msa-parsers 1.0.6 → 5.0.4
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/LICENSE +21 -0
- package/dist/gff/gffToInterPro.test.d.ts +1 -0
- package/dist/gff/gffToInterPro.test.js +181 -0
- package/dist/gff/gffToInterPro.test.js.map +1 -0
- package/dist/gff/interProToGFF.test.d.ts +1 -0
- package/dist/gff/interProToGFF.test.js +189 -0
- package/dist/gff/interProToGFF.test.js.map +1 -0
- package/dist/gff/parseGFF.test.d.ts +1 -0
- package/dist/gff/parseGFF.test.js +92 -0
- package/dist/gff/parseGFF.test.js.map +1 -0
- package/dist/msa/A3mMSA.test.d.ts +1 -0
- package/dist/msa/A3mMSA.test.js +155 -0
- package/dist/msa/A3mMSA.test.js.map +1 -0
- package/dist/msa/index.test.d.ts +1 -0
- package/dist/msa/index.test.js +60 -0
- package/dist/msa/index.test.js.map +1 -0
- package/dist/msa/stockholmParser.test.d.ts +1 -0
- package/dist/msa/stockholmParser.test.js +111 -0
- package/dist/msa/stockholmParser.test.js.map +1 -0
- package/package.json +8 -8
package/LICENSE
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MIT License
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Copyright (c) 2023 Colin Diesh
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.
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export {};
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import { describe, expect, test } from 'vitest';
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import { gffToInterProResponse, gffToInterProResults } from "./gffToInterPro.js";
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describe('gffToInterProResults', () => {
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test('converts empty array', () => {
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expect(gffToInterProResults([])).toEqual({});
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});
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test('converts single GFF record', () => {
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const records = [
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{
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seq_id: 'seq1',
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source: 'Pfam',
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type: 'protein_match',
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start: 10,
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end: 50,
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score: 0,
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strand: '.',
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phase: '.',
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Name: 'PF00001',
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signature_desc: '7tm_1',
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description: 'GPCR family',
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},
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];
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const result = gffToInterProResults(records);
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expect(result).toHaveProperty('seq1');
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expect(result.seq1?.matches).toHaveLength(1);
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expect(result.seq1?.matches[0]?.signature.entry).toEqual({
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accession: 'PF00001',
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name: '7tm_1',
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description: 'GPCR family',
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});
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expect(result.seq1?.matches[0]?.locations).toEqual([{ start: 10, end: 50 }]);
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expect(result.seq1?.xref).toEqual([{ id: 'seq1' }]);
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});
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test('groups multiple records for same sequence', () => {
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const records = [
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{
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seq_id: 'seq1',
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source: 'Pfam',
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type: 'protein_match',
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start: 10,
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end: 50,
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score: 0,
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strand: '.',
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phase: '.',
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Name: 'PF00001',
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},
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{
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seq_id: 'seq1',
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source: 'SMART',
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type: 'protein_match',
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start: 60,
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end: 100,
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score: 0,
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strand: '.',
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phase: '.',
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Name: 'SM00001',
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},
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];
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const result = gffToInterProResults(records);
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expect(Object.keys(result)).toHaveLength(1);
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expect(result.seq1?.matches).toHaveLength(2);
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});
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test('handles multiple sequences', () => {
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const records = [
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{
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seq_id: 'seq1',
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source: 'Pfam',
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type: 'protein_match',
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start: 10,
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end: 50,
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score: 0,
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strand: '.',
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phase: '.',
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Name: 'PF00001',
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},
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{
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seq_id: 'seq2',
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source: 'Pfam',
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type: 'protein_match',
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start: 5,
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end: 40,
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score: 0,
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strand: '.',
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phase: '.',
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Name: 'PF00002',
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},
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];
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const result = gffToInterProResults(records);
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expect(Object.keys(result)).toHaveLength(2);
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expect(result).toHaveProperty('seq1');
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expect(result).toHaveProperty('seq2');
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});
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test('combines locations for same accession', () => {
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const records = [
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{
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seq_id: 'seq1',
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source: 'Pfam',
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type: 'protein_match',
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start: 10,
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end: 50,
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score: 0,
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strand: '.',
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phase: '.',
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Name: 'PF00001',
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},
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{
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seq_id: 'seq1',
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source: 'Pfam',
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type: 'protein_match',
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start: 100,
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end: 150,
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score: 0,
