msa-parsers 5.0.7 → 5.0.13

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

@@ -1,20 +0,0 @@
-import type { GFFRecord, InterProScanResponse, InterProScanResults } from '../types.ts';
-/**
- * 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/src/gff/gffToInterPro.js

@@ -1,83 +0,0 @@
-/**
- * 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/src/gff/gffToInterPro.js.map

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

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

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

@@ -1,181 +0,0 @@
-import { describe, expect, test } from 'vitest';
-import { gffToInterProResponse, gffToInterProResults } from "./gffToInterPro.js";
-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/src/gff/gffToInterPro.test.js.map

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

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

package/dist/src/gff/index.js

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

package/dist/src/gff/index.js.map

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

@@ -1,9 +0,0 @@
-import type { InterProScanResults } from '../types.ts';
-/**
- * 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/src/gff/interProToGFF.js

@@ -1,48 +0,0 @@
-/**
- * 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/src/gff/interProToGFF.js.map

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

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

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

@@ -1,189 +0,0 @@
-import { describe, expect, test } from 'vitest';
-import { interProResponseToGFF, interProToGFF } from "./interProToGFF.js";
-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/src/gff/interProToGFF.test.js.map

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

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

package/dist/src/gff/parseGFF.js

@@ -1,41 +0,0 @@
-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/src/gff/parseGFF.js.map

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

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