msa-parsers 5.3.0 → 5.4.0

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Files changed (20) hide show
  1. package/dist/index.d.ts +1 -1
  2. package/dist/msa/A3mMSA.js +8 -0
  3. package/dist/msa/A3mMSA.js.map +1 -1
  4. package/dist/msa/StockholmMSA.js +11 -1
  5. package/dist/msa/StockholmMSA.js.map +1 -1
  6. package/dist/msa/impgIntegration.test.d.ts +1 -0
  7. package/dist/msa/impgIntegration.test.js +49 -0
  8. package/dist/msa/impgIntegration.test.js.map +1 -0
  9. package/dist/msa/index.d.ts +2 -1
  10. package/dist/msa/index.js +20 -1
  11. package/dist/msa/index.js.map +1 -1
  12. package/dist/msa/index.test.js +16 -0
  13. package/dist/msa/index.test.js.map +1 -1
  14. package/package.json +1 -1
  15. package/src/index.ts +1 -1
  16. package/src/msa/A3mMSA.ts +9 -0
  17. package/src/msa/StockholmMSA.ts +11 -1
  18. package/src/msa/impgIntegration.test.ts +57 -0
  19. package/src/msa/index.test.ts +18 -0
  20. package/src/msa/index.ts +26 -1
package/dist/index.d.ts CHANGED
@@ -1,5 +1,5 @@
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  export * from './types.ts';
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  export { generateNodeIds } from './util.ts';
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  export { A3mMSA, ClustalMSA, EmfMSA, FastaMSA, StockholmMSA, getUngappedSequence, parseEmfTree, parseMSA, parseNewick, stockholmSniff, } from './msa/index.ts';
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- export type { MSAParserType } from './msa/index.ts';
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+ export type { MSAFormat, MSAParserType } from './msa/index.ts';
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  export { gffToInterProResponse, gffToInterProResults, interProResponseToGFF, interProToGFF, parseGFF, } from './gff/index.ts';
package/dist/msa/A3mMSA.js CHANGED
@@ -76,6 +76,14 @@ export default class A3mMSA extends BaseMSA {
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  if (seqs.length < 2) {
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  return false;
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  }
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+ // A true aligned FASTA (e.g. impg's fasta-aln output from soft-masked
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+ // references) has all rows the same total length. A3M's defining feature is
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+ // variable-length rows, since lowercase inserts live outside the fixed match
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+ // grid. So equal-length rows are an alignment, not A3M, even when lowercase
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+ // soft-masking is present.
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+ if (new Set(seqs.map(s => s.length)).size === 1) {
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+ return false;
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+ }
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  let hasLowercase = false;
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  let firstMatchLen = -1;
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  let sameMatchLength = true;
package/dist/msa/A3mMSA.js.map CHANGED
@@ -1 +1 @@
1
- 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1
+ 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package/dist/msa/StockholmMSA.js CHANGED
@@ -85,9 +85,19 @@ export default class StockholmMSA extends BaseMSA {
85
85
  id: 'secondaryStruct',
86
86
  name: 'Secondary-structure',
87
87
  data: this.secondaryStructureConsensus,
88
+ // WUSS notation pairs base-paired columns as open/close brackets of
89
+ // several nesting types (<>, (), [], {}); color all opens one way and
90
+ // closes the other so every helix (e.g. the tRNA acceptor stem, which
91
+ // is written with parens) is highlighted, not just the <> arms.