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strand: '.',
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phase: '.',
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Name: 'PF00001',
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},
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];
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const result = gffToInterProResults(records);
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expect(result.seq1?.matches).toHaveLength(1);
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expect(result.seq1?.matches[0]?.locations).toHaveLength(2);
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expect(result.seq1?.matches[0]?.locations).toEqual([
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{ start: 10, end: 50 },
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{ start: 100, end: 150 },
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]);
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});
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test('uses ID as fallback for Name', () => {
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const records = [
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{
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seq_id: 'seq1',
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source: 'Source',
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type: 'protein_match',
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start: 10,
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end: 50,
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score: 0,
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strand: '.',
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phase: '.',
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ID: 'domain_123',
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},
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];
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const result = gffToInterProResults(records);
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expect(result.seq1?.matches[0]?.signature.entry?.accession).toBe('domain_123');
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});
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test('generates fallback accession from source and positions', () => {
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const records = [
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{
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seq_id: 'seq1',
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source: 'CustomSource',
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type: 'protein_match',
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start: 10,
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end: 50,
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score: 0,
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strand: '.',
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phase: '.',
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},
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];
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const result = gffToInterProResults(records);
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expect(result.seq1?.matches[0]?.signature.entry?.accession).toBe('CustomSource_10_50');
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});
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});
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describe('gffToInterProResponse', () => {
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test('wraps results in response format', () => {
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const records = [
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{
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seq_id: 'seq1',
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source: 'Pfam',
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type: 'protein_match',
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start: 10,
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end: 50,
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score: 0,
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strand: '.',
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phase: '.',
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Name: 'PF00001',
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},
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];
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const response = gffToInterProResponse(records);
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expect(response).toHaveProperty('results');
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expect(response.results).toHaveLength(1);
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expect(response.results[0]?.xref[0]?.id).toBe('seq1');
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});
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});
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//# sourceMappingURL=gffToInterPro.test.js.map
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{"version":3,"file":"gffToInterPro.test.js","sourceRoot":"","sources":["../../src/gff/gffToInterPro.test.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,QAAQ,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,QAAQ,CAAA;AAE/C,OAAO,EAAE,qBAAqB,EAAE,oBAAoB,EAAE,MAAM,oBAAoB,CAAA;AAIhF,QAAQ,CAAC,sBAAsB,EAAE,GAAG,EAAE;IACpC,IAAI,CAAC,sBAAsB,EAAE,GAAG,EAAE;QAChC,MAAM,CAAC,oBAAoB,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,EAAE,CAAC,CAAA;IAC9C,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,4BAA4B,EAAE,GAAG,EAAE;QACtC,MAAM,OAAO,GAAgB;YAC3B;gBACE,MAAM,EAAE,MAAM;gBACd,MAAM,EAAE,MAAM;gBACd,IAAI,EAAE,eAAe;gBACrB,KAAK,EAAE,EAAE;gBACT,GAAG,EAAE,EAAE;gBACP,KAAK,EAAE,CAAC;gBACR,MAAM,EAAE,GAAG;gBACX,KAAK,EAAE,GAAG;gBACV,IAAI,EAAE,SAAS;gBACf,cAAc,EAAE,OAAO;gBACvB,WAAW,EAAE,aAAa;aAC3B;SACF,CAAA;QACD,MAAM,MAAM,GAAG,oBAAoB,CAAC,OAAO,CAAC,CAAA;QAE5C,MAAM,CAAC,MAAM,CAAC,CAAC,cAAc,CAAC,MAAM,CAAC,CAAA;QACrC,MAAM,CAAC,MAAM,CAAC,IAAI,EAAE,OAAO,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,CAAA;QAC5C,MAAM,CAAC,MAAM,CAAC,IAAI,EAAE,OAAO,CAAC,CAAC,CAAC,EAAE,SAAS,CAAC,KAAK,CAAC,CAAC,OAAO,CAAC;YACvD,SAAS,EAAE,SAAS;YACpB,IAAI,EAAE,OAAO;YACb,WAAW,EAAE,aAAa;SAC3B,CAAC,CAAA;QACF,MAAM,CAAC,MAAM,CAAC,IAAI,EAAE,OAAO,CAAC,CAAC,CAAC,EAAE,SAAS,CAAC,CAAC,OAAO,CAAC,CAAC,EAAE,KAAK,EAAE,EAAE,EAAE,GAAG,EAAE,EAAE,EAAE,CAAC,CAAC,CAAA;QAC5E,MAAM,CAAC,MAAM,CAAC,IAAI,EAAE,IAAI,CAAC,CAAC,OAAO,CAAC,CAAC,EAAE,EAAE,EAAE,MAAM,EAAE,CAAC,CAAC,CAAA;IACrD,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,2CAA2C,EAAE,GAAG,EAAE;QACrD,MAAM,OAAO,GAAgB;YAC3B;gBACE,MAAM,EAAE,MAAM;gBACd,MAAM,EAAE,MAAM;gBACd,IAAI,EAAE,eAAe;gBACrB,KAAK,EAAE,EAAE;gBACT,GAAG,EAAE,EAAE;gBACP,KAAK,EAAE,CAAC;gBACR,MAAM,EAAE,GAAG;gBACX,KAAK,EAAE,GAAG;gBACV,IAAI,EAAE,SAAS;aAChB;YACD;gBACE,MAAM,EAAE,MAAM;gBACd,MAAM,EAAE,OAAO;gBACf,IAAI,EAAE,eAAe;gBACrB,KAAK,EAAE,EAAE;gBACT,GAAG,EAAE,GAAG;gBACR,KAAK,EAAE,CAAC;gBACR,MAAM,EAAE,GAAG;gBACX,KAAK,EAAE,GAAG;gBACV,IAAI,EAAE,SAAS;aAChB;SACF,CAAA;QACD,MAAM,MAAM,GAAG,oBAAoB,CAAC,OAAO,CAAC,CAAA;QAE5C,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,CAAA;QAC3C,MAAM,CAAC,MAAM,CAAC,IAAI,EAAE,OAAO,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,CAAA;IAC9C,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,4BAA4B,EAAE,GAAG,EAAE;QACtC,MAAM,OAAO,GAAgB;YAC3B;gBACE,MAAM,EAAE,MAAM;gBACd,MAAM,EAAE,MAAM;gBACd,IAAI,EAAE,eAAe;gBACrB,KAAK,EAAE,EAAE;gBACT,GAAG,EAAE,EAAE;gBACP,KAAK,EAAE,CAAC;gBACR,MAAM,EAAE,GAAG;gBACX,KAAK,EAAE,GAAG;gBACV,IAAI,EAAE,SAAS;aAChB;YACD;gBACE,MAAM,EAAE,MAAM;gBACd,MAAM,EAAE,MAAM;gBACd,IAAI,EAAE,eAAe;gBACrB,KAAK,EAAE,CAAC;gBACR,GAAG,EAAE,EAAE;gBACP,KAAK,EAAE,CAAC;gBACR,MAAM,EAAE,GAAG;gBACX,KAAK,EAAE,GAAG;gBACV,IAAI,EAAE,SAAS;aAChB;SACF,CAAA;QACD,MAAM,MAAM,GAAG,oBAAoB,CAAC,OAAO,CAAC,CAAA;QAE5C,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,CAAA;QAC3C,MAAM,CAAC,MAAM,CAAC,CAAC,cAAc,CAAC,MAAM,CAAC,CAAA;QACrC,MAAM,CAAC,MAAM,CAAC,CAAC,cAAc,CAAC,MAAM,CAAC,CAAA;IACvC,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,uCAAuC,EAAE,GAAG,EAAE;QACjD,MAAM,OAAO,GAAgB;YAC3B;gBACE,MAAM,EAAE,MAAM;gBACd,MAAM,EAAE,MAAM;gBACd,IAAI,EAAE,eAAe;gBACrB,KAAK,EAAE,EAAE;gBACT,GAAG,EAAE,EAAE;gBACP,KAAK,EAAE,CAAC;gBACR,MAAM,EAAE,GAAG;gBACX,KAAK,EAAE,GAAG;gBACV,IAAI,EAAE,SAAS;aAChB;YACD;gBACE,MAAM,EAAE,MAAM;gBACd,MAAM,EAAE,MAAM;gBACd,IAAI,EAAE,eAAe;gBACrB,KAAK,EAAE,GAAG;gBACV,GAAG,EAAE,GAAG;gBACR,KAAK,EAAE,CAAC;gBACR,MAAM,EAAE,GAAG;gBACX,KAAK,EAAE,GAAG;gBACV,IAAI,EAAE,SAAS;aAChB;SACF,CAAA;QACD,MAAM,MAAM,GAAG,oBAAoB,CAAC,OAAO,CAAC,CAAA;QAE5C,MAAM,CAAC,MAAM,CAAC,IAAI,EAAE,OAAO,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,CAAA;QAC5C,MAAM,CAAC,MAAM,CAAC,IAAI,EAAE,OAAO,CAAC,CAAC,CAAC,EAAE,SAAS,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,CAAA;QAC1D,MAAM,CAAC,MAAM,CAAC,IAAI,EAAE,OAAO,CAAC,CAAC,CAAC,EAAE,SAAS,CAAC,CAAC,OAAO,CAAC;YACjD,EAAE,KAAK,EAAE,EAAE,EAAE,GAAG,EAAE,EAAE,EAAE;YACtB,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE;SACzB,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,8BAA8B,EAAE,GAAG,EAAE;QACxC,MAAM,OAAO,GAAgB;YAC3B;gBACE,MAAM,EAAE,MAAM;gBACd,MAAM,EAAE,QAAQ;gBAChB,IAAI,EAAE,eAAe;gBACrB,KAAK,EAAE,EAAE;gBACT