msa-parsers 5.4.0 → 5.5.0
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.d.ts +0 -10
- package/dist/gff/gffToInterPro.js +37 -5
- package/dist/gff/gffToInterPro.js.map +1 -1
- package/dist/gff/gffToInterPro.test.js +60 -0
- package/dist/gff/gffToInterPro.test.js.map +1 -1
- package/dist/gff/parseGFF.js +9 -1
- package/dist/gff/parseGFF.js.map +1 -1
- package/dist/msa/FastaMSA.d.ts +1 -0
- package/dist/msa/FastaMSA.js +7 -3
- package/dist/msa/FastaMSA.js.map +1 -1
- package/dist/msa/StockholmMSA.js +6 -2
- package/dist/msa/StockholmMSA.js.map +1 -1
- package/dist/msa/index.test.js +12 -0
- package/dist/msa/index.test.js.map +1 -1
- package/dist/msa/stockholmParser.js +16 -30
- package/dist/msa/stockholmParser.js.map +1 -1
- package/dist/types.d.ts +2 -0
- package/package.json +2 -2
- package/src/gff/gffToInterPro.test.ts +63 -0
- package/src/gff/gffToInterPro.ts +46 -7
- package/src/gff/parseGFF.ts +9 -1
- package/src/msa/FastaMSA.ts +8 -3
- package/src/msa/StockholmMSA.ts +7 -3
- package/src/msa/index.test.ts +14 -0
- package/src/msa/stockholmParser.ts +20 -30
- package/src/types.ts +5 -1
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@@ -1,14 +1,4 @@
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import type { GFFRecord, InterProScanResponse, InterProScanResults } from '../types.ts';
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/**
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* Convert GFF records to InterProScan format
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*
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* InterProScan GFF3 output format:
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* - seq_id: sequence identifier
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* - source: database/signature (e.g., "Pfam", "SMART")
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* - type: usually "protein_match"
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* - start/end: domain positions (1-based)
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* - Attributes: Name (accession), signature_desc (name), Dbxref, etc.
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*/
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export declare function gffToInterProResults(gffRecords: GFFRecord[]): Record<string, InterProScanResults>;
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/**
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* Create a full InterProScanResponse from GFF records
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@@ -8,6 +8,30 @@
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* - start/end: domain positions (1-based)
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* - Attributes: Name (accession), signature_desc (name), Dbxref, etc.
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*/
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// Feature types that read as a directional "gene" and get an arrowhead in the
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// overlay. Exon/CDS/UTR/domain features deliberately stay rectangular blocks —
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// turning every exon into an arrow is misleading, since exons are segments of a
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// single transcript, not independently-oriented genes.
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const GENE_LEVEL_TYPES = new Set([
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'gene',
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'pseudogene',
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'mRNA',
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'transcript',
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'primary_transcript',
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'ncRNA',
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'tRNA',
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'rRNA',
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'snRNA',
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'snoRNA',
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'miRNA',
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'lnc_RNA',
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]);
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// +1/-1 for a stranded gene-level feature, undefined otherwise (which the
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// renderer draws as a plain block).
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function geneStrand({ type, strand }) {
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const directional = strand === '+' ? 1 : strand === '-' ? -1 : undefined;
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return GENE_LEVEL_TYPES.has(type) ? directional : undefined;
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}
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export function gffToInterProResults(gffRecords) {
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const bySequence = new Map();
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for (const record of gffRecords) {
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@@ -35,16 +59,24 @@ export function gffToInterProResults(gffRecords) {
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record.Note ||
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name;
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if (!matchInfo.has(accession)) {
