msa-parsers 5.6.2 → 5.7.0
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/dist/gff/gffToInterPro.test.js +1 -1
- package/dist/gff/index.js +3 -3
- package/dist/gff/interProToGFF.test.js +1 -1
- package/dist/gff/parseGFF.test.js +1 -1
- package/dist/index.d.ts +1 -1
- package/dist/index.js +3 -5
- package/dist/index.js.map +1 -1
- package/dist/msa/A3mMSA.js +1 -1
- package/dist/msa/A3mMSA.test.js +1 -1
- package/dist/msa/BaseMSA.js.map +1 -1
- package/dist/msa/ClustalMSA.js +1 -1
- package/dist/msa/EmfMSA.js +1 -1
- package/dist/msa/FastaMSA.js +1 -1
- package/dist/msa/StockholmMSA.js +5 -5
- package/dist/msa/StockholmMSA.js.map +1 -1
- package/dist/msa/impgIntegration.test.js +3 -3
- package/dist/msa/index.js +11 -11
- package/dist/msa/index.js.map +1 -1
- package/dist/msa/index.test.js +5 -5
- package/dist/msa/parseNewick.js.map +1 -1
- package/dist/msa/stockholmParser.test.js +1 -1
- package/package.json +3 -3
- package/src/index.ts +1 -1
- package/src/msa/BaseMSA.ts +2 -1
- package/src/msa/StockholmMSA.ts +2 -2
- package/src/msa/index.ts +5 -1
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@@ -1,5 +1,5 @@
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import { describe, expect, test } from 'vitest';
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import { gffToInterProResponse, gffToInterProResults } from
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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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package/dist/gff/index.js
CHANGED
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@@ -1,4 +1,4 @@
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export { parseGFF } from
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export { gffToInterProResponse, gffToInterProResults } from
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export { interProResponseToGFF, interProToGFF } from
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export { parseGFF } from './parseGFF.js';
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export { gffToInterProResponse, gffToInterProResults } from './gffToInterPro.js';
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export { interProResponseToGFF, interProToGFF } from './interProToGFF.js';
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//# sourceMappingURL=index.js.map
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@@ -1,5 +1,5 @@
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import { describe, expect, test } from 'vitest';
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import { interProResponseToGFF, interProToGFF } from
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import { interProResponseToGFF, interProToGFF } from './interProToGFF.js';
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describe('interProToGFF', () => {
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test('converts empty results', () => {
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const gff = interProToGFF({});
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package/dist/index.d.ts
CHANGED
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@@ -1,4 +1,4 @@
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export * from './types.ts';
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export type * 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 { MSAFormat, MSAParserType } from './msa/index.ts';
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package/dist/index.js
CHANGED
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// Types
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export * from "./types.js";
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// Utilities
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export { generateNodeIds } from
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export { generateNodeIds } from './util.js';
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// MSA parsers
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export { A3mMSA, ClustalMSA, EmfMSA, FastaMSA, StockholmMSA, getUngappedSequence, parseEmfTree, parseMSA, parseNewick, stockholmSniff, } from