,GAAG,EAAE,EAAE;gBACP,KAAK,EAAE,CAAC;gBACR,MAAM,EAAE,GAAG;gBACX,KAAK,EAAE,GAAG;gBACV,EAAE,EAAE,YAAY;aACjB;SACF,CAAA;QACD,MAAM,MAAM,GAAG,oBAAoB,CAAC,OAAO,CAAC,CAAA;QAE5C,MAAM,CAAC,MAAM,CAAC,IAAI,EAAE,OAAO,CAAC,CAAC,CAAC,EAAE,SAAS,CAAC,KAAK,EAAE,SAAS,CAAC,CAAC,IAAI,CAC9D,YAAY,CACb,CAAA;IACH,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,wDAAwD,EAAE,GAAG,EAAE;QAClE,MAAM,OAAO,GAAgB;YAC3B;gBACE,MAAM,EAAE,MAAM;gBACd,MAAM,EAAE,cAAc;gBACtB,IAAI,EAAE,eAAe;gBACrB,KAAK,EAAE,EAAE;gBACT,GAAG,EAAE,EAAE;gBACP,KAAK,EAAE,CAAC;gBACR,MAAM,EAAE,GAAG;gBACX,KAAK,EAAE,GAAG;aACX;SACF,CAAA;QACD,MAAM,MAAM,GAAG,oBAAoB,CAAC,OAAO,CAAC,CAAA;QAE5C,MAAM,CAAC,MAAM,CAAC,IAAI,EAAE,OAAO,CAAC,CAAC,CAAC,EAAE,SAAS,CAAC,KAAK,EAAE,SAAS,CAAC,CAAC,IAAI,CAC9D,oBAAoB,CACrB,CAAA;IACH,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA;AAEF,QAAQ,CAAC,uBAAuB,EAAE,GAAG,EAAE;IACrC,IAAI,CAAC,kCAAkC,EAAE,GAAG,EAAE;QAC5C,MAAM,OAAO,GAAgB;YAC3B;gBACE,MAAM,EAAE,MAAM;gBACd,MAAM,EAAE,MAAM;gBACd,IAAI,EAAE,eAAe;gBACrB,KAAK,EAAE,EAAE;gBACT,GAAG,EAAE,EAAE;gBACP,KAAK,EAAE,CAAC;gBACR,MAAM,EAAE,GAAG;gBACX,KAAK,EAAE,GAAG;gBACV,IAAI,EAAE,SAAS;aAChB;SACF,CAAA;QACD,MAAM,QAAQ,GAAG,qBAAqB,CAAC,OAAO,CAAC,CAAA;QAE/C,MAAM,CAAC,QAAQ,CAAC,CAAC,cAAc,CAAC,SAAS,CAAC,CAAA;QAC1C,MAAM,CAAC,QAAQ,CAAC,OAAO,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,CAAA;QACxC,MAAM,CAAC,QAAQ,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;IACvD,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA"}
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export {};
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1
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import { describe, expect, test } from 'vitest';
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2
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import { interProResponseToGFF, interProToGFF } from "./interProToGFF.js";
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3
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describe('interProToGFF', () => {
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4
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test('converts empty results', () => {
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5
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const gff = interProToGFF({});
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6
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expect(gff).toBe('##gff-version 3');
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7
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});
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8
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test('converts single result', () => {
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9
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const results = {
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10
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seq1: {
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11
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matches: [
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{
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13
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signature: {
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14
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entry: {
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15
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accession: 'PF00001',
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16
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name: '7tm_1',
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17
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description: 'GPCR family',
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18
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},
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19
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},
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locations: [{ start: 10, end: 50 }],
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21
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},
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],
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xref: [{ id: 'seq1' }],
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},
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25
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};
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26
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const gff = interProToGFF(results);
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27
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const lines = gff.split('\n');
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28
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expect(lines[0]).toBe('##gff-version 3');
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29
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expect(lines[1]).toContain('seq1');
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30
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expect(lines[1]).toContain('InterProScan');
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31
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expect(lines[1]).toContain('protein_match');
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32
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expect(lines[1]).toContain('10');
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33
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expect(lines[1]).toContain('50');
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34
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expect(lines[1]).toContain('Name=PF00001');
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35
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expect(lines[1]).toContain('signature_desc=7tm_1');
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36
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expect(lines[1]).toContain('description=GPCR%20family');
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37
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});
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38
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+
test('handles multiple locations', () => {
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39
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const results = {
|
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40
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seq1: {
|
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41
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+
matches: [
|
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42
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{
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43
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signature: {
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44
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entry: {
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45
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accession: 'PF00001',
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46
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name: 'domain',
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47
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description: 'test',
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48
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},
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49
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+
},
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50
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locations: [
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51
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{ start: 10, end: 50 },
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52
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{ start: 100, end: 150 },
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53
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],
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54
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},
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55
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],
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56
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xref: [{ id: 'seq1' }],
|
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57
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+
},
|
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58
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+
};
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59
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+
const gff = interProToGFF(results);
|
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60
|
+
const lines = gff.split('\n');
|
|
61
|
+
expect(lines).toHaveLength(3);
|
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62
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+
expect(lines[1]).toContain('10\t50');
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63
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+