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matchInfo.set(accession, {
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matchInfo.set(accession, {
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name,
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description,
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accession,
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featureType: record.type,
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});
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}
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const location = {
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start: record.start,
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end: record.end,
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strand: geneStrand(record),
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};
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const locations = matchesByAccession.get(accession);
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if (locations) {
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locations.push(
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locations.push(location);
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}
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else {
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matchesByAccession.set(accession, [
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{ start: record.start, end: record.end },
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]);
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matchesByAccession.set(accession, [location]);
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}
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}
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const matches = [];
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"gffToInterPro.js","sourceRoot":"","sources":["../../src/gff/gffToInterPro.ts"],"names":[],"mappings":"AAMA;;;;;;;;;GASG;AACH,MAAM,UAAU,oBAAoB,CAClC,UAAuB;IAEvB,MAAM,UAAU,GAAG,IAAI,GAAG,EAAuB,CAAA;IAEjD,KAAK,MAAM,MAAM,IAAI,UAAU,EAAE,CAAC;QAChC,MAAM,QAAQ,GAAG,UAAU,CAAC,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;QAC9C,IAAI,QAAQ,EAAE,CAAC;YACb,QAAQ,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;QACvB,CAAC;aAAM,CAAC;YACN,UAAU,CAAC,GAAG,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,MAAM,CAAC,CAAC,CAAA;QACzC,CAAC;IACH,CAAC;IAED,MAAM,OAAO,GAAwC,EAAE,CAAA;IAEvD,KAAK,MAAM,CAAC,KAAK,EAAE,OAAO,CAAC,IAAI,UAAU,EAAE,CAAC;QAC1C,MAAM,kBAAkB,GAAG,IAAI,GAAG,EAG/B,CAAA;QACH,MAAM,SAAS,GAAG,IAAI,GAAG,
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{"version":3,"file":"gffToInterPro.js","sourceRoot":"","sources":["../../src/gff/gffToInterPro.ts"],"names":[],"mappings":"AAMA;;;;;;;;;GASG;AACH,8EAA8E;AAC9E,+EAA+E;AAC/E,gFAAgF;AAChF,uDAAuD;AACvD,MAAM,gBAAgB,GAAG,IAAI,GAAG,CAAC;IAC/B,MAAM;IACN,YAAY;IACZ,MAAM;IACN,YAAY;IACZ,oBAAoB;IACpB,OAAO;IACP,MAAM;IACN,MAAM;IACN,OAAO;IACP,QAAQ;IACR,OAAO;IACP,SAAS;CACV,CAAC,CAAA;AAEF,0EAA0E;AAC1E,oCAAoC;AACpC,SAAS,UAAU,CAAC,EAAE,IAAI,EAAE,MAAM,EAAa;IAC7C,MAAM,WAAW,GAAG,MAAM,KAAK,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,MAAM,KAAK,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;IACxE,OAAO,gBAAgB,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,SAAS,CAAA;AAC7D,CAAC;AAED,MAAM,UAAU,oBAAoB,CAClC,UAAuB;IAEvB,MAAM,UAAU,GAAG,IAAI,GAAG,EAAuB,CAAA;IAEjD,KAAK,MAAM,MAAM,IAAI,UAAU,EAAE,CAAC;QAChC,MAAM,QAAQ,GAAG,UAAU,CAAC,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;QAC9C,IAAI,QAAQ,EAAE,CAAC;YACb,QAAQ,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;QACvB,CAAC;aAAM,CAAC;YACN,UAAU,CAAC,GAAG,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,MAAM,CAAC,CAAC,CAAA;QACzC,CAAC;IACH,CAAC;IAED,MAAM,OAAO,GAAwC,EAAE,CAAA;IAEvD,KAAK,MAAM,CAAC,KAAK,EAAE,OAAO,CAAC,IAAI,UAAU,EAAE,CAAC;QAC1C,MAAM,kBAAkB,GAAG,IAAI,GAAG,EAG/B,CAAA;QACH,MAAM,SAAS,GAAG,IAAI,GAAG,EAQtB,CAAA;QAEH,KAAK,MAAM,MAAM,IAAI,OAAO,EAAE,CAAC;YAC7B,MAAM,SAAS,GACZ,MAAM,CAAC,IAAe;gBACtB,MAAM,CAAC,EAAa;gBACrB,GAAG,MAAM,CAAC,MAAM,IAAI,MAAM,CAAC,KAAK,IAAI,MAAM,CAAC,GAAG,EAAE,CAAA;YAClD,MAAM,IAAI,GACP,MAAM,CAAC,cAAyB;gBAChC,MAAM,CAAC,IAAe;gBACvB,SAAS,CAAA;YACX,MAAM,WAAW,GACd,MAAM,CAAC,aAAwB;gBAC/B,MAAM,CAAC,WAAsB;gBAC7B,MAAM,CAAC,IAAe;gBACvB,IAAI,CAAA;YAEN,IAAI,CAAC,SAAS,CAAC,GAAG,CAAC,SAAS,CAAC,EAAE,CAAC;gBAC9B,SAAS,CAAC,GAAG,CAAC,SAAS,EAAE;oBACvB,IAAI;oBACJ,WAAW;oBACX,SAAS;oBACT,WAAW,EAAE,MAAM,CAAC,IAAI;iBACzB,CAAC,CAAA;YACJ,CAAC;YAED,MAAM,QAAQ,GAAG;gBACf,KAAK,EAAE,MAAM,CAAC,KAAK;gBACnB,GAAG,EAAE,MAAM,CAAC,GAAG;gBACf,MAAM,EAAE,UAAU,CAAC,MAAM,CAAC;aAC3B,CAAA;YACD,MAAM,SAAS,GAAG,kBAAkB,CAAC,GAAG,CAAC,SAAS,CAAC,CAAA;YACnD,IAAI,SAAS,EAAE,CAAC;gBACd,SAAS,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAA;YAC1B,CAAC;iBAAM,CAAC;gBACN,kBAAkB,CAAC,GAAG,CAAC,SAAS,EAAE,CAAC,QAAQ,CAAC,CAAC,CAAA;YAC/C,CAAC;QACH,CAAC;QAED,MAAM,OAAO,GAAG,EAAE,CAAA;QAClB,KAAK,MAAM,CAAC,SAAS,EAAE,SAAS,CAAC,IAAI,kBAAkB,EAAE,CAAC;YACxD,MAAM,IAAI,GAAG,SAAS,CAAC,GAAG,CAAC,SAAS,CAAE,CAAA;YACtC,OAAO,CAAC,IAAI,CAAC;gBACX,SAAS,EAAE;oBACT,KAAK,EAAE,IAAI;iBACZ;gBACD,SAAS;aACV,CAAC,CAAA;QACJ,CAAC;QAED,OAAO,CAAC,KAAK,CAAC,GAAG;YACf,OAAO;YACP,IAAI,EAAE,CAAC,EAAE,EAAE,EAAE,KAAK,EAAE,CAAC;SACtB,CAAA;IACH,CAAC;IAED,OAAO,OAAO,CAAA;AAChB,CAAC;AAED;;GAEG;AACH,MAAM,UAAU,qBAAqB,CACnC,UAAuB;IAEvB,MAAM,UAAU,GAAG,oBAAoB,CAAC,UAAU,CAAC,CAAA;IACnD,OAAO;QACL,OAAO,EAAE,MAAM,CAAC,MAAM,CAAC,UAAU,CAAC;KACnC,CAAA;AACH,CAAC"}