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export { A3mMSA, ClustalMSA, EmfMSA, FastaMSA, StockholmMSA, getUngappedSequence, parseEmfTree, parseMSA, parseNewick, stockholmSniff, } from './msa/index.js';
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// GFF parsing
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export { gffToInterProResponse, gffToInterProResults, interProResponseToGFF, interProToGFF, parseGFF, } from
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export { gffToInterProResponse, gffToInterProResults, interProResponseToGFF, interProToGFF, parseGFF, } from './gff/index.js';
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//# sourceMappingURL=index.js.map
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package/dist/index.js.map
CHANGED
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@@ -1 +1 @@
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{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"
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{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAGA,YAAY;AACZ,OAAO,EAAE,eAAe,EAAE,MAAM,WAAW,CAAA;AAE3C,cAAc;AACd,OAAO,EACL,MAAM,EACN,UAAU,EACV,MAAM,EACN,QAAQ,EACR,YAAY,EACZ,mBAAmB,EACnB,YAAY,EACZ,QAAQ,EACR,WAAW,EACX,cAAc,GACf,MAAM,gBAAgB,CAAA;AAGvB,cAAc;AACd,OAAO,EACL,qBAAqB,EACrB,oBAAoB,EACpB,qBAAqB,EACrB,aAAa,EACb,QAAQ,GACT,MAAM,gBAAgB,CAAA"}
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package/dist/msa/A3mMSA.js
CHANGED
package/dist/msa/A3mMSA.test.js
CHANGED
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import { describe, expect, test } from 'vitest';
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import A3mMSA from
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import A3mMSA from './A3mMSA.js';
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// A3M format rules (see https://yanglab.qd.sdu.edu.cn/trRosetta/msa_format.html):
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//
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// - Uppercase letters = "match columns" (aligned positions shared by all seqs)
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package/dist/msa/BaseMSA.js.map
CHANGED
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{"version":3,"file":"BaseMSA.js","sourceRoot":"","sources":["../../src/msa/BaseMSA.ts"],"names":[],"mappings":"AAEA,MAAM,CAAC,OAAO,OAAgB,OAAO;IAMnC,OAAO;QACL,OAAO;YACL,EAAE,EAAE,MAAM;YACV,IAAI,EAAE,MAAM;YACZ,MAAM,EAAE,IAAI;YACZ,QAAQ,EAAE,IAAI,CAAC,QAAQ,EAAE,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;gBACrC,EAAE,EAAE,IAAI;gBACR,QAAQ,EAAE,EAAE;gBACZ,IAAI;aACL,CAAC,CAAC;SACJ,CAAA;IACH,CAAC;IAED,UAAU,CAAC,KAAa;QACtB,OAAO,
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{"version":3,"file":"BaseMSA.js","sourceRoot":"","sources":["../../src/msa/BaseMSA.ts"],"names":[],"mappings":"AAEA,MAAM,CAAC,OAAO,OAAgB,OAAO;IAMnC,OAAO;QACL,OAAO;YACL,EAAE,EAAE,MAAM;YACV,IAAI,EAAE,MAAM;YACZ,MAAM,EAAE,IAAI;YACZ,QAAQ,EAAE,IAAI,CAAC,QAAQ,EAAE,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;gBACrC,EAAE,EAAE,IAAI;gBACR,QAAQ,EAAE,EAAE;gBACZ,IAAI;aACL,CAAC,CAAC;SACJ,CAAA;IACH,CAAC;IAED,UAAU,CAAC,KAAa;QACtB,OAAO,SAEM,CAAA;IACf,CAAC;IAED,aAAa;QACX,OAAO,EAAE,CAAA;IACX,CAAC;IAED,SAAS;QACP,OAAO,EAAE,CAAA;IACX,CAAC;IAED,IAAI,cAAc;QAChB,OAAO,EAAE,CAAA;IACX,CAAC;IAED,IAAI,YAAY;QACd,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,IAAI,2BAA2B;QAC7B,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,IAAI,MAAM;QAMR,OAAO,EAAE,CAAA;IACX,CAAC;CACF"}
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package/dist/msa/ClustalMSA.js
CHANGED
package/dist/msa/EmfMSA.js
CHANGED
package/dist/msa/FastaMSA.js
CHANGED
package/dist/msa/StockholmMSA.js
CHANGED
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import
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import
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import
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import
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import { generateNodeIds } from '../util.js';