expect(lines[2]).toContain('100\t150');
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64
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+
});
|
|
65
|
+
test('handles multiple sequences', () => {
|
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66
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+
const results = {
|
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67
|
+
seq1: {
|
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68
|
+
matches: [
|
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69
|
+
{
|
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70
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+
signature: {
|
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71
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+
entry: {
|
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72
|
+
accession: 'PF00001',
|
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73
|
+
name: 'domain1',
|
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74
|
+
description: 'test1',
|
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75
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+
},
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76
|
+
},
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77
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+
locations: [{ start: 10, end: 50 }],
|
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78
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+
},
|
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79
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+
],
|
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80
|
+
xref: [{ id: 'seq1' }],
|
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81
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+
},
|
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82
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+
seq2: {
|
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83
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+
matches: [
|
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84
|
+
{
|
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85
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+
signature: {
|
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86
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+
entry: {
|
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87
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+
accession: 'PF00002',
|
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88
|
+
name: 'domain2',
|
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89
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+
description: 'test2',
|
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90
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+
},
|
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91
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+
},
|
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92
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+
locations: [{ start: 5, end: 40 }],
|
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93
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+
},
|
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94
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+
],
|
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95
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+
xref: [{ id: 'seq2' }],
|
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96
|
+
},
|
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97
|
+
};
|
|
98
|
+
const gff = interProToGFF(results);
|
|
99
|
+
const lines = gff.split('\n');
|
|
100
|
+
expect(lines).toHaveLength(3);
|
|
101
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+
expect(lines.some(l => l.includes('seq1'))).toBe(true);
|
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102
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+
expect(lines.some(l => l.includes('seq2'))).toBe(true);
|
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103
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+
});
|
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104
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+
test('skips matches without entry', () => {
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105
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+
const results = {
|
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106
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+
seq1: {
|
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107
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+
matches: [
|
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108
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+
{
|
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109
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+
signature: {},
|
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110
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+
locations: [{ start: 10, end: 50 }],
|
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111
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+
},
|
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112
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+
],
|
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113
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+
xref: [{ id: 'seq1' }],
|
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114
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+
},
|
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115
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+
};
|
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116
|
+
const gff = interProToGFF(results);
|
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117
|
+
const lines = gff.split('\n');
|
|
118
|
+
expect(lines).toHaveLength(1);
|
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119
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+
expect(lines[0]).toBe('##gff-version 3');
|
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120
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+
});
|
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121
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+
test('URL-encodes special characters in attributes', () => {
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122
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+
const results = {
|
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123
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+
seq1: {
|
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124
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+
matches: [
|
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125
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+
{
|
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126
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+
signature: {
|
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127
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+
entry: {
|
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128
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+
accession: 'PF00001',
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129
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+
name: 'test;name=value',
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130
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+
description: 'description with spaces',
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131
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+
},
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132
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+
},
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133
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+
locations: [{ start: 10, end: 50 }],
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134
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+
},
|
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135
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+
],
|
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136
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+
xref: [{ id: 'seq1' }],
|
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137
|
+
},
|
|
138
|
+
};
|
|
139
|
+
const gff = interProToGFF(results);
|
|
140
|
+
expect(gff).toContain('signature_desc=test%3Bname%3Dvalue');
|
|
141
|
+
expect(gff).toContain('description=description%20with%20spaces');
|
|
142
|
+
});
|
|
143
|
+
});
|
|
144
|
+
describe('interProResponseToGFF', () => {
|
|
145
|
+
test('converts array of results', () => {
|
|
146
|
+
const results = [
|
|
147
|
+
{
|
|
148
|
+
matches: [
|
|
149
|
+
{
|
|
150
|
+
signature: {
|
|
151
|
+
entry: {
|
|
152
|
+
accession: 'PF00001',
|
|
153
|
+
name: 'domain',
|
|
154
|
+
description: 'test',
|
|
155
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+
},
|
|
156
|
+
},
|
|
157
|
+
locations: [{ start: 10, end: 50 }],
|
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158
|
+
},
|
|
159
|
+
],
|
|
160
|
+
xref: [{ id: 'seq1' }],
|
|
161
|
+
},
|
|
162
|
+
];
|
|
163
|
+
const gff = interProResponseToGFF(results);
|
|
164
|
+
expect(gff).toContain('##gff-version 3');
|
|
165
|
+