88
92
  customColorScheme: {
89
- '>': 'pink',
90
93
  '<': 'lightblue',
94
+ '(': 'lightblue',
95
+ '[': 'lightblue',
96
+ '{': 'lightblue',
97
+ '>': 'pink',
98
+ ')': 'pink',
99
+ ']': 'pink',
100
+ '}': 'pink',
91
101
  },
92
102
  },
93
103
  ];
package/dist/msa/StockholmMSA.js.map CHANGED
@@ -1 +1 @@
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+ {"version":3,"file":"StockholmMSA.js","sourceRoot":"","sources":["../../src/msa/StockholmMSA.ts"],"names":[],"mappings":"AAAA,OAAO,WAAW,MAAM,kBAAkB,CAAA;AAC1C,OAAO,EAAE,QAAQ,EAAE,MAAM,sBAAsB,CAAA;AAC/C,OAAO,EAAE,eAAe,EAAE,MAAM,YAAY,CAAA;AAC5C,OAAO,OAAO,MAAM,cAAc,CAAA;AAKlC,MAAM,CAAC,OAAO,OAAO,YAAa,SAAQ,OAAO;IACvC,IAAI,CAAiB;IACrB,GAAG,CAAe;IAE1B,YAAY,IAAY,EAAE,gBAAwB;QAChD,KAAK,EAAE,CAAA;QACP,MAAM,GAAG,GAAG,QAAQ,CAAC,IAAI,CAAC,CAAA;QAC1B,IAAI,CAAC,IAAI,GAAG,GAAG,CAAA;QACf,IAAI,CAAC,GAAG,GAAG,GAAG,CAAC,gBAAgB,CAAE,CAAA;IACnC,CAAC;IAED,MAAM;QACJ,OAAO,IAAI,CAAC,GAAG,CAAA;IACjB,CAAC;IAED,MAAM,CAAC,IAAY;QACjB,OAAO,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,IAAI,CAAC,IAAI,EAAE,CAAA;IACrC,CAAC;IAED,QAAQ;QACN,MAAM,IAAI,GAAG,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,CAAE,CAAA;QAC9C,OAAO,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,MAAM,CAAA;IACjC,CAAC;IAED,IAAI,cAAc;QAChB,OAAO,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,GAAG,EAAE,GAAG,EAAE,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,aAAa,GAAG,GAAG,CAAC,EAAE,CAAC,CAAA;IAC9E,CAAC;IAED,SAAS;QACP,MAAM,SAAS,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,IAAI,EAAE,CAAA;QACtC,MAAM,SAAS,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,IAAI,EAAE,CAAA;QACtC,OAAO;YACL,OAAO,EAAE,IAAI,CAAC,GAAG,CAAC,EAAE;YACpB,UAAU,EAAE,MAAM,CAAC,WAAW,CAC5B,MAAM,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CACrD;YACD,MAAM,EAAE,MAAM,CAAC,WAAW,CACxB,MAAM,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,CAC7D;SACF,CAAA;IACH,CAAC;IAED,UAAU,CAAC,OAAe;QACxB,OAAO;YACL,IAAI,EAAE,OAAO;YACb,SAAS,EAAE,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC;YACzC,MAAM,EAAE,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,OAAO,CAAC,EAAE,IAAI,CAAC,IAAI,CAAC;SAC9C,CAAA;IACH,CAAC;IAED,QAAQ;QACN,OAAO,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;IACtC,CAAC;IAED,aAAa;QACX,MAAM,QAAQ,GAAG,sCAAsC,CAAA;QACvD,MAAM,SAAS,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,IAAI,EAAE,CAAA;QACtC,MAAM,MAAM,GAGR,EAAE,CAAA;QACN,KAAK,MAAM,CAAC,EAAE,EAAE,MAAM,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,SAAS,CAAC,EAAE,CAAC;YACrD,KAAK,MAAM,EAAE,IAAI,MAAM,EAAE,CAAC;gBACxB,MAAM,KAAK,GAAG,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;gBAC/B,IAAI,KAAK,EAAE,CAAC;oBACV,CAAC;oBAAA,CAAC,MAAM,CAAC,EAAE,CAAC,KAAK,EAAE,CAAC,CAAC,IAAI,CAAC;wBACxB,GAAG,EAAE,KAAK,CAAC,CAAC,CAAE,CAAC,WAAW,EAAE;wBAC5B,KAAK,EAAE,KAAK,CAAC,CAAC,CAAE;wBAChB,QAAQ,EAAE,CAAC,KAAK,CAAC,CAAC,CAAE;wBACpB,MAAM,EAAE,CAAC,KAAK,CAAC,CAAC,CAAE;qBACnB,CAAC,CAAA;gBACJ,CAAC;YACH,CAAC;QACH,CAAC;QACD,OAAO,MAAM,CAAA;IACf,CAAC;IAED,OAAO;QACL,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAA;QAChC,OAAO,IAAI,CAAC,CAAC,CAAC,eAAe,CAAC,WAAW,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,EAAE,CAAA;IACpE,CAAC;IAED,IAAI,YAAY;QACd,OAAO,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,QAAQ,CAAA;IAC7B,CAAC;IAED,IAAI,2BAA2B;QAC7B,OAAO,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,OAAO,CAAA;IAC5B,CAAC;IAED,IAAI,MAAM;QAMR,OAAO;YACL;gBACE,EAAE,EAAE,cAAc;gBAClB,IAAI,EAAE,oBAAoB;gBAC1B,IAAI,EAAE,IAAI,CAAC,YAAY;gBACvB,iBAAiB,EAAE,EAAE;aACtB;YACD;gBACE,EAAE,EAAE,iBAAiB;gBACrB,IAAI,EAAE,qBAAqB;gBAC3B,IAAI,EAAE,IAAI,CAAC,2BAA2B;gBACtC,oEAAoE;gBACpE,sEAAsE;gBACtE,sEAAsE;gBACtE,gEAAgE;gBAChE,iBAAiB,EAAE;oBACjB,GAAG,EAAE,WAAW;oBAChB,GAAG,EAAE,WAAW;oBAChB,GAAG,EAAE,WAAW;oBAChB,GAAG,EAAE,WAAW;oBAChB,GAAG,EAAE,MAAM;oBACX,GAAG,EAAE,MAAM;oBACX,GAAG,EAAE,MAAM;oBACX,GAAG,EAAE,MAAM;iBACZ;aACF;SACF,CAAA;IACH,CAAC;CACF;AAED,OAAO,EAAE,KAAK,IAAI,cAAc,EAAE,MAAM,sBAAsB,CAAA"}
package/dist/msa/impgIntegration.test.d.ts ADDED
@@ -0,0 +1 @@
1
+ export {};
package/dist/msa/impgIntegration.test.js ADDED
@@ -0,0 +1,49 @@
1
+ import { describe, expect, test } from 'vitest';
2
+ import A3mMSA from "./A3mMSA.js";
3
+ import FastaMSA from "./FastaMSA.js";
4
+ import { parseMSA } from "./index.js";
5
+ // impg (https://github.com/pangenome/impg) pipes `impg query -o fasta-aln` into
6
+ // scripts/faln2html.py, which feeds the FASTA string to
7
+ // MSAModelF().create({ data: { msa } }). These tests pin the behavior that
8
+ // integration relies on.
9
+ describe('impg fasta-aln integration', () => {
10
+ // PanSN-style names + region coordinates with colons, dash gaps, uppercase
11
+ const block = `>HG002#1#chr1:1000-1040
12
+ ACGTACGT--ACGTNNNNACGTACGTACGTACGTACGT
13
+ >HG003#1#chr1:1000-1040
14
+ ACGTAC-TGGACGTNNNNACGTAC--ACGTACGTACGT
15
+ >CHM13#0#chr1:1000-1040
16
+ ACGTACGTGGACGTNNNNACGT----ACGTACGTACGT`;
17
+ test('uppercase block is parsed as FASTA, not A3M/Clustal', () => {
18
+ const msa = parseMSA(block);
19
+ expect(msa).toBeInstanceOf(FastaMSA);
20
+ expect(msa.getNames()).toEqual([
21
+ 'HG002#1#chr1:1000-1040',
22
+ 'HG003#1#chr1:1000-1040',
23
+ 'CHM13#0#chr1:1000-1040',
24
+ ]);
25
+ expect(msa.getWidth()).toBe(38);
26
+ });
27
+ test('rows are retrievable by their colon-containing region name', () => {
28
+ const msa = parseMSA(block);
29
+ expect(msa.getRow('HG002#1#chr1:1000-1040')).toBe('ACGTACGT--ACGTNNNNACGTACGTACGTACGTACGT');
30
+ });
31
+ // If impg extracts from a soft-masked reference FASTA, aligned rows carry
32
+ // lowercase bases. A3M sniff runs before FASTA and triggers on
33
+ // hasLowercase && equal upper+dash match-length across rows -- which these
34
+ // rows satisfy by coincidence. The rows are all the same total length though,
35
+ // so they are a real alignment and must parse as FASTA, not A3M (A3M would
36
+ // strip the lowercase into separate insert columns and break alignment).
