EAAE,CAAC,CACjC,CAAA;AACH,CAAC;AAED,MAAM,UAAU,QAAQ,CAAC,GAAY;IACnC,IAAI,CAAC,GAAG,EAAE,CAAC;QACT,OAAO,EAAE,CAAA;IACX,CAAC;IACD,OAAO,GAAG;SACP,KAAK,CAAC,IAAI,CAAC;SACX,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;SAClB,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,UAAU,CAAC,GAAG,CAAC,CAAC;SACtC,GAAG,CAAC,CAAC,CAAC,EAAE;QACP,MAAM,KAAK,GAAG,CAAC,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAC3B,MAAM,CAAC,MAAM,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,EAAE,GAAG,EAAE,KAAK,EAAE,MAAM,EAAE,KAAK,CAAC,GAAG,KAAK,CAAA;QACtE,MAAM,IAAI,GAAG,KAAK,CAAC,CAAC,CAAC,CAAA;QAErB,OAAO;YACL,MAAM,EAAE,MAAM,IAAI,EAAE;YACpB,MAAM,EAAE,MAAM,IAAI,EAAE;YACpB,IAAI,EAAE,IAAI,IAAI,EAAE;YAChB,KAAK,EAAE,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC;YACzB,GAAG,EAAE,MAAM,CAAC,GAAG,CAAC,IAAI,CAAC;YACrB,KAAK,EAAE,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC;YACzB,MAAM,EAAE,MAAM,IAAI,GAAG;YACrB,KAAK,EAAE,KAAK,IAAI,GAAG;YACnB,GAAG,eAAe,CAAC,IAAI,CAAC;SACzB,CAAA;IACH,CAAC,CAAC,CAAA;AACN,CAAC"}

package/dist/gff/parseGFF.test.d.ts

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