expect(gff).toContain('seq1');
|
|
166
|
+
});
|
|
167
|
+
test('handles results without xref', () => {
|
|
168
|
+
const results = [
|
|
169
|
+
{
|
|
170
|
+
matches: [
|
|
171
|
+
{
|
|
172
|
+
signature: {
|
|
173
|
+
entry: {
|
|
174
|
+
accession: 'PF00001',
|
|
175
|
+
name: 'domain',
|
|
176
|
+
description: 'test',
|
|
177
|
+
},
|
|
178
|
+
},
|
|
179
|
+
locations: [{ start: 10, end: 50 }],
|
|
180
|
+
},
|
|
181
|
+
],
|
|
182
|
+
xref: [],
|
|
183
|
+
},
|
|
184
|
+
];
|
|
185
|
+
const gff = interProResponseToGFF(results);
|
|
186
|
+
expect(gff).toBe('##gff-version 3');
|
|
187
|
+
});
|
|
188
|
+
});
|
|
189
|
+
//# sourceMappingURL=interProToGFF.test.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
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@@ -0,0 +1 @@
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1
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+
export {};
|
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@@ -0,0 +1,92 @@
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|
|
1
|
+
import { describe, expect, test } from 'vitest';
|
|
2
|
+
import { parseGFF } from "./parseGFF.js";
|
|
3
|
+
describe('parseGFF', () => {
|
|
4
|
+
test('parses empty string', () => {
|
|
5
|
+
expect(parseGFF('')).toEqual([]);
|
|
6
|
+
expect(parseGFF(undefined)).toEqual([]);
|
|
7
|
+
});
|
|
8
|
+
test('parses basic GFF3 line', () => {
|
|
9
|
+
const gff = 'seq1\tInterProScan\tprotein_match\t10\t50\t.\t+\t.\tName=PF00001';
|
|
10
|
+
const result = parseGFF(gff);
|
|
11
|
+
expect(result).toHaveLength(1);
|
|
12
|
+
expect(result[0]).toEqual({
|
|
13
|
+
seq_id: 'seq1',
|
|
14
|
+
source: 'InterProScan',
|
|
15
|
+
type: 'protein_match',
|
|
16
|
+
start: 10,
|
|
17
|
+
end: 50,
|
|
18
|
+
score: 0,
|
|
19
|
+
strand: '+',
|
|
20
|
+
phase: '.',
|
|
21
|
+
Name: 'PF00001',
|
|
22
|
+
});
|
|
23
|
+
});
|
|
24
|
+
test('parses multiple attributes', () => {
|
|
25
|
+
const gff = 'seq1\tPfam\tprotein_match\t10\t50\t1.5\t.\t.\tName=PF00001;signature_desc=7tm_1;description=GPCR';
|
|
26
|
+
const result = parseGFF(gff);
|
|
27
|
+
expect(result[0]).toMatchObject({
|
|
28
|
+
Name: 'PF00001',
|
|
29
|
+
signature_desc: '7tm_1',
|
|
30
|
+
description: 'GPCR',
|
|
31
|
+
});
|
|
32
|
+
});
|
|
33
|
+
test('handles URL-encoded attribute values', () => {
|
|
34
|
+
const gff = 'seq1\tSource\ttype\t1\t10\t.\t.\t.\tNote=Hello%20World%3B%3D';
|
|
35
|
+
const result = parseGFF(gff);
|
|
36
|
+
expect(result[0]?.Note).toBe('Hello World;=');
|
|
37
|
+
});
|
|
38
|
+
test('skips comment lines', () => {
|
|
39
|
+
const gff = `##gff-version 3
|
|
40
|
+
# This is a comment
|
|
41
|
+
seq1\tSource\ttype\t1\t10\t.\t.\t.\tName=test`;
|
|
42
|
+
const result = parseGFF(gff);
|
|
43
|
+
expect(result).toHaveLength(1);
|
|
44
|
+
expect(result[0]?.seq_id).toBe('seq1');
|
|
45
|
+
});
|
|
46
|
+
test('skips empty lines', () => {
|
|
47
|
+
const gff = `seq1\tSource\ttype\t1\t10\t.\t.\t.\tName=test1
|
|
48
|
+
|
|
49
|
+
seq2\tSource\ttype\t20\t30\t.\t.\t.\tName=test2`;
|
|
50
|
+
const result = parseGFF(gff);
|
|
51
|
+
expect(result).toHaveLength(2);
|
|
52
|
+
});
|
|
53
|
+
test('handles missing attributes column', () => {
|
|
54
|
+
const gff = 'seq1\tSource\ttype\t1\t10\t.\t.\t.';
|
|
55
|
+
const result = parseGFF(gff);
|
|
56
|
+
expect(result).toHaveLength(1);
|
|
57
|
+
expect(result[0]?.seq_id).toBe('seq1');
|
|
58
|
+
});
|
|
59
|
+
test('handles partial GFF lines gracefully', () => {
|
|
60
|
+
const gff = 'seq1\tSource\ttype';
|
|
61
|
+
const result = parseGFF(gff);
|
|
62
|
+
expect(result).toHaveLength(1);
|
|
63
|
+
expect(result[0]).toMatchObject({
|
|
64
|
+
seq_id: 'seq1',
|
|
65
|
+
source: 'Source',
|
|
66
|
+
type: 'type',
|
|
67
|
+
start: 0,
|
|
68
|
+
end: 0,
|
|
69
|
+
});
|
|
70
|
+
});
|
|
71
|
+
test('parses numeric score', () => {
|
|
72
|
+
const gff = 'seq1\tSource\ttype\t1\t10\t45.6\t.\t.\tName=test';
|
|
73
|
+
const result = parseGFF(gff);
|
|
74
|
+
expect(result[0]?.score).toBe(45.6);
|
|
75
|
+
});
|
|
76
|
+
test('handles comma-separated values in attributes', () => {
|
|
77
|
+
const gff = 'seq1\tSource\ttype\t1\t10\t.\t.\t.\tOntology_term=GO:0001,GO:0002';
|
|
78
|
+
const result = parseGFF(gff);
|
|
79
|
+
expect(result[0]?.Ontology_term).toBe('GO:0001 GO:0002');
|
|
80
|
+
});
|
|
81
|
+
test('parses multiple lines', () => {
|
|
82
|
+
const gff = `seq1\tPfam\tprotein_match\t10\t50\t.\t.\t.\tName=PF00001
|
|
83
|
+
seq1\tSMART\tprotein_match\t60\t100\t.\t.\t.\tName=SM00001
|
|
84
|
+
seq2\tPfam\tprotein_match\t5\t40\t.\t.\t.\tName=PF00002`;
|
|
85
|
+
const result = parseGFF(gff);
|
|
86
|
+
expect(result).toHaveLength(3);
|
|
87
|
+
expect(result[0]?.seq_id).toBe('seq1');
|
|
88
|
+
expect(result[1]?.seq_id).toBe('seq1');
|
|
89
|
+
expect(result[2]?.seq_id).toBe('seq2');
|
|
90
|
+
});
|
|
91
|
+
});
|
|
92
|
+
//# sourceMappingURL=parseGFF.test.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"parseGFF.test.js","sourceRoot":"","sources":["../../src/gff/parseGFF.test.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,QAAQ,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,QAAQ,CAAA;AAE/C,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAExC,QAAQ,CAAC,UAAU,EAAE,GAAG,EAAE;IACxB,IAAI,CAAC,qBAAqB,EAAE,GAAG,EAAE;QAC/B,MAAM,CAAC,QAAQ,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,EAAE,CAAC,CAAA;QAChC,MAAM,CAAC,QAAQ,CAAC,SAAS,CAAC,CAAC,CAAC,OAAO,CAAC,EAAE,CAAC,CAAA;IACzC,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,wBAAwB,EAAE,GAAG,EAAE;QAClC,MAAM,GAAG,GACP,kEAAkE,CAAA;QACpE,MAAM,MAAM,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAA;QAC5B,MAAM,CAAC,MAAM,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,CAAA;QAC9B,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC;YACxB,MAAM,EAAE,MAAM;YACd,MAAM,EAAE,cAAc;YACtB,IAAI,EAAE,eAAe;YACrB,KAAK,EAAE,EAAE;YACT,GAAG,EAAE,EAAE;YACP,KAAK,EAAE,CAAC;YACR,MAAM,EAAE,GAAG;YACX,KAAK,EAAE,GAAG;YACV,IAAI,EAAE,SAAS;SAChB,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,4BAA4B,EAAE,GAAG,EAAE;QACtC,MAAM,GAAG,GACP,kGAAkG,CAAA;QACpG,MAAM,MAAM,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAA;QAC5B,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,aAAa,CAAC;YAC9B,IAAI,EAAE,SAAS;YACf,cAAc,EAAE,OAAO;YACvB,WAAW,EAAE,MAAM;SACpB,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,sCAAsC,EAAE,GAAG,EAAE;QAChD,MAAM,GAAG,GAAG,8DAA8D,CAAA;QAC1E,MAAM,MAAM,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAA;QAC5B,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,IAAI,CAAC,CAAC,IAAI,CAAC,eAAe,CAAC,CAAA;IAC/C,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,qBAAqB,EAAE,GAAG,EAAE;QAC/B,MAAM,GAAG,GAAG;;8CAE8B,CAAA;QAC1C,MAAM,MAAM,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAA;QAC5B,MAAM,CAAC,MAAM,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,CAAA;QAC9B,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,MAAM,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;IACxC,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,mBAAmB,EAAE,GAAG,EAAE;QAC7B,MAAM,GAAG,GAAG;;gDAEgC,CAAA;QAC5C,MAAM,MAAM,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAA;QAC5B,MAAM,CAAC,MAAM,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,CAAA;IAChC,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,mCAAmC,EAAE,GAAG,EAAE;QAC7C,MAAM,GAAG,GAAG,oCAAoC,CAAA;QAChD,MAAM,MAAM,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAA;QAC5B,MAAM,CAAC,MAAM,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,CAAA;QAC9B,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,MAAM,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;IACxC,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,sCAAsC,EAAE,GAAG,EAAE;QAChD,MAAM,GAAG,GAAG,oBAAoB,CAAA;QAChC,MAAM,MAAM,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAA;QAC5B,MAAM,CAAC,MAAM,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,CAAA;QAC9B,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,aAAa,CAAC;YAC9B,MAAM,EAAE,MAAM;YACd,MAAM,EAAE,QAAQ;YAChB,IAAI,EAAE,MAAM;YACZ,KAAK,EAAE,CAAC;YACR,GAAG,EAAE,CAAC;SACP,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,sBAAsB,EAAE,GAAG,EAAE;QAChC,MAAM,GAAG,GAAG,kDAAkD,CAAA;QAC9D,MAAM,MAAM,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAA;QAC5B,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,KAAK,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;IACrC,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,8CAA8C,EAAE,GAAG,EAAE;QACxD,MAAM,GAAG,GACP,mEAAmE,CAAA;QACrE,MAAM,MAAM,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAA;QAC5B,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,aAAa,CAAC,CAAC,IAAI,CAAC,iBAAiB,CAAC,CAAA;IAC1D,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,uBAAuB,EAAE,GAAG,EAAE;QACjC,MAAM,GAAG,GAAG;;wDAEwC,CAAA;QACpD,MAAM,MAAM,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAA;QAC5B,MAAM,CAAC,MAAM,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,CAAA;QAC9B,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,MAAM,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;QACtC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,MAAM,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;QACtC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,MAAM,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;IACxC,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA"}