37
+ const softMasked = `>HG002#1#chr1:1000-1030
38
+ acgtACGTAC--GTACGTACGTACGTacgt
39
+ >HG003#1#chr1:1000-1030
40
+ ACGTacgtAC--GTACGTacgtACGTACGT`;
41
+ test('soft-masked equal-length block parses as FASTA, not A3M', () => {
42
+ const msa = parseMSA(softMasked);
43
+ expect(msa).toBeInstanceOf(FastaMSA);
44
+ expect(msa).not.toBeInstanceOf(A3mMSA);
45
+ const rows = msa.getNames().map(n => msa.getRow(n));
46
+ expect(new Set(rows.map(r => r.length)).size).toBe(1);
47
+ });
48
+ });
49
+ //# sourceMappingURL=impgIntegration.test.js.map
package/dist/msa/impgIntegration.test.js.map ADDED
@@ -0,0 +1 @@
1
+ {"version":3,"file":"impgIntegration.test.js","sourceRoot":"","sources":["../../src/msa/impgIntegration.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,QAAQ,MAAM,eAAe,CAAA;AACpC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,gFAAgF;AAChF,wDAAwD;AACxD,2EAA2E;AAC3E,yBAAyB;AAEzB,QAAQ,CAAC,4BAA4B,EAAE,GAAG,EAAE;IAC1C,2EAA2E;IAC3E,MAAM,KAAK,GAAG;;;;;uCAKuB,CAAA;IAErC,IAAI,CAAC,qDAAqD,EAAE,GAAG,EAAE;QAC/D,MAAM,GAAG,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;QAC3B,MAAM,CAAC,GAAG,CAAC,CAAC,cAAc,CAAC,QAAQ,CAAC,CAAA;QACpC,MAAM,CAAC,GAAG,CAAC,QAAQ,EAAE,CAAC,CAAC,OAAO,CAAC;YAC7B,wBAAwB;YACxB,wBAAwB;YACxB,wBAAwB;SACzB,CAAC,CAAA;QACF,MAAM,CAAC,GAAG,CAAC,QAAQ,EAAE,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;IACjC,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,4DAA4D,EAAE,GAAG,EAAE;QACtE,MAAM,GAAG,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;QAC3B,MAAM,CAAC,GAAG,CAAC,MAAM,CAAC,wBAAwB,CAAC,CAAC,CAAC,IAAI,CAC/C,wCAAwC,CACzC,CAAA;IACH,CAAC,CAAC,CAAA;IAEF,0EAA0E;IAC1E,+DAA+D;IAC/D,2EAA2E;IAC3E,8EAA8E;IAC9E,2EAA2E;IAC3E,yEAAyE;IACzE,MAAM,UAAU,GAAG;;;+BAGU,CAAA;IAE7B,IAAI,CAAC,yDAAyD,EAAE,GAAG,EAAE;QACnE,MAAM,GAAG,GAAG,QAAQ,CAAC,UAAU,CAAC,CAAA;QAChC,MAAM,CAAC,GAAG,CAAC,CAAC,cAAc,CAAC,QAAQ,CAAC,CAAA;QACpC,MAAM,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,cAAc,CAAC,MAAM,CAAC,CAAA;QACtC,MAAM,IAAI,GAAG,GAAG,CAAC,QAAQ,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAA;QACnD,MAAM,CAAC,IAAI,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;IACvD,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA"}
package/dist/msa/index.d.ts CHANGED
@@ -6,7 +6,8 @@ import StockholmMSA from './StockholmMSA.ts';
6
6
  export { parseEmfTree } from 'emf-js';
7
7
  export { default as parseNewick } from './parseNewick.ts';
8
8
  export type MSAParserType = StockholmMSA | A3mMSA | FastaMSA | EmfMSA | ClustalMSA;
9
- export declare function parseMSA(text: string, currentAlignment?: number): MSAParserType;
9
+ export type MSAFormat = 'stockholm' | 'a3m' | 'fasta' | 'emf' | 'clustal';
10
+ export declare function parseMSA(text: string, currentAlignment?: number, format?: MSAFormat): MSAParserType;
10
11
  /**
11
12
  * Get ungapped sequence from an aligned row
12
13
  */
package/dist/msa/index.js CHANGED
@@ -5,7 +5,26 @@ import FastaMSA from "./FastaMSA.js";
5
5
  import StockholmMSA, { stockholmSniff } from "./StockholmMSA.js";
6
6
  export { parseEmfTree } from 'emf-js';
7
7
  export { default as parseNewick } from "./parseNewick.js";
