msa-parsers 1.0.5 → 5.0.3

package/dist/gff/gffToInterPro.test.js

@@ -1,181 +0,0 @@
-import { describe, expect, test } from 'vitest';
-import { gffToInterProResponse, gffToInterProResults } from './gffToInterPro';
-describe('gffToInterProResults', () => {
-    test('converts empty array', () => {
-        expect(gffToInterProResults([])).toEqual({});
-    });
-    test('converts single GFF record', () => {
-        const records = [
-            {
-                seq_id: 'seq1',
-                source: 'Pfam',
-                type: 'protein_match',
-                start: 10,
-                end: 50,
-                score: 0,
-                strand: '.',
-                phase: '.',
-                Name: 'PF00001',
-                signature_desc: '7tm_1',
-                description: 'GPCR family',
-            },
-        ];
-        const result = gffToInterProResults(records);
-        expect(result).toHaveProperty('seq1');
-        expect(result.seq1?.matches).toHaveLength(1);
-        expect(result.seq1?.matches[0]?.signature.entry).toEqual({
-            accession: 'PF00001',
-            name: '7tm_1',
-            description: 'GPCR family',
-        });
-        expect(result.seq1?.matches[0]?.locations).toEqual([{ start: 10, end: 50 }]);
-        expect(result.seq1?.xref).toEqual([{ id: 'seq1' }]);
-    });
-    test('groups multiple records for same sequence', () => {
-        const records = [
-            {
-                seq_id: 'seq1',
-                source: 'Pfam',
-                type: 'protein_match',
-                start: 10,
-                end: 50,
-                score: 0,
-                strand: '.',
-                phase: '.',
-                Name: 'PF00001',
-            },
-            {
-                seq_id: 'seq1',
-                source: 'SMART',
-                type: 'protein_match',
-                start: 60,
-                end: 100,
-                score: 0,
-                strand: '.',
-                phase: '.',
-                Name: 'SM00001',
-            },
-        ];
-        const result = gffToInterProResults(records);
-        expect(Object.keys(result)).toHaveLength(1);
-        expect(result.seq1?.matches).toHaveLength(2);
-    });
-    test('handles multiple sequences', () => {
-        const records = [
-            {
-                seq_id: 'seq1',
-                source: 'Pfam',
-                type: 'protein_match',
-                start: 10,
-                end: 50,
-                score: 0,
-                strand: '.',
-                phase: '.',
-                Name: 'PF00001',
-            },
-            {
-                seq_id: 'seq2',
-                source: 'Pfam',
-                type: 'protein_match',
-                start: 5,
-                end: 40,
-                score: 0,
-                strand: '.',
-                phase: '.',
-                Name: 'PF00002',
-            },
-        ];
-        const result = gffToInterProResults(records);
-        expect(Object.keys(result)).toHaveLength(2);
-        expect(result).toHaveProperty('seq1');
-        expect(result).toHaveProperty('seq2');
-    });
-    test('combines locations for same accession', () => {
-        const records = [
-            {
-                seq_id: 'seq1',
-                source: 'Pfam',
-                type: 'protein_match',
-                start: 10,
-                end: 50,
-                score: 0,
-                strand: '.',
-                phase: '.',
-                Name: 'PF00001',
-            },
-            {
-                seq_id: 'seq1',
-                source: 'Pfam',
-                type: 'protein_match',
-                start: 100,
-                end: 150,
-                score: 0,
-                strand: '.',
-                phase: '.',
-                Name: 'PF00001',
-            },
-        ];
-        const result = gffToInterProResults(records);
-        expect(result.seq1?.matches).toHaveLength(1);
-        expect(result.seq1?.matches[0]?.locations).toHaveLength(2);
-        expect(result.seq1?.matches[0]?.locations).toEqual([
-            { start: 10, end: 50 },
-            { start: 100, end: 150 },
-        ]);
-    });
-    test('uses ID as fallback for Name', () => {
-        const records = [
-            {
-                seq_id: 'seq1',
-                source: 'Source',
-                type: 'protein_match',
-                start: 10,
-                end: 50,
-                score: 0,
-                strand: '.',
-                phase: '.',
-                ID: 'domain_123',
-            },
-        ];
-        const result = gffToInterProResults(records);
-        expect(result.seq1?.matches[0]?.signature.entry?.accession).toBe('domain_123');
-    });
-    test('generates fallback accession from source and positions', () => {
-        const records = [
-            {
-                seq_id: 'seq1',
-                source: 'CustomSource',
-                type: 'protein_match',
-                start: 10,
-                end: 50,
-                score: 0,
-                strand: '.',
-                phase: '.',
-            },
-        ];
-        const result = gffToInterProResults(records);
-        expect(result.seq1?.matches[0]?.signature.entry?.accession).toBe('CustomSource_10_50');
-    });
-});
-describe('gffToInterProResponse', () => {
-    test('wraps results in response format', () => {
-        const records = [
-            {
-                seq_id: 'seq1',
-                source: 'Pfam',
-                type: 'protein_match',
-                start: 10,
-                end: 50,
-                score: 0,
-                strand: '.',
-                phase: '.',
-                Name: 'PF00001',
-            },
-        ];
-        const response = gffToInterProResponse(records);
-        expect(response).toHaveProperty('results');
-        expect(response.results).toHaveLength(1);
-        expect(response.results[0]?.xref[0]?.id).toBe('seq1');
-    });
-});
-//# sourceMappingURL=gffToInterPro.test.js.map

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

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

package/dist/gff/interProToGFF.test.js

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

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

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

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

package/dist/gff/parseGFF.test.js

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

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

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

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

package/dist/msa/A3mMSA.test.js

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

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

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package/dist/msa/index.test.d.ts

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