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1
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+
export {};
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@@ -0,0 +1,155 @@
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1
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+
import { describe, expect, test } from 'vitest';
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2
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+
import A3mMSA from "./A3mMSA.js";
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3
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+
describe('A3mMSA', () => {
|
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4
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+
describe('sniff', () => {
|
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5
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+
test('returns false for non-FASTA text', () => {
|
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6
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+
expect(A3mMSA.sniff('not fasta')).toBe(false);
|
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7
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+
expect(A3mMSA.sniff('CLUSTAL W')).toBe(false);
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8
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+
});
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9
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+
test('returns false for regular FASTA', () => {
|
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10
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+
const fasta = `>seq1
|
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11
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+
ACDEFGHIKLMNPQRSTVWY
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12
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+
>seq2
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13
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+
ACDEFGHIKLMNPQRSTVWY`;
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14
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+
expect(A3mMSA.sniff(fasta)).toBe(false);
|
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15
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+
});
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16
|
+
test('returns true for A3M format', () => {
|
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17
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+
const a3m = `>seq1
|
|
18
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+
ACDEFghiKLMNPQ
|
|
19
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+
>seq2
|
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20
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+
ACDEF---KLMNPQ`;
|
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21
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+
expect(A3mMSA.sniff(a3m)).toBe(true);
|
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22
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+
});
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23
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+
test('returns false for single sequence', () => {
|
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24
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+
const a3m = `>seq1
|
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25
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+
ACDEFghiKLMNPQ`;
|
|
26
|
+
expect(A3mMSA.sniff(a3m)).toBe(false);
|
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27
|
+
});
|
|
28
|
+
});
|
|
29
|
+
describe('parsing', () => {
|
|
30
|
+
test('parses simple A3M', () => {
|
|
31
|
+
const a3m = `>seq1
|
|
32
|
+
ACDEFghiKLMNPQ
|
|
33
|
+
>seq2
|
|
34
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+
ACDEF---KLMNPQ`;
|
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35
|
+
const msa = new A3mMSA(a3m);
|
|
36
|
+
expect(msa.getNames()).toEqual(['seq1', 'seq2']);
|
|
37
|
+
const seq1 = msa.getRow('seq1');
|
|
38
|
+
const seq2 = msa.getRow('seq2');
|
|
39
|
+
expect(seq1.length).toBe(seq2.length);
|
|
40
|
+
expect(seq1).toContain('GHI');
|
|
41
|
+
});
|
|
42
|
+
test('expands lowercase insertions', () => {
|
|
43
|
+
const a3m = `>seq1
|
|
44
|
+
ACabc
|
|
45
|
+
>seq2
|
|
46
|
+
AC---`;
|
|
47
|
+
const msa = new A3mMSA(a3m);
|
|
48
|
+
const seq1 = msa.getRow('seq1');
|
|
49
|
+
const seq2 = msa.getRow('seq2');
|
|
50
|
+
expect(seq1).toBe('ACABC');
|
|
51
|
+
expect(seq2).toBe('AC...');
|
|
52
|
+
});
|
|
53
|
+
test('handles multiple insertions', () => {
|
|
54
|
+
const a3m = `>seq1
|
|
55
|
+
AabcDdefG
|
|
56
|
+
>seq2
|
|
57
|
+
A---D---G`;
|
|
58
|
+
const msa = new A3mMSA(a3m);
|
|
59
|
+
const seq1 = msa.getRow('seq1');
|
|
60
|
+
const seq2 = msa.getRow('seq2');
|
|
61
|
+
expect(seq1.length).toBe(seq2.length);
|
|
62
|
+
});
|
|
63
|
+
test('getWidth returns correct width', () => {
|
|
64
|
+
const a3m = `>seq1
|
|
65
|
+
ACDEF
|
|
66
|
+
>seq2
|
|
67
|
+
ACDEF`;
|
|
68
|
+
const msa = new A3mMSA(a3m);
|
|
69
|
+
expect(msa.getWidth()).toBe(5);
|
|
70
|
+
});
|
|
71
|
+
test('getMSA returns seqdata', () => {
|
|
72
|
+
const a3m = `>seq1
|
|
73
|
+
ACDEF
|
|
74
|
+
>seq2
|
|
75
|
+
GHIKL`;
|
|
76
|
+
const msa = new A3mMSA(a3m);
|
|
77
|
+
const data = msa.getMSA();
|
|
78
|
+
expect(data.seqdata).toHaveProperty('seq1');
|
|
79
|
+
expect(data.seqdata).toHaveProperty('seq2');
|
|
80
|
+
});
|
|
81
|
+
test('getTree returns noTree structure', () => {
|
|
82
|
+
const a3m = `>seq1
|
|
83
|
+
ACDEF
|
|
84
|
+
>seq2
|
|
85
|
+
GHIKL`;
|
|
86
|
+
const msa = new A3mMSA(a3m);
|
|
87
|
+
const tree = msa.getTree();
|
|
88
|
+
expect(tree.noTree).toBe(true);
|
|
89
|
+
expect(tree.children).toHaveLength(2);
|
|
90
|
+
});
|
|
91
|
+
test('handles empty sequences', () => {
|
|
92
|
+
const a3m = `>seq1
|
|
93
|
+
ACDEF`;
|
|
94
|
+
const msa = new A3mMSA(a3m);
|
|
95
|
+
expect(msa.getNames()).toEqual(['seq1']);
|
|
96
|
+
});
|
|
97
|
+
test('handles sequences with only ID on defline', () => {
|
|
98
|
+
const a3m = `>seq1 description here
|
|
99
|
+
ACDEF
|
|
100
|
+
>seq2 another description
|
|
101
|
+
GHIKL`;
|
|
102
|
+
const msa = new A3mMSA(a3m);
|
|
103
|
+
expect(msa.getNames()).toEqual(['seq1', 'seq2']);
|
|
104
|
+
});
|
|
105
|
+
test('preserves sequence order', () => {
|
|
106
|
+
const a3m = `>z_seq
|
|
107
|
+
AAAAA
|
|
108
|
+
>a_seq
|
|
109
|
+
CCCCC
|
|
110
|
+
>m_seq
|
|
111
|
+
DDDDD`;
|
|
112
|
+
const msa = new A3mMSA(a3m);
|
|
113
|
+
expect(msa.getNames()).toEqual(['z_seq', 'a_seq', 'm_seq']);
|
|
114
|
+
});
|
|
115
|
+
});
|
|
116
|
+
describe('properties', () => {
|
|
117
|
+
test('alignmentNames is empty array', () => {
|
|
118
|
+
const a3m = `>seq1
|
|
119
|
+
ACDEF`;
|
|
120
|
+
const msa = new A3mMSA(a3m);
|
|
121
|
+
expect(msa.alignmentNames).toEqual([]);
|
|
122
|
+
});
|
|
123
|
+
test('seqConsensus is undefined', () => {
|
|
124
|
+
const a3m = `>seq1
|
|
125
|
+
ACDEF`;
|
|
126
|
+
const msa = new A3mMSA(a3m);
|
|
127
|
+
expect(msa.seqConsensus).toBeUndefined();
|
|
128
|
+
});
|
|
129
|
+
test('secondaryStructureConsensus is undefined', () => {
|
|
130
|
+
const a3m = `>seq1
|
|
131
|
+
ACDEF`;
|
|
132
|
+
const msa = new A3mMSA(a3m);
|
|
133
|
+
expect(msa.secondaryStructureConsensus).toBeUndefined();
|
|
134
|
+
});
|
|
135
|
+
test('tracks is empty array', () => {
|
|
136
|
+
const a3m = `>seq1
|
|
137
|
+
ACDEF`;
|
|
138
|
+
const msa = new A3mMSA(a3m);
|
|
139
|
+
expect(msa.tracks).toEqual([]);
|
|
140
|
+
});
|
|
141
|
+
test('getStructures returns empty object', () => {
|
|
142
|
+
const a3m = `>seq1
|
|
143
|
+
ACDEF`;
|
|
144
|
+
const msa = new A3mMSA(a3m);
|
|
145
|
+
expect(msa.getStructures()).toEqual({});
|
|
146
|
+
});
|
|
147
|
+
test('getHeader returns empty object', () => {
|
|
148
|
+
const a3m = `>seq1
|
|
149
|
+
ACDEF`;
|
|
150
|
+
const msa = new A3mMSA(a3m);
|
|
151
|
+
expect(msa.getHeader()).toEqual({});
|
|
152
|
+
});
|
|
153
|
+
});
|
|
154
|
+
});
|
|
155
|
+