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@@ -27,6 +27,7 @@ describe('gffToInterProResults', () => {
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accession: 'PF00001',
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name: '7tm_1',
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description: 'GPCR family',
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featureType: 'protein_match',
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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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{ start: 100, end: 150 },
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]);
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});
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test('gives gene-level features a direction but leaves exons/domains as blocks', () => {
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const records = [
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{
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seq_id: 'seq1',
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source: 'x',
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type: 'gene',
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start: 5,
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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: 'GENEA',
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},
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{
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seq_id: 'seq1',
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source: 'x',
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type: 'mRNA',
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start: 60,
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end: 90,
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score: 0,
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strand: '-',
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phase: '.',
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Name: 'GENEB',
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},
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{
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seq_id: 'seq1',
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source: 'x',
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type: 'exon',
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start: 5,
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end: 20,
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score: 0,
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strand: '+',
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phase: '.',
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Name: 'exon-1',
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},
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{
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seq_id: 'seq1',
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source: 'x',
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type: 'protein_match',
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start: 5,
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end: 20,
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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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const byAccession = Object.fromEntries(result.seq1.matches.map(m => [
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m.signature.entry.accession,
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m.locations[0].strand,
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]));
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expect(byAccession).toEqual({
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GENEA: 1, // + gene -> arrow right
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GENEB: -1, // - gene -> arrow left
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'exon-1': undefined, // exon stays a block even though it is stranded
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PF00001: undefined, // protein domain stays a block
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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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{"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;
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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;YAC1B,WAAW,EAAE,eAAe;SAC7B,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,0EAA0E,EAAE,GAAG,EAAE;QACpF,MAAM,OAAO,GAAgB;YAC3B;gBACE,MAAM,EAAE,MAAM;gBACd,MAAM,EAAE,GAAG;gBACX,IAAI,EAAE,MAAM;gBACZ,KAAK,EAAE,CAAC;gBACR,GAAG,EAAE,EAAE;gBACP,KAAK,EAAE,CAAC;gBACR,MAAM,EAAE,GAAG;gBACX,KAAK,EAAE,GAAG;gBACV,IAAI,EAAE,OAAO;aACd;YACD;gBACE,MAAM,EAAE,MAAM;gBACd,MAAM,EAAE,GAAG;gBACX,IAAI,EAAE,MAAM;gBACZ,KAAK,EAAE,EAAE;gBACT,GAAG,EAAE,EAAE;gBACP,KAAK,EAAE,CAAC;gBACR,MAAM,EAAE,GAAG;gBACX,KAAK,EAAE,GAAG;gBACV,IAAI,EAAE,OAAO;aACd;YACD;gBACE,MAAM,EAAE,MAAM;gBACd,MAAM,EAAE,GAAG;gBACX,IAAI,EAAE,MAAM;gBACZ,KAAK,EAAE,CAAC;gBACR,GAAG,EAAE,EAAE;gBACP,KAAK,EAAE,CAAC;gBACR,MAAM,EAAE,GAAG;gBACX,KAAK,EAAE,GAAG;gBACV,IAAI,EAAE,QAAQ;aACf;YACD;gBACE,MAAM,EAAE,MAAM;gBACd,MAAM,EAAE,GAAG;gBACX,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;QAC5C,MAAM,WAAW,GAAG,MAAM,CAAC,WAAW,CACpC,MAAM,CAAC,IAAK,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC;YAC5B,CAAC,CAAC,SAAS,CAAC,KAAM,CAAC,SAAS;YAC5B,CAAC,CAAC,SAAS,CAAC,CAAC,CAAE,CAAC,MAAM;SACvB,CAAC,CACH,CAAA;QACD,MAAM,CAAC,WAAW,CAAC,CAAC,OAAO,CAAC;YAC1B,KAAK,EAAE,CAAC,EAAE,wBAAwB;YAClC,KAAK,EAAE,CAAC,CAAC,EAAE,uBAAuB;YAClC,QAAQ,EAAE,SAAS,EAAE,gDAAgD;YACrE,OAAO,EAAE,SAAS,EAAE,+BAA+B;SACpD,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"}