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import BaseMSA from './BaseMSA.js';
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import parseNewick from './parseNewick.js';
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import { parseAll } from './stockholmParser.js';
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export default class StockholmMSA extends BaseMSA {
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data;
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MSA;
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];
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}
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}
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export { sniff as stockholmSniff } from
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export { sniff as stockholmSniff } from './stockholmParser.js';
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//# sourceMappingURL=StockholmMSA.js.map
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{"version":3,"file":"StockholmMSA.js","sourceRoot":"","sources":["../../src/msa/StockholmMSA.ts"],"names":[],"mappings":"AAAA,OAAO,
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{"version":3,"file":"StockholmMSA.js","sourceRoot":"","sources":["../../src/msa/StockholmMSA.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,eAAe,EAAE,MAAM,YAAY,CAAA;AAC5C,OAAO,OAAO,MAAM,cAAc,CAAA;AAClC,OAAO,WAAW,MAAM,kBAAkB,CAAA;AAC1C,OAAO,EAAE,QAAQ,EAAE,MAAM,sBAAsB,CAAA;AAK/C,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,MAAM,GAAG,GAAG,GAAG,CAAC,gBAAgB,CAAC,IAAI,GAAG,CAAC,CAAC,CAAC,CAAA;QAC3C,IAAI,CAAC,GAAG,EAAE,CAAC;YACT,MAAM,IAAI,KAAK,CAAC,uCAAuC,CAAC,CAAA;QAC1D,CAAC;QACD,IAAI,CAAC,GAAG,GAAG,GAAG,CAAA;IAChB,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,CAAC,CAAA;QAC7C,OAAO,IAAI,KAAK,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,MAAM,CAAA;IAC1D,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"}
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import { describe, expect, test } from 'vitest';
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import A3mMSA from
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import FastaMSA from
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import { parseMSA } from
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import A3mMSA from './A3mMSA.js';
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import FastaMSA from './FastaMSA.js';
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import { parseMSA } from './index.js';
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// impg (https://github.com/pangenome/impg) pipes `impg query -o fasta-aln` into
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// scripts/faln2html.py, which feeds the FASTA string to
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// MSAModelF().create({ data: { msa } }). These tests pin the behavior that
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package/dist/msa/index.js
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import A3mMSA from
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import ClustalMSA from
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import EmfMSA from
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import FastaMSA from
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import StockholmMSA, { stockholmSniff } from
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import A3mMSA from './A3mMSA.js';
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import ClustalMSA from './ClustalMSA.js';
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import EmfMSA from './EmfMSA.js';
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import FastaMSA from './FastaMSA.js';
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import StockholmMSA, { stockholmSniff } from './StockholmMSA.js';
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export { parseEmfTree } from 'emf-js';
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export { default as parseNewick } from