//# sourceMappingURL=A3mMSA.test.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"A3mMSA.test.js","sourceRoot":"","sources":["../../src/msa/A3mMSA.test.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,QAAQ,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,QAAQ,CAAA;AAE/C,OAAO,MAAM,MAAM,aAAa,CAAA;AAEhC,QAAQ,CAAC,QAAQ,EAAE,GAAG,EAAE;IACtB,QAAQ,CAAC,OAAO,EAAE,GAAG,EAAE;QACrB,IAAI,CAAC,kCAAkC,EAAE,GAAG,EAAE;YAC5C,MAAM,CAAC,MAAM,CAAC,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;YAC7C,MAAM,CAAC,MAAM,CAAC,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;QAC/C,CAAC,CAAC,CAAA;QAEF,IAAI,CAAC,iCAAiC,EAAE,GAAG,EAAE;YAC3C,MAAM,KAAK,GAAG;;;qBAGC,CAAA;YACf,MAAM,CAAC,MAAM,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;QACzC,CAAC,CAAC,CAAA;QAEF,IAAI,CAAC,6BAA6B,EAAE,GAAG,EAAE;YACvC,MAAM,GAAG,GAAG;;;eAGH,CAAA;YACT,MAAM,CAAC,MAAM,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QACtC,CAAC,CAAC,CAAA;QAEF,IAAI,CAAC,mCAAmC,EAAE,GAAG,EAAE;YAC7C,MAAM,GAAG,GAAG;eACH,CAAA;YACT,MAAM,CAAC,MAAM,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;QACvC,CAAC,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;IAEF,QAAQ,CAAC,SAAS,EAAE,GAAG,EAAE;QACvB,IAAI,CAAC,mBAAmB,EAAE,GAAG,EAAE;YAC7B,MAAM,GAAG,GAAG;;;eAGH,CAAA;YACT,MAAM,GAAG,GAAG,IAAI,MAAM,CAAC,GAAG,CAAC,CAAA;YAE3B,MAAM,CAAC,GAAG,CAAC,QAAQ,EAAE,CAAC,CAAC,OAAO,CAAC,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC,CAAA;YAChD,MAAM,IAAI,GAAG,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;YAC/B,MAAM,IAAI,GAAG,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;YAE/B,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;YACrC,MAAM,CAAC,IAAI,CAAC,CAAC,SAAS,CAAC,KAAK,CAAC,CAAA;QAC/B,CAAC,CAAC,CAAA;QAEF,IAAI,CAAC,8BAA8B,EAAE,GAAG,EAAE;YACxC,MAAM,GAAG,GAAG;;;MAGZ,CAAA;YACA,MAAM,GAAG,GAAG,IAAI,MAAM,CAAC,GAAG,CAAC,CAAA;YAE3B,MAAM,IAAI,GAAG,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;YAC/B,MAAM,IAAI,GAAG,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;YAE/B,MAAM,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;YAC1B,MAAM,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;QAC5B,CAAC,CAAC,CAAA;QAEF,IAAI,CAAC,6BAA6B,EAAE,GAAG,EAAE;YACvC,MAAM,GAAG,GAAG;;;UAGR,CAAA;YACJ,MAAM,GAAG,GAAG,IAAI,MAAM,CAAC,GAAG,CAAC,CAAA;YAE3B,MAAM,IAAI,GAAG,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;YAC/B,MAAM,IAAI,GAAG,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;YAE/B,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;QACvC,CAAC,CAAC,CAAA;QAEF,IAAI,CAAC,gCAAgC,EAAE,GAAG,EAAE;YAC1C,MAAM,GAAG,GAAG;;;MAGZ,CAAA;YACA,MAAM,GAAG,GAAG,IAAI,MAAM,CAAC,GAAG,CAAC,CAAA;YAE3B,MAAM,CAAC,GAAG,CAAC,QAAQ,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;QAChC,CAAC,CAAC,CAAA;QAEF,IAAI,CAAC,wBAAwB,EAAE,GAAG,EAAE;YAClC,MAAM,GAAG,GAAG;;;MAGZ,CAAA;YACA,MAAM,GAAG,GAAG,IAAI,MAAM,CAAC,GAAG,CAAC,CAAA;YAC3B,MAAM,IAAI,GAAG,GAAG,CAAC,MAAM,EAAE,CAAA;YAEzB,MAAM,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,cAAc,CAAC,MAAM,CAAC,CAAA;YAC3C,MAAM,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,cAAc,CAAC,MAAM,CAAC,CAAA;QAC7C,CAAC,CAAC,CAAA;QAEF,IAAI,CAAC,kCAAkC,EAAE,GAAG,EAAE;YAC5C,MAAM,GAAG,GAAG;;;MAGZ,CAAA;YACA,MAAM,GAAG,GAAG,IAAI,MAAM,CAAC,GAAG,CAAC,CAAA;YAC3B,MAAM,IAAI,GAAG,GAAG,CAAC,OAAO,EAAE,CAAA;YAE1B,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;YAC9B,MAAM,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,CAAA;QACvC,CAAC,CAAC,CAAA;QAEF,IAAI,CAAC,yBAAyB,EAAE,GAAG,EAAE;YACnC,MAAM,GAAG,GAAG;MACZ,CAAA;YACA,MAAM,GAAG,GAAG,IAAI,MAAM,CAAC,GAAG,CAAC,CAAA;YAE3B,MAAM,CAAC,GAAG,CAAC,QAAQ,EAAE,CAAC,CAAC,OAAO,CAAC,CAAC,MAAM,CAAC,CAAC,CAAA;QAC1C,CAAC,CAAC,CAAA;QAEF,IAAI,CAAC,2CAA2C,EAAE,GAAG,EAAE;YACrD,MAAM,GAAG,GAAG;;;MAGZ,CAAA;YACA,MAAM,GAAG,GAAG,IAAI,MAAM,CAAC,GAAG,CAAC,CAAA;YAE3B,MAAM,CAAC,GAAG,CAAC,QAAQ,EAAE,CAAC,CAAC,OAAO,CAAC,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC,CAAA;QAClD,CAAC,CAAC,CAAA;QAEF,IAAI,CAAC,0BAA0B,EAAE,GAAG,EAAE;YACpC,MAAM,GAAG,GAAG;;;;;MAKZ,CAAA;YACA,MAAM,GAAG,GAAG,IAAI,MAAM,CAAC,GAAG,CAAC,CAAA;YAE3B,MAAM,CAAC,GAAG,CAAC,QAAQ,EAAE,CAAC,CAAC,OAAO,CAAC,CAAC,OAAO,EAAE,OAAO,EAAE,OAAO,CAAC,CAAC,CAAA;QAC7D,CAAC,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;IAEF,QAAQ,CAAC,YAAY,EAAE,GAAG,EAAE;QAC1B,IAAI,CAAC,+BAA+B,EAAE,GAAG,EAAE;YACzC,MAAM,GAAG,GAAG;MACZ,CAAA;YACA,MAAM,GAAG,GAAG,IAAI,MAAM,CAAC,GAAG,CAAC,CAAA;YAE3B,MAAM,CAAC,GAAG,CAAC,cAAc,CAAC,CAAC,OAAO,CAAC,EAAE,CAAC,CAAA;QACxC,CAAC,CAAC,CAAA;QAEF,IAAI,CAAC,2BAA2B,EAAE,GAAG,EAAE;YACrC,MAAM,GAAG,GAAG;MACZ,CAAA;YACA,MAAM,GAAG,GAAG,IAAI,MAAM,CAAC,GAAG,CAAC,CAAA;YAE3B,MAAM,CAAC,GAAG,CAAC,YAAY,CAAC,CAAC,aAAa,EAAE,CAAA;QAC1C,CAAC,CAAC,CAAA;QAEF,IAAI,CAAC,0CAA0C,EAAE,GAAG,EAAE;YACpD,MAAM,GAAG,GAAG;MACZ,CAAA;YACA,MAAM,GAAG,GAAG,IAAI,MAAM,CAAC,GAAG,CAAC,CAAA;YAE3B,MAAM,CAAC,GAAG,CAAC,2BAA2B,CAAC,CAAC,aAAa,EAAE,CAAA;QACzD,CAAC,CAAC,CAAA;QAEF,IAAI,CAAC,uBAAuB,EAAE,GAAG,EAAE;YACjC,MAAM,GAAG,GAAG;MACZ,CAAA;YACA,MAAM,GAAG,GAAG,IAAI,MAAM,CAAC,GAAG,CAAC,CAAA;YAE3B,MAAM,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC,OAAO,CAAC,EAAE,CAAC,CAAA;QAChC,CAAC,CAAC,CAAA;QAEF,IAAI,CAAC,oCAAoC,EAAE,GAAG,EAAE;YAC9C,MAAM,GAAG,GAAG;MACZ,CAAA;YACA,MAAM,GAAG,GAAG,IAAI,MAAM,CAAC,GAAG,CAAC,CAAA;YAE3B,MAAM,CAAC,GAAG,CAAC,aAAa,EAAE,CAAC,CAAC,OAAO,CAAC,EAAE,CAAC,CAAA;QACzC,CAAC,CAAC,CAAA;QAEF,IAAI,CAAC,gCAAgC,EAAE,GAAG,EAAE;YAC1C,MAAM,GAAG,GAAG;MACZ,CAAA;YACA,MAAM,GAAG,GAAG,IAAI,MAAM,CAAC,GAAG,CAAC,CAAA;YAE3B,MAAM,CAAC,GAAG,CAAC,SAAS,EAAE,CAAC,CAAC,OAAO,CAAC,EAAE,CAAC,CAAA;QACrC,CAAC,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA"}
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
export {};
|
|
@@ -0,0 +1,60 @@
|
|
|
1
|
+
import { describe, expect, test } from 'vitest';
|
|
2
|
+
import A3mMSA from "./A3mMSA.js";
|
|
3
|
+
import ClustalMSA from "./ClustalMSA.js";
|
|
4
|
+
import FastaMSA from "./FastaMSA.js";
|
|
5
|
+
import { getUngappedSequence, parseMSA } from "./index.js";
|
|
6
|
+
describe('parseMSA', () => {
|
|
7
|
+
test('parses FASTA format', () => {
|
|
8
|
+
const fasta = `>seq1
|
|
9
|
+
ACDEF
|
|
10
|
+
>seq2
|
|
11
|
+
GHIKL`;
|
|
12
|
+
const msa = parseMSA(fasta);
|
|
13
|
+
expect(msa).toBeInstanceOf(FastaMSA);
|
|
14
|
+
expect(msa.getNames()).toEqual(['seq1', 'seq2']);
|
|
15
|
+
});
|
|
16
|
+
test('parses A3M format', () => {
|
|
17
|
+
const a3m = `>seq1
|
|
18
|
+
ACDEFghiKLMNPQ
|
|
19
|
+
>seq2
|
|
20
|
+
ACDEF---KLMNPQ`;
|
|
21
|
+
const msa = parseMSA(a3m);
|
|
22
|
+
expect(msa).toBeInstanceOf(A3mMSA);
|
|
23
|
+
});
|
|
24
|
+
test('parses Clustal format', () => {
|
|
25
|
+
const clustal = `CLUSTAL W (1.83) multiple sequence alignment
|
|
26
|
+
|
|
27
|
+
seq1 ACDEFGHIKL
|
|
28
|
+
seq2 ACDEFGHIKL
|
|
29
|
+
**********`;
|
|
30
|
+
const msa = parseMSA(clustal);
|
|
31
|
+
expect(msa).toBeInstanceOf(ClustalMSA);
|
|
32
|
+
});
|
|
33
|
+
test('defaults to Clustal for unknown format', () => {
|
|
34
|
+
const unknown = `some unknown format
|
|
35
|
+
that doesn't match anything`;
|
|
36
|
+
const msa = parseMSA(unknown);
|
|
37
|
+
expect(msa).toBeInstanceOf(ClustalMSA);
|
|
38
|
+
});
|
|
39
|
+
});
|
|
40
|
+
describe('getUngappedSequence', () => {
|
|
41
|
+
test('removes dashes', () => {
|
|
42
|
+
expect(getUngappedSequence('AC--DEF')).toBe('ACDEF');
|
|
43
|
+
});
|
|
44
|
+
test('removes dots', () => {
|
|
45
|
+
expect(getUngappedSequence('AC..DEF')).toBe('ACDEF');
|
|
46
|
+
});
|
|
47
|
+
test('removes mixed gaps', () => {
|
|
48
|
+
expect(getUngappedSequence('A-C.D--E..F')).toBe('ACDEF');
|
|
49
|
+
});
|
|
50
|
+
test('handles empty string', () => {
|
|
51
|
+
expect(getUngappedSequence('')).toBe('');
|
|
52
|
+
});
|
|
53
|
+
test('handles string with only gaps', () => {
|
|
54
|
+
expect(getUngappedSequence('---...')).toBe('');
|
|
55
|
+
});
|
|
56
|
+
test('handles string with no gaps', () => {
|
|
57
|
+
expect(getUngappedSequence('ACDEF')).toBe('ACDEF');
|
|
58
|
+
});
|
|
59
|
+
});
|
|
60
|
+
//# sourceMappingURL=index.test.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"index.test.js","sourceRoot":"","sources":["../../src/msa/index.test.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,QAAQ,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,QAAQ,CAAA;AAE/C,OAAO,MAAM,MAAM,aAAa,CAAA;AAChC,OAAO,UAAU,MAAM,iBAAiB,CAAA;AACxC,OAAO,QAAQ,MAAM,eAAe,CAAA;AACpC,OAAO,EAAE,mBAAmB,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAE1D,QAAQ,CAAC,UAAU,EAAE,GAAG,EAAE;IACxB,IAAI,CAAC,qBAAqB,EAAE,GAAG,EAAE;QAC/B,MAAM,KAAK,GAAG;;;MAGZ,CAAA;QACF,MAAM,GAAG,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;QAE3B,MAAM,CAAC,GAAG,CAAC,CAAC,cAAc,CAAC,QAAQ,CAAC,CAAA;QACpC,MAAM,CAAC,GAAG,CAAC,QAAQ,EAAE,CAAC,CAAC,OAAO,CAAC,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC,CAAA;IAClD,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,mBAAmB,EAAE,GAAG,EAAE;QAC7B,MAAM,GAAG,GAAG;;;eAGD,CAAA;QACX,MAAM,GAAG,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAA;QAEzB,MAAM,CAAC,GAAG,CAAC,CAAC,cAAc,CAAC,MAAM,CAAC,CAAA;IACpC,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,uBAAuB,EAAE,GAAG,EAAE;QACjC,MAAM,OAAO,GAAG;;;;qBAIC,CAAA;QACjB,MAAM,GAAG,GAAG,QAAQ,CAAC,OAAO,CAAC,CAAA;QAE7B,MAAM,CAAC,GAAG,CAAC,CAAC,cAAc,CAAC,UAAU,CAAC,CAAA;IACxC,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,wCAAwC,EAAE,GAAG,EAAE;QAClD,MAAM,OAAO,GAAG;4BACQ,CAAA;QACxB,MAAM,GAAG,GAAG,QAAQ,CAAC,OAAO,CAAC,CAAA;QAE7B,MAAM,CAAC,GAAG,CAAC,CAAC,cAAc,CAAC,UAAU,CAAC,CAAA;IACxC,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA;AAEF,QAAQ,CAAC,qBAAqB,EAAE,GAAG,EAAE;IACnC,IAAI,CAAC,gBAAgB,EAAE,GAAG,EAAE;QAC1B,MAAM,CAAC,mBAAmB,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;IACtD,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,cAAc,EAAE,GAAG,EAAE;QACxB,MAAM,CAAC,mBAAmB,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;IACtD,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,oBAAoB,EAAE,GAAG,EAAE;QAC9B,MAAM,CAAC,mBAAmB,CAAC,aAAa,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;IAC1D,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,sBAAsB,EAAE,GAAG,EAAE;QAChC,MAAM,CAAC,mBAAmB,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;IAC1C,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,+BAA+B,EAAE,GAAG,EAAE;QACzC,MAAM,CAAC,mBAAmB,CAAC,QAAQ,CAAC,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;IAChD,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,6BAA6B,EAAE,GAAG,EAAE;QACvC,MAAM,CAAC,mBAAmB,CAAC,OAAO,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;IACpD,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA"}
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
export {};
|
|
@@ -0,0 +1,111 @@
|
|
|
1
|
+
import { describe, expect, test } from 'vitest';
|
|
2
|
+