8
- export function parseMSA(text, currentAlignment = 0) {
8
+ // when `format` is given the heuristic sniffing is bypassed -- callers that
9
+ // already know the format (e.g. impg emitting fasta-aln) can force it rather
10
+ // than rely on auto-detection, which is necessarily ambiguous between formats
11
+ // that share a leading '>' (fasta vs a3m)
12
+ export function parseMSA(text, currentAlignment = 0, format) {
13
+ if (format === 'stockholm') {
14
+ return new StockholmMSA(text, currentAlignment);
15
+ }
16
+ if (format === 'a3m') {
17
+ return new A3mMSA(text);
18
+ }
19
+ if (format === 'fasta') {
20
+ return new FastaMSA(text);
21
+ }
22
+ if (format === 'emf') {
23
+ return new EmfMSA(text);
24
+ }
25
+ if (format === 'clustal') {
26
+ return new ClustalMSA(text);
27
+ }
9
28
  if (stockholmSniff(text)) {
10
29
  return new StockholmMSA(text, currentAlignment);
11
30
  }
package/dist/msa/index.js.map CHANGED
@@ -1 +1 @@
1
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+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/msa/index.ts"],"names":[],"mappings":"AAAA,OAAO,MAAM,MAAM,aAAa,CAAA;AAChC,OAAO,UAAU,MAAM,iBAAiB,CAAA;AACxC,OAAO,MAAM,MAAM,aAAa,CAAA;AAChC,OAAO,QAAQ,MAAM,eAAe,CAAA;AACpC,OAAO,YAAY,EAAE,EAAE,cAAc,EAAE,MAAM,mBAAmB,CAAA;AAEhE,OAAO,EAAE,YAAY,EAAE,MAAM,QAAQ,CAAA;AACrC,OAAO,EAAE,OAAO,IAAI,WAAW,EAAE,MAAM,kBAAkB,CAAA;AAWzD,4EAA4E;AAC5E,6EAA6E;AAC7E,8EAA8E;AAC9E,0CAA0C;AAC1C,MAAM,UAAU,QAAQ,CACtB,IAAY,EACZ,gBAAgB,GAAG,CAAC,EACpB,MAAkB;IAElB,IAAI,MAAM,KAAK,WAAW,EAAE,CAAC;QAC3B,OAAO,IAAI,YAAY,CAAC,IAAI,EAAE,gBAAgB,CAAC,CAAA;IACjD,CAAC;IACD,IAAI,MAAM,KAAK,KAAK,EAAE,CAAC;QACrB,OAAO,IAAI,MAAM,CAAC,IAAI,CAAC,CAAA;IACzB,CAAC;IACD,IAAI,MAAM,KAAK,OAAO,EAAE,CAAC;QACvB,OAAO,IAAI,QAAQ,CAAC,IAAI,CAAC,CAAA;IAC3B,CAAC;IACD,IAAI,MAAM,KAAK,KAAK,EAAE,CAAC;QACrB,OAAO,IAAI,MAAM,CAAC,IAAI,CAAC,CAAA;IACzB,CAAC;IACD,IAAI,MAAM,KAAK,SAAS,EAAE,CAAC;QACzB,OAAO,IAAI,UAAU,CAAC,IAAI,CAAC,CAAA;IAC7B,CAAC;IACD,IAAI,cAAc,CAAC,IAAI,CAAC,EAAE,CAAC;QACzB,OAAO,IAAI,YAAY,CAAC,IAAI,EAAE,gBAAgB,CAAC,CAAA;IACjD,CAAC;IACD,IAAI,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC;QACvB,OAAO,IAAI,MAAM,CAAC,IAAI,CAAC,CAAA;IACzB,CAAC;IACD,IAAI,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE,CAAC;QACzB,OAAO,IAAI,QAAQ,CAAC,IAAI,CAAC,CAAA;IAC3B,CAAC;IACD,IAAI,IAAI,CAAC,UAAU,CAAC,KAAK,CAAC,EAAE,CAAC;QAC3B,OAAO,IAAI,MAAM,CAAC,IAAI,CAAC,CAAA;IACzB,CAAC;IACD,OAAO,IAAI,UAAU,CAAC,IAAI,CAAC,CAAA;AAC7B,CAAC;AAED;;GAEG;AACH,MAAM,UAAU,mBAAmB,CAAC,UAAkB;IACpD,OAAO,UAAU,CAAC,UAAU,CAAC,OAAO,EAAE,EAAE,CAAC,CAAA;AAC3C,CAAC;AAED,OAAO,EAAE,OAAO,IAAI,MAAM,EAAE,MAAM,aAAa,CAAA;AAC/C,OAAO,EAAE,OAAO,IAAI,UAAU,EAAE,MAAM,iBAAiB,CAAA;AACvD,OAAO,EAAE,OAAO,IAAI,MAAM,EAAE,MAAM,aAAa,CAAA;AAC/C,OAAO,EAAE,OAAO,IAAI,QAAQ,EAAE,MAAM,eAAe,CAAA;AACnD,OAAO,EAAE,OAAO,IAAI,YAAY,EAAE,cAAc,EAAE,MAAM,mBAAmB,CAAA"}
package/dist/msa/index.test.js CHANGED
@@ -37,6 +37,22 @@ that doesn't match anything`;
37
37
  const msa = parseMSA(unknown);
38
38
  expect(msa).toBeInstanceOf(ClustalMSA);
39
39
  });
40
+ test('explicit format bypasses auto-detection', () => {
41