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export { default as parseNewick } from './parseNewick.js';
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// when `format` is given the heuristic sniffing is bypassed -- callers that
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// already know the format (e.g. impg emitting fasta-aln) can force it rather
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// than rely on auto-detection, which is necessarily ambiguous between formats
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export function getUngappedSequence(alignedSeq) {
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return alignedSeq.replaceAll(/[.-]/g, '');
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}
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export { default as A3mMSA } from
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export { default as ClustalMSA } from
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export { default as EmfMSA } from
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export { default as FastaMSA } from
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export { default as StockholmMSA, stockholmSniff } from
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export { default as A3mMSA } from './A3mMSA.js';
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export { default as ClustalMSA } from './ClustalMSA.js';
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export { default as EmfMSA } from './EmfMSA.js';
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export { default as FastaMSA } from './FastaMSA.js';
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export { default as StockholmMSA, stockholmSniff } from './StockholmMSA.js';
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//# sourceMappingURL=index.js.map
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package/dist/msa/index.js.map
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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;
|
|
1
|
+
{"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
|
@@ -1,9 +1,9 @@
|
|
|
1
1
|
import { describe, expect, test } from 'vitest';
|
|
2
|
-
import A3mMSA from
|
|
3
|
-
import ClustalMSA from
|
|
4
|
-
import FastaMSA from
|
|
5
|
-
import { getUngappedSequence, parseMSA } from
|
|
6
|
-
import parseNewick from
|
|
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
|
+
import parseNewick from './parseNewick.js';
|
|
7
7
|
describe('parseMSA', () => {
|
|
8
8
|
test('parses FASTA format', () => {
|
|
9
9
|
const fasta = `>seq1
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"parseNewick.js","sourceRoot":"","sources":["../../src/msa/parseNewick.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA0DG;AACH,MAAM,CAAC,OAAO,UAAU,KAAK,CAAC,CAAS;IACrC,MAAM,SAAS,GAAG,EAAE,CAAA;IAEpB,mFAAmF;IACnF,MAAM,WAAW,GAAa,EAAE,CAAA;IAChC,MAAM,YAAY,GAAG,CAAC,CAAC,OAAO,CAAC,mBAAmB,EAAE,CAAC,CAAC,EAAE,KAAa,EAAE,EAAE;QACvE,MAAM,GAAG,GAAG,WAAW,CAAC,MAAM,CAAA;QAC9B,WAAW,CAAC,IAAI,CAAC,KAAK,CAAC,UAAU,CAAC,IAAI,EAAE,GAAG,CAAC,CAAC,CAAA;QAC7C,OAAO,MAAM,GAAG,IAAI,CAAA;IACtB,CAAC,CAAC,CAAA;IAEF,IAAI,IAAI,GAAG,EAAyB,CAAA;IACpC,MAAM,MAAM,GAAG,YAAY,CAAC,KAAK,CAAC,qBAAqB,CAAC,CAAA;IACxD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QACvC,MAAM,GAAG,GAAG,MAAM,CAAC,CAAC,CAAE,CAAA;QACtB,MAAM,KAAK,GAAG,GAAG,CAAC,OAAO,CACvB,cAAc,EACd,CAAC,CAAC,EAAE,GAAW,EAAE,EAAE,CAAC,WAAW,CAAC,MAAM,CAAC,GAAG,CAAC,CAAE,CAC9C,CAAA;QACD,MAAM,OAAO,GAAG,EAAE,CAAA;QAClB,QAAQ,KAAK,EAAE,CAAC;YACd,KAAK,GAAG,EAAE,eAAe;gBACvB,IAAI,CAAC,QAAQ,GAAG,CAAC,OAAO,CAAC,CAAA;gBACzB,SAAS,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;gBACpB,IAAI,GAAG,OAAO,CAAA;gBACd,MAAK;YACP,KAAK,GAAG,EAAE,iBAAiB;gBACzB,SAAS,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,EAAE,QAAQ,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;gBACxC,IAAI,GAAG,OAAO,CAAA;gBACd,MAAK;YACP,KAAK,GAAG,EAAE,qBAAqB;gBAC7B,IAAI,GAAG,SAAS,CAAC,GAAG,EAAG,CAAA;gBACvB,MAAK;YACP,KAAK,GAAG,EAAE,uBAAuB;gBAC/B,MAAK;YACP,
|
|
1
|
+