|
package/dist/gff/parseGFF.js
CHANGED
|
@@ -20,9 +20,17 @@ function parseAttributes(col9) {
|
|
|
20
20
|
const eq = f.indexOf('=');
|
|
21
21
|
const key = (eq === -1 ? f : f.slice(0, eq)).trim();
|
|
22
22
|
const val = eq === -1 ? undefined : f.slice(eq + 1);
|
|
23
|
+
// split on comma (the GFF3 multi-value separator) BEFORE decoding, so a
|
|
24
|
+
// literal comma encoded as %2C survives the split and isn't mistaken
|
|
25
|
+
// for a separator
|
|
23
26
|
return [
|
|
24
27
|
key,
|
|
25
|
-
val
|
|
28
|
+
val
|
|
29
|
+
? val
|
|
30
|
+
.split(',')
|
|
31
|
+
.map(v => safeDecode(v).trim())
|
|
32
|
+
.join(' ')
|
|
33
|
+
: undefined,
|
|
26
34
|
];
|
|
27
35
|
})
|
|
28
36
|
.filter(([key]) => key !== ''));
|
package/dist/gff/parseGFF.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"parseGFF.js","sourceRoot":"","sources":["../../src/gff/parseGFF.ts"],"names":[],"mappings":"AAEA,8EAA8E;AAC9E,kEAAkE;AAClE,SAAS,UAAU,CAAC,GAAW;IAC7B,IAAI,CAAC;QACH,OAAO,kBAAkB,CAAC,GAAG,CAAC,CAAA;IAChC,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,GAAG,CAAA;IACZ,CAAC;AACH,CAAC;AAED,SAAS,eAAe,CAAC,IAAa;IACpC,IAAI,CAAC,IAAI,EAAE,CAAC;QACV,OAAO,EAAE,CAAA;IACX,CAAC;IACD,OAAO,MAAM,CAAC,WAAW,CACvB,IAAI;SACD,KAAK,CAAC,GAAG,CAAC;SACV,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;SAClB,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;SAChB,GAAG,CAAC,CAAC,CAAC,EAAE;QACP,MAAM,EAAE,GAAG,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,CAAA;QACzB,MAAM,GAAG,GAAG,CAAC,EAAE,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAA;QACnD,MAAM,GAAG,GAAG,EAAE,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,EAAE,GAAG,CAAC,CAAC,CAAA;QACnD,OAAO;YACL,GAAG;YACH,GAAG,CAAC,CAAC,CAAC,
|
|
1
|
+
{"version":3,"file":"parseGFF.js","sourceRoot":"","sources":["../../src/gff/parseGFF.ts"],"names":[],"mappings":"AAEA,8EAA8E;AAC9E,kEAAkE;AAClE,SAAS,UAAU,CAAC,GAAW;IAC7B,IAAI,CAAC;QACH,OAAO,kBAAkB,CAAC,GAAG,CAAC,CAAA;IAChC,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,GAAG,CAAA;IACZ,CAAC;AACH,CAAC;AAED,SAAS,eAAe,CAAC,IAAa;IACpC,IAAI,CAAC,IAAI,EAAE,CAAC;QACV,OAAO,EAAE,CAAA;IACX,CAAC;IACD,OAAO,MAAM,CAAC,WAAW,CACvB,IAAI;SACD,KAAK,CAAC,GAAG,CAAC;SACV,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;SAClB,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;SAChB,GAAG,CAAC,CAAC,CAAC,EAAE;QACP,MAAM,EAAE,GAAG,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,CAAA;QACzB,MAAM,GAAG,GAAG,CAAC,EAAE,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAA;QACnD,MAAM,GAAG,GAAG,EAAE,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,EAAE,GAAG,CAAC,CAAC,CAAA;QACnD,wEAAwE;QACxE,qEAAqE;QACrE,kBAAkB;QAClB,OAAO;YACL,GAAG;YACH,GAAG;gBACD,CAAC,CAAC,GAAG;qBACA,KAAK,CAAC,GAAG,CAAC;qBACV,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;qBAC9B,IAAI,CAAC,GAAG,CAAC;gBACd,CAAC,CAAC,SAAS;SACd,CAAA;IACH,CAAC,CAAC;SACD,MAAM,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,GAAG,KAAK,EAAE,CAAC,CACjC,CAAA;AACH,CAAC;AAED,MAAM,UAAU,QAAQ,CAAC,GAAY;IACnC,IAAI,CAAC,GAAG,EAAE,CAAC;QACT,OAAO,EAAE,CAAA;IACX,CAAC;IACD,OAAO,GAAG;SACP,KAAK,CAAC,IAAI,CAAC;SACX,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;SAClB,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,UAAU,CAAC,GAAG,CAAC,CAAC;SACtC,GAAG,CAAC,CAAC,CAAC,EAAE;QACP,MAAM,KAAK,GAAG,CAAC,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAC3B,MAAM,CAAC,MAAM,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,EAAE,GAAG,EAAE,KAAK,EAAE,MAAM,EAAE,KAAK,CAAC,GAAG,KAAK,CAAA;QACtE,MAAM,IAAI,GAAG,KAAK,CAAC,CAAC,CAAC,CAAA;QAErB,OAAO;YACL,MAAM,EAAE,MAAM,IAAI,EAAE;YACpB,MAAM,EAAE,MAAM,IAAI,EAAE;YACpB,IAAI,EAAE,IAAI,IAAI,EAAE;YAChB,KAAK,EAAE,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC;YACzB,GAAG,EAAE,MAAM,CAAC,GAAG,CAAC,IAAI,CAAC;YACrB,KAAK,EAAE,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC;YACzB,MAAM,EAAE,MAAM,IAAI,GAAG;YACrB,KAAK,EAAE,KAAK,IAAI,GAAG;YACnB,GAAG,eAAe,CAAC,IAAI,CAAC;SACzB,CAAA;IACH,CAAC,CAAC,CAAA;AACN,CAAC"}
|
package/dist/msa/FastaMSA.d.ts
CHANGED
package/dist/msa/FastaMSA.js
CHANGED
|
@@ -1,6 +1,9 @@
|
|
|
1
1
|
import BaseMSA from "./BaseMSA.js";
|
|
2
2
|
export default class FastaMSA extends BaseMSA {
|
|
3
3
|
MSA;
|
|
4
|
+
// explicit insertion-ordered ids: object key order reorders integer-like
|
|
5
|
+
// keys (e.g. a numeric ">123" defline) to the front, scrambling row order
|
|
6
|
+
orderedNames = [];
|
|
4
7
|
constructor(text) {
|
|
5
8
|
super();
|
|
6
9
|
const seqdata = {};
|
|
@@ -18,6 +21,7 @@ export default class FastaMSA extends BaseMSA {
|
|
|
18
21
|
const id = spaceIdx === -1 ? defLine : defLine.slice(0, spaceIdx);
|
|
19
22
|
if (id) {
|
|
20
23
|
seqdata[id] = entry.slice(newlineIdx + 1).replaceAll(/\s/g, '');
|
|
24
|
+
this.orderedNames.push(id);
|
|
21
25
|
if (id.includes(':')) {
|
|
22
26
|
colonNormalized[id.replaceAll(':', '_')] = id;
|
|
23
27
|
}
|
|
@@ -29,7 +33,7 @@ export default class FastaMSA extends BaseMSA {
|
|
|
29
33
|
return this.MSA;
|
|
30
34
|
}
|
|
31
35
|
getNames() {
|
|
32
|
-
return
|
|
36
|
+
return this.orderedNames;
|
|
33
37
|
}
|
|
34
38
|
getRow(name) {
|
|
35
39
|
return (this.MSA.seqdata[name] ??