+ // a3m-looking input (lowercase inserts, differing row lengths) forced to
42
+ // FASTA, and FASTA-looking input forced to A3M
43
+ const a3mLooking = `>seq1
44
+ ACDEFghiKLMNPQ
45
+ >seq2
46
+ ACDEFKLMNPQ`;
47
+ expect(parseMSA(a3mLooking)).toBeInstanceOf(A3mMSA);
48
+ expect(parseMSA(a3mLooking, 0, 'fasta')).toBeInstanceOf(FastaMSA);
49
+ const fastaLooking = `>seq1
50
+ ACDEF
51
+ >seq2
52
+ GHIKL`;
53
+ expect(parseMSA(fastaLooking)).toBeInstanceOf(FastaMSA);
54
+ expect(parseMSA(fastaLooking, 0, 'a3m')).toBeInstanceOf(A3mMSA);
55
+ });
40
56
  });
41
57
  describe('FastaMSA colon-in-name lookup', () => {
42
58
  const fasta = `>EU105457.1|chr09:67680268..67675529_LTR/Copia
package/dist/msa/index.test.js.map CHANGED
@@ -1 +1 @@
1
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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;AAC1D,OAAO,WAAW,MAAM,kBAAkB,CAAA;AAE1C,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;;;YAGJ,CAAA;QACR,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;IAEF,IAAI,CAAC,yCAAyC,EAAE,GAAG,EAAE;QACnD,yEAAyE;QACzE,+CAA+C;QAC/C,MAAM,UAAU,GAAG;;;YAGX,CAAA;QACR,MAAM,CAAC,QAAQ,CAAC,UAAU,CAAC,CAAC,CAAC,cAAc,CAAC,MAAM,CAAC,CAAA;QACnD,MAAM,CAAC,QAAQ,CAAC,UAAU,EAAE,CAAC,EAAE,OAAO,CAAC,CAAC,CAAC,cAAc,CAAC,QAAQ,CAAC,CAAA;QAEjE,MAAM,YAAY,GAAG;;;MAGnB,CAAA;QACF,MAAM,CAAC,QAAQ,CAAC,YAAY,CAAC,CAAC,CAAC,cAAc,CAAC,QAAQ,CAAC,CAAA;QACvD,MAAM,CAAC,QAAQ,CAAC,YAAY,EAAE,CAAC,EAAE,KAAK,CAAC,CAAC,CAAC,cAAc,CAAC,MAAM,CAAC,CAAA;IACjE,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA;AAEF,QAAQ,CAAC,+BAA+B,EAAE,GAAG,EAAE;IAC7C,MAAM,KAAK,GAAG;;;WAGL,CAAA;IAET,IAAI,CAAC,8CAA8C,EAAE,GAAG,EAAE;QACxD,MAAM,GAAG,GAAG,IAAI,QAAQ,CAAC,KAAK,CAAC,CAAA;QAC/B,MAAM,CAAC,GAAG,CAAC,MAAM,CAAC,+CAA+C,CAAC,CAAC,CAAC,IAAI,CACtE,YAAY,CACb,CAAA;IACH,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,iFAAiF,EAAE,GAAG,EAAE;QAC3F,MAAM,GAAG,GAAG,IAAI,QAAQ,CAAC,KAAK,CAAC,CAAA;QAC/B,MAAM,CAAC,GAAG,CAAC,MAAM,CAAC,+CAA+C,CAAC,CAAC,CAAC,IAAI,CACtE,YAAY,CACb,CAAA;IACH,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,8EAA8E,EAAE,GAAG,EAAE;QACxF,MAAM,GAAG,GAAG,IAAI,QAAQ,CAAC,KAAK,CAAC,CAAA;QAC/B,MAAM,CAAC,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,YAAY,CAAC,CAAA;IAC/C,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA;AAEF,QAAQ,CAAC,4BAA4B,EAAE,GAAG,EAAE;IAC1C,IAAI,CAAC,qDAAqD,EAAE,GAAG,EAAE;QAC/D,MAAM,GAAG,GAAG,IAAI,QAAQ,CAAC,sCAAsC,CAAC,CAAA;QAChE,MAAM,CAAC,GAAG,CAAC,QAAQ,EAAE,CAAC,CAAC,OAAO,CAAC,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC,CAAA;QAChD,MAAM,CAAC,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;IAC1C,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA;AAEF,QAAQ,CAAC,iCAAiC,EAAE,GAAG,EAAE;IAC/C,IAAI,CAAC,uCAAuC,EAAE,GAAG,EAAE;QACjD,MAAM,IAAI,GAAG,WAAW,CACtB,iEAAiE,CAClE,CAAA;QACD,MAAM,KAAK,GAAG,IAAI,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAA0B,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAA;QACvE,MAAM,CAAC,KAAK,CAAC,CAAC,SAAS,CAAC,+CAA+C,CAAC,CAAA;IAC1E,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,8CAA8C,EAAE,GAAG,EAAE;QACxD,MAAM,IAAI,GAAG,WAAW,CAAC,gCAAgC,CAAC,CAAA;QAC1D,MAAM,KAAK,GAAG,IAAI,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAA0B,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAA;QACvE,MAAM,CAAC,KAAK,CAAC,CAAC,SAAS,CAAC,aAAa,CAAC,CAAA;IACxC,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,sCAAsC,EAAE,GAAG,EAAE;QAChD,MAAM,IAAI,GAAG,WAAW,CAAC,sBAAsB,CAAC,CAAA;QAChD,MAAM,KAAK,GAAG,IAAI,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAA0B,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAA;QACvE,MAAM,CAAC,KAAK,CAAC,CAAC,OAAO,CAAC,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC,CAAA;IACzC,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"}
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "msa-parsers",
3
- "version": "5.3.0",
3
+ "version": "5.4.0",
4
4
  "license": "MIT",
5
5
  "type": "module",
6
6
  "repository": {
package/src/index.ts CHANGED
@@ -17,7 +17,7 @@ export {
17
17
  parseNewick,
18
18
  stockholmSniff,
19
19
  } from './msa/index.ts'
20
- export type { MSAParserType } from './msa/index.ts'
20
+ export type { MSAFormat, MSAParserType } from './msa/index.ts'
21
21
 
22
22
  // GFF parsing
23
23
  export {
package/src/msa/A3mMSA.ts CHANGED
@@ -87,6 +87,15 @@ export default class A3mMSA extends BaseMSA {
87
87
  return false
88
88
  }
89
89
 
90
+ // A true aligned FASTA (e.g. impg's fasta-aln output from soft-masked
91
+ // references) has all rows the same total length. A3M's defining feature is
92
+ // variable-length rows, since lowercase inserts live outside the fixed match
93
+ // grid. So equal-length rows are an alignment, not A3M, even when lowercase
94
+ // soft-masking is present.
95
+ if (new Set(seqs.map(s => s.length)).size === 1) {
96
+ return false
97
+ }
98
+
90
99
  let hasLowercase = false
91
100
  let firstMatchLen = -1
92
101
  let sameMatchLength = true
package/src/msa/StockholmMSA.ts CHANGED
@@ -113,9 +113,19 @@ export default class StockholmMSA extends BaseMSA {
113
113
  id: 'secondaryStruct',
114
114
  name: 'Secondary-structure',
115
115
  data: this.secondaryStructureConsensus,
116
+ // WUSS notation pairs base-paired columns as open/close brackets of
117
+ // several nesting types (<>, (), [], {}); color all opens one way and
118
+ // closes the other so every helix (e.g. the tRNA acceptor stem, which
119
+ // is written with parens) is highlighted, not just the <> arms.
116
120
  customColorScheme: {
117
- '>': 'pink',
118
121
  '<': 'lightblue',
122
+ '(': 'lightblue',
123
+ '[': 'lightblue',
124
+ '{': 'lightblue',
125
+ '>': 'pink',
126
+ ')': 'pink',
127
+ ']': 'pink',
128
+ '}': 'pink',
119
129
  },
120
130
  },
121
131
  ]
package/src/msa/impgIntegration.test.ts ADDED
@@ -0,0 +1,57 @@
1
+ import { describe, expect, test } from 'vitest'
2
+
3
+ import A3mMSA from './A3mMSA.ts'
4
+ import FastaMSA from './FastaMSA.ts'
5
+ import { parseMSA } from './index.ts'
6
+
7
+ // impg (https://github.com/pangenome/impg) pipes `impg query -o fasta-aln` into
8
+ // scripts/faln2html.py, which feeds the FASTA string to
9
+ // MSAModelF().create({ data: { msa } }). These tests pin the behavior that
10
+ // integration relies on.