import { parse, parseAll, sniff } from "./stockholmParser.js";
|
|
3
|
+
describe('stockholmParser', () => {
|
|
4
|
+
describe('sniff', () => {
|
|
5
|
+
test('returns true for Stockholm format', () => {
|
|
6
|
+
expect(sniff('# STOCKHOLM 1.0\n')).toBe(true);
|
|
7
|
+
});
|
|
8
|
+
test('returns false for non-Stockholm format', () => {
|
|
9
|
+
expect(sniff('>seq1\nACDEF')).toBe(false);
|
|
10
|
+
expect(sniff('CLUSTAL W')).toBe(false);
|
|
11
|
+
});
|
|
12
|
+
});
|
|
13
|
+
describe('parseAll', () => {
|
|
14
|
+
test('parses simple Stockholm file', () => {
|
|
15
|
+
const stockholm = `# STOCKHOLM 1.0
|
|
16
|
+
seq1 ACDEFGHIKL
|
|
17
|
+
seq2 ACDEFGHIKL
|
|
18
|
+
//`;
|
|
19
|
+
const result = parseAll(stockholm);
|
|
20
|
+
expect(result).toHaveLength(1);
|
|
21
|
+
expect(result[0]?.seqdata).toEqual({
|
|
22
|
+
seq1: 'ACDEFGHIKL',
|
|
23
|
+
seq2: 'ACDEFGHIKL',
|
|
24
|
+
});
|
|
25
|
+
expect(result[0]?.seqname).toEqual(['seq1', 'seq2']);
|
|
26
|
+
});
|
|
27
|
+
test('parses GF lines', () => {
|
|
28
|
+
const stockholm = `# STOCKHOLM 1.0
|
|
29
|
+
#=GF DE Description of the alignment
|
|
30
|
+
#=GF NH (A:0.1,B:0.2);
|
|
31
|
+
seq1 ACDEF
|
|
32
|
+
//`;
|
|
33
|
+
const result = parseAll(stockholm);
|
|
34
|
+
expect(result[0]?.gf.DE).toEqual(['Description of the alignment']);
|
|
35
|
+
expect(result[0]?.gf.NH).toEqual(['(A:0.1,B:0.2);']);
|
|
36
|
+
});
|
|
37
|
+
test('parses GC lines', () => {
|
|
38
|
+
const stockholm = `# STOCKHOLM 1.0
|
|
39
|
+
seq1 ACDEF
|
|
40
|
+
#=GC seq_cons *****
|
|
41
|
+
#=GC SS_cons <<>>>
|
|
42
|
+
//`;
|
|
43
|
+
const result = parseAll(stockholm);
|
|
44
|
+
expect(result[0]?.gc.seq_cons).toBe('*****');
|
|
45
|
+
expect(result[0]?.gc.SS_cons).toBe('<<>>>');
|
|
46
|
+
});
|
|
47
|
+
test('parses GS lines', () => {
|
|
48
|
+
const stockholm = `# STOCKHOLM 1.0
|
|
49
|
+
#=GS seq1 AC P12345
|
|
50
|
+
#=GS seq1 DR PDB; 1ABC A; 1-100
|
|
51
|
+
seq1 ACDEF
|
|
52
|
+
//`;
|
|
53
|
+
const result = parseAll(stockholm);
|
|
54
|
+
expect(result[0]?.gs.AC?.seq1).toEqual(['P12345']);
|
|
55
|
+
expect(result[0]?.gs.DR?.seq1).toEqual(['PDB; 1ABC A; 1-100']);
|
|
56
|
+
});
|
|
57
|
+
test('parses multiple alignments', () => {
|
|
58
|
+
const stockholm = `# STOCKHOLM 1.0
|
|
59
|
+
seq1 ACDEF
|
|
60
|
+
//
|
|
61
|
+
# STOCKHOLM 1.0
|
|
62
|
+
seq2 GHIKL
|
|
63
|
+
//`;
|
|
64
|
+
const result = parseAll(stockholm);
|
|
65
|
+
expect(result).toHaveLength(2);
|
|
66
|
+
expect(result[0]?.seqdata.seq1).toBe('ACDEF');
|
|
67
|
+
expect(result[1]?.seqdata.seq2).toBe('GHIKL');
|
|
68
|
+
});
|
|
69
|
+
test('concatenates interleaved sequence blocks', () => {
|
|
70
|
+
const stockholm = `# STOCKHOLM 1.0
|
|
71
|
+
seq1 ACDEF
|
|
72
|
+
seq2 GHIKL
|
|
73
|
+
|
|
74
|
+
seq1 MNOPQ
|
|
75
|
+
seq2 RSTUV
|
|
76
|
+
//`;
|
|
77
|
+
const result = parseAll(stockholm);
|
|
78
|
+
expect(result[0]?.seqdata.seq1).toBe('ACDEFMNOPQ');
|
|
79
|
+
expect(result[0]?.seqdata.seq2).toBe('GHIKLRSTUV');
|
|
80
|
+
});
|
|
81
|
+
test('handles file without trailing //', () => {
|
|
82
|
+
const stockholm = `# STOCKHOLM 1.0
|
|
83
|
+
seq1 ACDEF`;
|
|
84
|
+
const result = parseAll(stockholm);
|
|
85
|
+
expect(result).toHaveLength(1);
|
|
86
|
+
expect(result[0]?.seqdata.seq1).toBe('ACDEF');
|
|
87
|
+
});
|
|
88
|
+
});
|
|
89
|
+
describe('parse', () => {
|
|
90
|
+
test('returns single alignment', () => {
|
|
91
|
+
const stockholm = `# STOCKHOLM 1.0
|
|
92
|
+
seq1 ACDEF
|
|
93
|
+
//`;
|
|
94
|
+
const result = parse(stockholm);
|
|
95
|
+
expect(result.seqdata.seq1).toBe('ACDEF');
|
|
96
|
+
});
|
|
97
|
+
test('throws on empty input', () => {
|
|
98
|
+
expect(() => parse('')).toThrow('No alignments found');
|
|
99
|
+
});
|
|
100
|
+
test('throws on multiple alignments', () => {
|
|
101
|
+
const stockholm = `# STOCKHOLM 1.0
|
|
102
|
+
seq1 ACDEF
|
|
103
|
+
//
|
|
104
|
+
# STOCKHOLM 1.0
|
|
105
|
+
seq2 GHIKL
|
|
106
|
+
//`;
|
|
107
|
+
expect(() => parse(stockholm)).toThrow('More than one alignment found');
|
|
108
|
+
});
|
|
109
|
+
});
|
|
110
|
+
});
|
|
111
|
+
//# sourceMappingURL=stockholmParser.test.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"stockholmParser.test.js","sourceRoot":"","sources":["../../src/msa/stockholmParser.test.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,QAAQ,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,QAAQ,CAAA;AAE/C,OAAO,EAAE,KAAK,EAAE,QAAQ,EAAE,KAAK,EAAE,MAAM,sBAAsB,CAAA;AAE7D,QAAQ,CAAC,iBAAiB,EAAE,GAAG,EAAE;IAC/B,QAAQ,CAAC,OAAO,EAAE,GAAG,EAAE;QACrB,IAAI,CAAC,mCAAmC,EAAE,GAAG,EAAE;YAC7C,MAAM,CAAC,KAAK,CAAC,mBAAmB,CAAC,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QAC/C,CAAC,CAAC,CAAA;QAEF,IAAI,CAAC,wCAAwC,EAAE,GAAG,EAAE;YAClD,MAAM,CAAC,KAAK,CAAC,cAAc,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;YACzC,MAAM,CAAC,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;QACxC,CAAC,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;IAEF,QAAQ,CAAC,UAAU,EAAE,GAAG,EAAE;QACxB,IAAI,CAAC,8BAA8B,EAAE,GAAG,EAAE;YACxC,MAAM,SAAS,GAAG;;;GAGrB,CAAA;YACG,MAAM,MAAM,GAAG,QAAQ,CAAC,SAAS,CAAC,CAAA;YAClC,MAAM,CAAC,MAAM,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,CAAA;YAC9B,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,OAAO,CAAC,CAAC,OAAO,CAAC;gBACjC,IAAI,EAAE,YAAY;gBAClB,IAAI,EAAE,YAAY;aACnB,CAAC,CAAA;YACF,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,OAAO,CAAC,CAAC,OAAO,CAAC,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC,CAAA;QACtD,CAAC,CAAC,CAAA;QAEF,IAAI,CAAC,iBAAiB,EAAE,GAAG,EAAE;YAC3B,MAAM,SAAS,GAAG;;;;GAIrB,CAAA;YACG,MAAM,MAAM,GAAG,QAAQ,CAAC,SAAS,CAAC,CAAA;YAClC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,EAAE,CAAC,CAAC,OAAO,CAAC,CAAC,8BAA8B,CAAC,CAAC,CAAA;YAClE,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,EAAE,CAAC,CAAC,OAAO,CAAC,CAAC,gBAAgB,CAAC,CAAC,CAAA;QACtD,CAAC,CAAC,CAAA;QAEF,IAAI,CAAC,iBAAiB,EAAE,GAAG,EAAE;YAC3B,MAAM,SAAS,GAAG;;;;GAIrB,CAAA;YACG,MAAM,MAAM,GAAG,QAAQ,CAAC,SAAS,CAAC,CAAA;YAClC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,QAAQ,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;YAC5C,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,OAAO,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;QAC7C,CAAC,CAAC,CAAA;QAEF,IAAI,CAAC,iBAAiB,EAAE,GAAG,EAAE;YAC3B,MAAM,SAAS,GAAG;;;;GAIrB,CAAA;YACG,MAAM,MAAM,GAAG,QAAQ,CAAC,SAAS,CAAC,CAAA;YAClC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,EAAE,EAAE,IAAI,CAAC,CAAC,OAAO,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAA;YAClD,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,EAAE,EAAE,IAAI,CAAC,CAAC,OAAO,CAAC,CAAC,oBAAoB,CAAC,CAAC,CAAA;QAChE,CAAC,CAAC,CAAA;QAEF,IAAI,CAAC,4BAA4B,EAAE,GAAG,EAAE;YACtC,MAAM,SAAS,GAAG;;;;;GAKrB,CAAA;YACG,MAAM,MAAM,GAAG,QAAQ,CAAC,SAAS,CAAC,CAAA;YAClC,MAAM,CAAC,MAAM,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,CAAA;YAC9B,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,OAAO,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;YAC7C,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,OAAO,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;QAC/C,CAAC,CAAC,CAAA;QAEF,IAAI,CAAC,0CAA0C,EAAE,GAAG,EAAE;YACpD,MAAM,SAAS,GAAG;;;;;;GAMrB,CAAA;YACG,MAAM,MAAM,GAAG,QAAQ,CAAC,SAAS,CAAC,CAAA;YAClC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,OAAO,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,YAAY,CAAC,CAAA;YAClD,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,OAAO,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,YAAY,CAAC,CAAA;QACpD,CAAC,CAAC,CAAA;QAEF,IAAI,CAAC,kCAAkC,EAAE,GAAG,EAAE;YAC5C,MAAM,SAAS,GAAG;YACZ,CAAA;YACN,MAAM,MAAM,GAAG,QAAQ,CAAC,SAAS,CAAC,CAAA;YAClC,MAAM,CAAC,MAAM,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,CAAA;YAC9B,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,OAAO,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;QAC/C,CAAC,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;IAEF,QAAQ,CAAC,OAAO,EAAE,GAAG,EAAE;QACrB,IAAI,CAAC,0BAA0B,EAAE,GAAG,EAAE;YACpC,MAAM,SAAS,GAAG;;GAErB,CAAA;YACG,MAAM,MAAM,GAAG,KAAK,CAAC,SAAS,CAAC,CAAA;YAC/B,MAAM,CAAC,MAAM,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;QAC3C,CAAC,CAAC,CAAA;QAEF,IAAI,CAAC,uBAAuB,EAAE,GAAG,EAAE;YACjC,MAAM,CAAC,GAAG,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,qBAAqB,CAAC,CAAA;QACxD,CAAC,CAAC,CAAA;QAEF,IAAI,CAAC,+BAA+B,EAAE,GAAG,EAAE;YACzC,MAAM,SAAS,GAAG;;;;;GAKrB,CAAA;YACG,MAAM,CAAC,GAAG,EAAE,CAAC,KAAK,CAAC,SAAS,CAAC,CAAC,CAAC,OAAO,CAAC,+BAA+B,CAAC,CAAA;QACzE,CAAC,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA"}
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "msa-parsers",
|
|
3
|
-
"version": "
|
|
3
|
+
"version": "5.0.4",
|
|
4
4
|
"license": "MIT",
|
|
5
5
|
"type": "module",
|
|
6
6
|
"exports": {
|
|
@@ -14,12 +14,6 @@
|
|
|
14
14
|
"dist",
|
|
15
15
|
"src"
|
|
16
16
|
],
|
|
17
|
-
"scripts": {
|
|
18
|
-
"clean": "rimraf dist",
|
|
19
|
-
"build": "tsc",
|
|
20
|
-
"watch": "tsc --watch",
|
|
21
|
-
"test": "vitest"
|
|
22
|
-
},
|
|
23
17
|
"dependencies": {
|
|
24
18
|
"clustal-js": "^2.0.13",
|
|
25
19
|
"emf-js": "^2.0.0"
|
|
@@ -30,5 +24,11 @@
|
|
|
30
24
|
"devDependencies": {
|
|
31
25
|
"typescript": "^5.9.3",
|
|
32
26
|
"vitest": "^4.0.18"
|
|
27
|
+
},
|
|
28
|
+
"scripts": {
|
|
29
|
+
"clean": "rimraf dist",
|
|
30
|
+
"build": "tsc",
|
|
31
|
+
"watch": "tsc --watch",
|
|
32
|
+
"test": "vitest"
|
|
33
33
|
}
|
|
34
|
-
}
|
|
34
|
+
}
|