|
|
@@ -37,8 +41,8 @@ export default class FastaMSA extends BaseMSA {
|
|
|
37
41
|
'');
|
|
38
42
|
}
|
|
39
43
|
getWidth() {
|
|
40
|
-
const name =
|
|
41
|
-
return this.getRow(name).length;
|
|
44
|
+
const name = this.orderedNames[0];
|
|
45
|
+
return name === undefined ? 0 : this.getRow(name).length;
|
|
42
46
|
}
|
|
43
47
|
}
|
|
44
48
|
//# sourceMappingURL=FastaMSA.js.map
|
package/dist/msa/FastaMSA.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"FastaMSA.js","sourceRoot":"","sources":["../../src/msa/FastaMSA.ts"],"names":[],"mappings":"AAAA,OAAO,OAAO,MAAM,cAAc,CAAA;AAElC,MAAM,CAAC,OAAO,OAAO,QAAS,SAAQ,OAAO;IACnC,GAAG,CAGV;IAED,YAAY,IAAY;QACtB,KAAK,EAAE,CAAA;QACP,MAAM,OAAO,GAA2B,EAAE,CAAA;QAC1C,MAAM,eAAe,GAA2B,EAAE,CAAA;QAClD,KAAK,MAAM,KAAK,IAAI,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,EAAE,CAAC;YACpC,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC;gBACtB,SAAQ;YACV,CAAC;YACD,MAAM,UAAU,GAAG,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,CAAA;YACtC,IAAI,UAAU,KAAK,CAAC,CAAC,EAAE,CAAC;gBACtB,SAAQ;YACV,CAAC;YACD,MAAM,OAAO,GAAG,KAAK,CAAC,KAAK,CAAC,CAAC,EAAE,UAAU,CAAC,CAAC,OAAO,CAAC,KAAK,EAAE,EAAE,CAAC,CAAA;YAC7D,MAAM,QAAQ,GAAG,OAAO,CAAC,OAAO,CAAC,GAAG,CAAC,CAAA;YACrC,MAAM,EAAE,GAAG,QAAQ,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,EAAE,QAAQ,CAAC,CAAA;YACjE,IAAI,EAAE,EAAE,CAAC;gBACP,OAAO,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,KAAK,CAAC,UAAU,GAAG,CAAC,CAAC,CAAC,UAAU,CAAC,KAAK,EAAE,EAAE,CAAC,CAAA;gBAC/D,IAAI,EAAE,CAAC,QAAQ,CAAC,GAAG,CAAC,EAAE,CAAC;oBACrB,eAAe,CAAC,EAAE,CAAC,UAAU,CAAC,GAAG,EAAE,GAAG,CAAC,CAAC,GAAG,EAAE,CAAA;gBAC/C,CAAC;YACH,CAAC;QACH,CAAC;QACD,IAAI,CAAC,GAAG,GAAG,EAAE,OAAO,EAAE,eAAe,EAAE,CAAA;IACzC,CAAC;IAED,MAAM;QACJ,OAAO,IAAI,CAAC,GAAG,CAAA;IACjB,CAAC;IAED,QAAQ;QACN,OAAO,
|
|
1
|
+
{"version":3,"file":"FastaMSA.js","sourceRoot":"","sources":["../../src/msa/FastaMSA.ts"],"names":[],"mappings":"AAAA,OAAO,OAAO,MAAM,cAAc,CAAA;AAElC,MAAM,CAAC,OAAO,OAAO,QAAS,SAAQ,OAAO;IACnC,GAAG,CAGV;IAED,yEAAyE;IACzE,0EAA0E;IAClE,YAAY,GAAa,EAAE,CAAA;IAEnC,YAAY,IAAY;QACtB,KAAK,EAAE,CAAA;QACP,MAAM,OAAO,GAA2B,EAAE,CAAA;QAC1C,MAAM,eAAe,GAA2B,EAAE,CAAA;QAClD,KAAK,MAAM,KAAK,IAAI,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,EAAE,CAAC;YACpC,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC;gBACtB,SAAQ;YACV,CAAC;YACD,MAAM,UAAU,GAAG,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,CAAA;YACtC,IAAI,UAAU,KAAK,CAAC,CAAC,EAAE,CAAC;gBACtB,SAAQ;YACV,CAAC;YACD,MAAM,OAAO,GAAG,KAAK,CAAC,KAAK,CAAC,CAAC,EAAE,UAAU,CAAC,CAAC,OAAO,CAAC,KAAK,EAAE,EAAE,CAAC,CAAA;YAC7D,MAAM,QAAQ,GAAG,OAAO,CAAC,OAAO,CAAC,GAAG,CAAC,CAAA;YACrC,MAAM,EAAE,GAAG,QAAQ,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,EAAE,QAAQ,CAAC,CAAA;YACjE,IAAI,EAAE,EAAE,CAAC;gBACP,OAAO,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,KAAK,CAAC,UAAU,GAAG,CAAC,CAAC,CAAC,UAAU,CAAC,KAAK,EAAE,EAAE,CAAC,CAAA;gBAC/D,IAAI,CAAC,YAAY,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;gBAC1B,IAAI,EAAE,CAAC,QAAQ,CAAC,GAAG,CAAC,EAAE,CAAC;oBACrB,eAAe,CAAC,EAAE,CAAC,UAAU,CAAC,GAAG,EAAE,GAAG,CAAC,CAAC,GAAG,EAAE,CAAA;gBAC/C,CAAC;YACH,CAAC;QACH,CAAC;QACD,IAAI,CAAC,GAAG,GAAG,EAAE,OAAO,EAAE,eAAe,EAAE,CAAA;IACzC,CAAC;IAED,MAAM;QACJ,OAAO,IAAI,CAAC,GAAG,CAAA;IACjB,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,YAAY,CAAA;IAC1B,CAAC;IAED,MAAM,CAAC,IAAY;QACjB,OAAO,CACL,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,IAAI,CAAC;YACtB,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,eAAe,CAAC,IAAI,CAAC,IAAI,EAAE,CAAC;YACtD,EAAE,CACH,CAAA;IACH,CAAC;IAED,QAAQ;QACN,MAAM,IAAI,GAAG,IAAI,CAAC,YAAY,CAAC,CAAC,CAAC,CAAA;QACjC,OAAO,IAAI,KAAK,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,MAAM,CAAA;IAC1D,CAAC;CACF"}
|
package/dist/msa/StockholmMSA.js
CHANGED
|
@@ -9,7 +9,11 @@ export default class StockholmMSA extends BaseMSA {
|
|
|
9
9
|
super();
|
|
10
10
|
const res = parseAll(text);
|
|
11
11
|
this.data = res;
|
|
12
|
-
|
|
12
|
+
const aln = res[currentAlignment] ?? res[0];
|
|
13
|
+
if (!aln) {
|
|
14
|
+
throw new Error('No alignments found in Stockholm file');
|
|
15
|
+
}
|
|
16
|
+
this.MSA = aln;
|
|
13
17
|
}
|
|
14
18
|
getMSA() {
|
|
15
19
|
return this.MSA;
|
|
@@ -19,7 +23,7 @@ export default class StockholmMSA extends BaseMSA {
|
|
|
19
23
|
}
|
|
20
24
|
getWidth() {
|
|
21
25
|
const name = Object.keys(this.MSA.seqdata)[0];
|
|
22
|
-
return this.getRow(name).length;
|
|
26
|
+
return name === undefined ? 0 : this.getRow(name).length;
|
|
23
27
|
}
|
|
24
28
|
get alignmentNames() {
|
|
25
29
|
return this.data.map((aln, idx) => aln.gf.DE?.[0] ?? `Alignment ${idx + 1}`);
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"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,
|
|
1
|
+
{"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,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"}
|
package/dist/msa/index.test.js
CHANGED
|
@@ -14,6 +14,18 @@ GHIKL`;
|
|
|
14
14
|
expect(msa).toBeInstanceOf(FastaMSA);
|
|
15
15
|
expect(msa.getNames()).toEqual(['seq1', 'seq2']);
|
|
16
16
|
});
|
|
17
|
+
test('preserves row order for numeric FASTA ids', () => {
|
|
18
|
+
// object key order would hoist integer-like keys ('10' before '2'),
|
|
19
|
+
// scrambling the alignment; getNames must keep file order
|
|
20
|
+
const fasta = `>3
|
|
21
|
+
ACDEF
|
|
22
|
+
>1
|
|
23
|
+
GHIKL
|
|
24
|
+
>2
|
|
25
|
+
MNPQR`;
|
|
26
|
+
const msa = parseMSA(fasta);
|
|
27
|
+
expect(msa.getNames()).toEqual(['3', '1', '2']);
|
|
28
|
+
});
|
|
17
29
|
test('parses A3M format', () => {
|
|
18
30
|
const a3m = `>seq1
|
|
19
31
|
ACDEFghiKLMNPQ
|
|
@@ -1 +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;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"}
|
|
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,2CAA2C,EAAE,GAAG,EAAE;QACrD,oEAAoE;QACpE,0DAA0D;QAC1D,MAAM,KAAK,GAAG;;;;;MAKZ,CAAA;QACF,MAAM,GAAG,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;QAE3B,MAAM,CAAC,GAAG,CAAC,QAAQ,EAAE,CAAC,CAAC,OAAO,CAAC,CAAC,GAAG,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC,CAAA;IACjD,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"}
|
|
@@ -13,6 +13,17 @@ function createStockholm() {
|
|
|
13
13
|
seqdata: {},
|
|
14
14
|
};
|
|
15
15
|
}
|
|
16
|
+
// records before a "# STOCKHOLM 1.0" header are an error in strict mode,
|
|
17
|
+
// otherwise they implicitly start a new alignment
|
|
18
|
+
function ensureStock(stock, strict) {