11
+
12
+ describe('impg fasta-aln integration', () => {
13
+ // PanSN-style names + region coordinates with colons, dash gaps, uppercase
14
+ const block = `>HG002#1#chr1:1000-1040
15
+ ACGTACGT--ACGTNNNNACGTACGTACGTACGTACGT
16
+ >HG003#1#chr1:1000-1040
17
+ ACGTAC-TGGACGTNNNNACGTAC--ACGTACGTACGT
18
+ >CHM13#0#chr1:1000-1040
19
+ ACGTACGTGGACGTNNNNACGT----ACGTACGTACGT`
20
+
21
+ test('uppercase block is parsed as FASTA, not A3M/Clustal', () => {
22
+ const msa = parseMSA(block)
23
+ expect(msa).toBeInstanceOf(FastaMSA)
24
+ expect(msa.getNames()).toEqual([
25
+ 'HG002#1#chr1:1000-1040',
26
+ 'HG003#1#chr1:1000-1040',
27
+ 'CHM13#0#chr1:1000-1040',
28
+ ])
29
+ expect(msa.getWidth()).toBe(38)
30
+ })
31
+
32
+ test('rows are retrievable by their colon-containing region name', () => {
33
+ const msa = parseMSA(block)
34
+ expect(msa.getRow('HG002#1#chr1:1000-1040')).toBe(
35
+ 'ACGTACGT--ACGTNNNNACGTACGTACGTACGTACGT',
36
+ )
37
+ })
38
+
39
+ // If impg extracts from a soft-masked reference FASTA, aligned rows carry
40
+ // lowercase bases. A3M sniff runs before FASTA and triggers on
41
+ // hasLowercase && equal upper+dash match-length across rows -- which these
42
+ // rows satisfy by coincidence. The rows are all the same total length though,
43
+ // so they are a real alignment and must parse as FASTA, not A3M (A3M would
44
+ // strip the lowercase into separate insert columns and break alignment).
45
+ const softMasked = `>HG002#1#chr1:1000-1030
46
+ acgtACGTAC--GTACGTACGTACGTacgt
47
+ >HG003#1#chr1:1000-1030
48
+ ACGTacgtAC--GTACGTacgtACGTACGT`
49
+
50
+ test('soft-masked equal-length block parses as FASTA, not A3M', () => {
51
+ const msa = parseMSA(softMasked)
52
+ expect(msa).toBeInstanceOf(FastaMSA)
53
+ expect(msa).not.toBeInstanceOf(A3mMSA)
54
+ const rows = msa.getNames().map(n => msa.getRow(n))
55
+ expect(new Set(rows.map(r => r.length)).size).toBe(1)
56
+ })
57
+ })
package/src/msa/index.test.ts CHANGED
@@ -46,6 +46,24 @@ that doesn't match anything`
46
46
 
47
47
  expect(msa).toBeInstanceOf(ClustalMSA)
48
48
  })
49
+
50
+ test('explicit format bypasses auto-detection', () => {
51
+ // a3m-looking input (lowercase inserts, differing row lengths) forced to
52
+ // FASTA, and FASTA-looking input forced to A3M
53
+ const a3mLooking = `>seq1
54
+ ACDEFghiKLMNPQ
55
+ >seq2
56
+ ACDEFKLMNPQ`
57
+ expect(parseMSA(a3mLooking)).toBeInstanceOf(A3mMSA)
58
+ expect(parseMSA(a3mLooking, 0, 'fasta')).toBeInstanceOf(FastaMSA)
59
+
60
+ const fastaLooking = `>seq1
61
+ ACDEF
62
+ >seq2
63
+ GHIKL`
64
+ expect(parseMSA(fastaLooking)).toBeInstanceOf(FastaMSA)
65
+ expect(parseMSA(fastaLooking, 0, 'a3m')).toBeInstanceOf(A3mMSA)
66
+ })
49
67
  })
50
68
 
51
69
  describe('FastaMSA colon-in-name lookup', () => {
package/src/msa/index.ts CHANGED
@@ -14,7 +14,32 @@ export type MSAParserType =
14
14
  | EmfMSA
15
15
  | ClustalMSA
16
16
 
17
- export function parseMSA(text: string, currentAlignment = 0): MSAParserType {
17
+ export type MSAFormat = 'stockholm' | 'a3m' | 'fasta' | 'emf' | 'clustal'
18
+
19
+ // when `format` is given the heuristic sniffing is bypassed -- callers that
20
+ // already know the format (e.g. impg emitting fasta-aln) can force it rather
21
+ // than rely on auto-detection, which is necessarily ambiguous between formats
22
+ // that share a leading '>' (fasta vs a3m)
23
+ export function parseMSA(
24
+ text: string,
25
+ currentAlignment = 0,
26
+ format?: MSAFormat,
27
+ ): MSAParserType {
28
+ if (format === 'stockholm') {
29
+ return new StockholmMSA(text, currentAlignment)
30
+ }
31
+ if (format === 'a3m') {
32
+ return new A3mMSA(text)
33
+ }
34
+ if (format === 'fasta') {
35
+ return new FastaMSA(text)
36
+ }
37
+ if (format === 'emf') {
38
+ return new EmfMSA(text)
39
+ }
40
+ if (format === 'clustal') {
41
+ return new ClustalMSA(text)
42
+ }
18
43
  if (stockholmSniff(text)) {
19
44
  return new StockholmMSA(text, currentAlignment)
20
45
  }