{"version":3,"file":"parseNewick.js","sourceRoot":"","sources":["../../src/msa/parseNewick.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA0DG;AACH,MAAM,CAAC,OAAO,UAAU,KAAK,CAAC,CAAS;IACrC,MAAM,SAAS,GAAG,EAAE,CAAA;IAEpB,mFAAmF;IACnF,MAAM,WAAW,GAAa,EAAE,CAAA;IAChC,MAAM,YAAY,GAAG,CAAC,CAAC,OAAO,CAAC,mBAAmB,EAAE,CAAC,CAAC,EAAE,KAAa,EAAE,EAAE;QACvE,MAAM,GAAG,GAAG,WAAW,CAAC,MAAM,CAAA;QAC9B,WAAW,CAAC,IAAI,CAAC,KAAK,CAAC,UAAU,CAAC,IAAI,EAAE,GAAG,CAAC,CAAC,CAAA;QAC7C,OAAO,MAAM,GAAG,IAAI,CAAA;IACtB,CAAC,CAAC,CAAA;IAEF,IAAI,IAAI,GAAG,EAAyB,CAAA;IACpC,MAAM,MAAM,GAAG,YAAY,CAAC,KAAK,CAAC,qBAAqB,CAAC,CAAA;IACxD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QACvC,MAAM,GAAG,GAAG,MAAM,CAAC,CAAC,CAAE,CAAA;QACtB,MAAM,KAAK,GAAG,GAAG,CAAC,OAAO,CACvB,cAAc,EACd,CAAC,CAAC,EAAE,GAAW,EAAE,EAAE,CAAC,WAAW,CAAC,MAAM,CAAC,GAAG,CAAC,CAAE,CAC9C,CAAA;QACD,MAAM,OAAO,GAAG,EAAE,CAAA;QAClB,QAAQ,KAAK,EAAE,CAAC;YACd,KAAK,GAAG,EAAE,eAAe;gBACvB,IAAI,CAAC,QAAQ,GAAG,CAAC,OAAO,CAAC,CAAA;gBACzB,SAAS,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;gBACpB,IAAI,GAAG,OAAO,CAAA;gBACd,MAAK;YACP,KAAK,GAAG,EAAE,iBAAiB;gBACzB,SAAS,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,EAAE,QAAQ,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;gBACxC,IAAI,GAAG,OAAO,CAAA;gBACd,MAAK;YACP,KAAK,GAAG,EAAE,qBAAqB;gBAC7B,IAAI,GAAG,SAAS,CAAC,GAAG,EAAG,CAAA;gBACvB,MAAK;YACP,KAAK,GAAG,EAAE,uBAAuB;gBAC/B,MAAK;YACP,SAAS,CAAC;gBACR,MAAM,CAAC,GAAG,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,CAAA;gBACxB,IAAI,CAAC,KAAK,GAAG,IAAI,CAAC,KAAK,GAAG,IAAI,CAAC,KAAK,GAAG,EAAE,CAAC;oBACxC,IAAI,CAAC,IAAI,GAAG,KAAK,CAAA;gBACnB,CAAC;qBAAM,IAAI,CAAC,KAAK,GAAG,EAAE,CAAC;oBACrB,IAAI,CAAC,MAAM,GAAG,MAAM,CAAC,UAAU,CAAC,KAAK,CAAC,CAAA;gBACxC,CAAC;YACH,CAAC;QACH,CAAC;IACH,CAAC;IACD,OAAO,IAAI,CAAA;AACb,CAAC"}
|
|
@@ -1,5 +1,5 @@
|
|
|
1
1
|
import { describe, expect, test } from 'vitest';
|
|
2
|
-
import { parse, parseAll, sniff } from
|
|
2
|
+
import { parse, parseAll, sniff } from './stockholmParser.js';
|
|
3
3
|
describe('stockholmParser', () => {
|
|
4
4
|
describe('sniff', () => {
|
|
5
5
|
test('returns true for Stockholm format', () => {
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "msa-parsers",
|
|
3
|
-
"version": "5.
|
|
3
|
+
"version": "5.7.0",
|
|
4
4
|
"license": "MIT",
|
|
5
5
|
"type": "module",
|
|
6
6
|
"repository": {
|
|
@@ -20,14 +20,14 @@
|
|
|
20
20
|
"src"
|
|
21
21
|
],
|
|
22
22
|
"dependencies": {
|
|
23
|
-
"clustal-js": "^2.0.
|
|
23
|
+
"clustal-js": "^2.0.17",
|
|
24
24
|
"emf-js": "^2.0.0"
|
|
25
25
|
},
|
|
26
26
|
"publishConfig": {
|
|
27
27
|
"access": "public"
|
|
28
28
|
},
|
|
29
29
|
"devDependencies": {
|
|
30
|
-
"typescript": "^
|
|
30
|
+
"typescript": "^7.0.2",
|
|
31
31
|
"vitest": "^4.1.10"
|
|
32
32
|
},
|
|
33
33
|
"scripts": {
|
package/src/index.ts
CHANGED
package/src/msa/BaseMSA.ts
CHANGED
|
@@ -21,7 +21,8 @@ export default abstract class BaseMSA {
|
|
|
21
21
|
|
|
22
22
|
getRowData(_name: string) {
|
|
23
23
|
return undefined as
|
|
24
|
-
{ name?: string; accession?: string; dbxref?: string }
|
|
24
|
+
| { name?: string; accession?: string; dbxref?: string }
|
|
25
|
+
| undefined
|
|
25
26
|
}
|
|
26
27
|
|
|
27
28
|
getStructures(): Record<string, unknown> {
|
package/src/msa/StockholmMSA.ts
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
|
-
import parseNewick from './parseNewick.ts'
|
|
2
|
-
import { parseAll } from './stockholmParser.ts'
|
|
3
1
|
import { generateNodeIds } from '../util.ts'
|
|
4
2
|
import BaseMSA from './BaseMSA.ts'
|
|
3
|
+
import parseNewick from './parseNewick.ts'
|
|
4
|
+
import { parseAll } from './stockholmParser.ts'
|
|
5
5
|
|
|
6
6
|
import type { NodeWithIds } from '../types.ts'
|
|
7
7
|
import type { StockholmData } from './stockholmParser.ts'
|
package/src/msa/index.ts
CHANGED
|
@@ -8,7 +8,11 @@ export { parseEmfTree } from 'emf-js'
|
|
|
8
8
|
export { default as parseNewick } from './parseNewick.ts'
|
|
9
9
|
|
|
10
10
|
export type MSAParserType =
|
|
11
|
-
|
|
11
|
+
| StockholmMSA
|
|
12
|
+
| A3mMSA
|
|
13
|
+
| FastaMSA
|
|
14
|
+
| EmfMSA
|
|
15
|
+
| ClustalMSA
|
|
12
16
|
|
|
13
17
|
export type MSAFormat = 'stockholm' | 'a3m' | 'fasta' | 'emf' | 'clustal'
|
|
14
18
|
|