|
|
19
|
+
if (stock) {
|
|
20
|
+
return stock;
|
|
21
|
+
}
|
|
22
|
+
if (strict) {
|
|
23
|
+
throw new Error('No format header: # STOCKHOLM 1.0');
|
|
24
|
+
}
|
|
25
|
+
return createStockholm();
|
|
26
|
+
}
|
|
16
27
|
const formatStartRegex = /^# STOCKHOLM 1.0/;
|
|
17
28
|
const formatEndRegex = /^\/\/\s*$/;
|
|
18
29
|
const gfRegex = /^#=GF\s+(\S+)\s+(.*?)\s*$/;
|
|
@@ -41,12 +52,7 @@ export function parseAll(text, opts) {
|
|
|
41
52
|
stock = null;
|
|
42
53
|
}
|
|
43
54
|
else if ((match = gfRegex.exec(line))) {
|
|
44
|
-
|
|
45
|
-
if (options.strict) {
|
|
46
|
-
throw new Error('No format header: # STOCKHOLM 1.0');
|
|
47
|
-
}
|
|
48
|
-
stock = createStockholm();
|
|
49
|
-
}
|
|
55
|
+
stock = ensureStock(stock, !!options.strict);
|
|
50
56
|
const tag = match[1];
|
|
51
57
|
if (!stock.gf[tag]) {
|
|
52
58
|
stock.gf[tag] = [];
|
|
@@ -54,12 +60,7 @@ export function parseAll(text, opts) {
|
|
|
54
60
|
stock.gf[tag].push(match[2]);
|
|
55
61
|
}
|
|
56
62
|
else if ((match = gcRegex.exec(line))) {
|
|
57
|
-
|
|
58
|
-
if (options.strict) {
|
|
59
|
-
throw new Error('No format header: # STOCKHOLM 1.0');
|
|
60
|
-
}
|
|
61
|
-
stock = createStockholm();
|
|
62
|
-
}
|
|
63
|
+
stock = ensureStock(stock, !!options.strict);
|
|
63
64
|
const tag = match[1];
|
|
64
65
|
if (!stock.gc[tag]) {
|
|
65
66
|
stock.gc[tag] = '';
|
|
@@ -67,12 +68,7 @@ export function parseAll(text, opts) {
|
|
|
67
68
|
stock.gc[tag] += match[2];
|
|
68
69
|
}
|
|
69
70
|
else if ((match = gsRegex.exec(line))) {
|
|
70
|
-
|
|
71
|
-
if (options.strict) {
|
|
72
|
-
throw new Error('No format header: # STOCKHOLM 1.0');
|
|
73
|
-
}
|
|
74
|
-
stock = createStockholm();
|
|
75
|
-
}
|
|
71
|
+
stock = ensureStock(stock, !!options.strict);
|
|
76
72
|
const seqname = match[1];
|
|
77
73
|
const tag = match[2];
|
|
78
74
|
const value = match[3];
|
|
@@ -85,12 +81,7 @@ export function parseAll(text, opts) {
|
|
|
85
81
|
stock.gs[tag][seqname].push(value);
|
|
86
82
|
}
|
|
87
83
|
else if ((match = grRegex.exec(line))) {
|
|
88
|
-
|
|
89
|
-
if (options.strict) {
|
|
90
|
-
throw new Error('No format header: # STOCKHOLM 1.0');
|
|
91
|
-
}
|
|
92
|
-
stock = createStockholm();
|
|
93
|
-
}
|
|
84
|
+
stock = ensureStock(stock, !!options.strict);
|
|
94
85
|
const seqname = match[1];
|
|
95
86
|
const tag = match[2];
|
|
96
87
|
const value = match[3];
|
|
@@ -103,12 +94,7 @@ export function parseAll(text, opts) {
|
|
|
103
94
|
stock.gr[tag][seqname] += value;
|
|
104
95
|
}
|
|
105
96
|
else if ((match = lineRegex.exec(line))) {
|
|
106
|
-
|
|
107
|
-
if (options.strict) {
|
|
108
|
-
throw new Error('No format header: # STOCKHOLM 1.0');
|
|
109
|
-
}
|
|
110
|
-
stock = createStockholm();
|
|
111
|
-
}
|
|
97
|
+
stock = ensureStock(stock, !!options.strict);
|
|
112
98
|
const seqname = match[1];
|
|
113
99
|
const seqdata = match[2];
|
|
114
100
|
if (!stock.seqdata[seqname]) {
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"stockholmParser.js","sourceRoot":"","sources":["../../src/msa/stockholmParser.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAWH,SAAS,eAAe;IACtB,OAAO;QACL,EAAE,EAAE,EAAE;QACN,EAAE,EAAE,EAAE;QACN,EAAE,EAAE,EAAE;QACN,EAAE,EAAE,EAAE;QACN,OAAO,EAAE,EAAE;QACX,OAAO,EAAE,EAAE;KACZ,CAAA;AACH,CAAC;AAED,MAAM,gBAAgB,GAAG,kBAAkB,CAAA;AAC3C,MAAM,cAAc,GAAG,WAAW,CAAA;AAClC,MAAM,OAAO,GAAG,2BAA2B,CAAA;AAC3C,MAAM,OAAO,GAAG,2BAA2B,CAAA;AAC3C,MAAM,OAAO,GAAG,mCAAmC,CAAA;AACnD,MAAM,OAAO,GAAG,mCAAmC,CAAA;AACnD,MAAM,SAAS,GAAG,uBAAuB,CAAA;AACzC,MAAM,aAAa,GAAG,IAAI,CAAA;AAE1B,MAAM,UAAU,KAAK,CAAC,IAAY;IAChC,OAAO,gBAAgB,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;AACpC,CAAC;AAED,MAAM,UAAU,QAAQ,CACtB,IAAY,EACZ,IAA4C;IAE5C,MAAM,OAAO,GAAG,IAAI,IAAI,EAAE,CAAA;IAC1B,MAAM,EAAE,GAAoB,EAAE,CAAA;IAC9B,IAAI,KAAK,GAAyB,IAAI,CAAA;IAEtC,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;IAC9B,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE,CAAC;QACzB,IAAI,KAA6B,CAAA;QAEjC,IAAI,gBAAgB,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;YAChC,KAAK,GAAG,eAAe,EAAE,CAAA;QAC3B,CAAC;aAAM,IAAI,cAAc,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;YACrC,IAAI,KAAK,EAAE,CAAC;gBACV,EAAE,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;YAChB,CAAC;YACD,KAAK,GAAG,IAAI,CAAA;QACd,CAAC;aAAM,IAAI,CAAC,KAAK,GAAG,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,EAAE,CAAC;YACxC,
|
|
1
|
+
{"version":3,"file":"stockholmParser.js","sourceRoot":"","sources":["../../src/msa/stockholmParser.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAWH,SAAS,eAAe;IACtB,OAAO;QACL,EAAE,EAAE,EAAE;QACN,EAAE,EAAE,EAAE;QACN,EAAE,EAAE,EAAE;QACN,EAAE,EAAE,EAAE;QACN,OAAO,EAAE,EAAE;QACX,OAAO,EAAE,EAAE;KACZ,CAAA;AACH,CAAC;AAED,yEAAyE;AACzE,kDAAkD;AAClD,SAAS,WAAW,CAClB,KAA2B,EAC3B,MAAe;IAEf,IAAI,KAAK,EAAE,CAAC;QACV,OAAO,KAAK,CAAA;IACd,CAAC;IACD,IAAI,MAAM,EAAE,CAAC;QACX,MAAM,IAAI,KAAK,CAAC,mCAAmC,CAAC,CAAA;IACtD,CAAC;IACD,OAAO,eAAe,EAAE,CAAA;AAC1B,CAAC;AAED,MAAM,gBAAgB,GAAG,kBAAkB,CAAA;AAC3C,MAAM,cAAc,GAAG,WAAW,CAAA;AAClC,MAAM,OAAO,GAAG,2BAA2B,CAAA;AAC3C,MAAM,OAAO,GAAG,2BAA2B,CAAA;AAC3C,MAAM,OAAO,GAAG,mCAAmC,CAAA;AACnD,MAAM,OAAO,GAAG,mCAAmC,CAAA;AACnD,MAAM,SAAS,GAAG,uBAAuB,CAAA;AACzC,MAAM,aAAa,GAAG,IAAI,CAAA;AAE1B,MAAM,UAAU,KAAK,CAAC,IAAY;IAChC,OAAO,gBAAgB,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;AACpC,CAAC;AAED,MAAM,UAAU,QAAQ,CACtB,IAAY,EACZ,IAA4C;IAE5C,MAAM,OAAO,GAAG,IAAI,IAAI,EAAE,CAAA;IAC1B,MAAM,EAAE,GAAoB,EAAE,CAAA;IAC9B,IAAI,KAAK,GAAyB,IAAI,CAAA;IAEtC,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;IAC9B,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE,CAAC;QACzB,IAAI,KAA6B,CAAA;QAEjC,IAAI,gBAAgB,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;YAChC,KAAK,GAAG,eAAe,EAAE,CAAA;QAC3B,CAAC;aAAM,IAAI,cAAc,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;YACrC,IAAI,KAAK,EAAE,CAAC;gBACV,EAAE,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;YAChB,CAAC;YACD,KAAK,GAAG,IAAI,CAAA;QACd,CAAC;aAAM,IAAI,CAAC,KAAK,GAAG,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,EAAE,CAAC;YACxC,KAAK,GAAG,WAAW,CAAC,KAAK,EAAE,CAAC,CAAC,OAAO,CAAC,MAAM,CAAC,CAAA;YAC5C,MAAM,GAAG,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;YACrB,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC;gBACnB,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,EAAE,CAAA;YACpB,CAAC;YACD,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAE,CAAC,CAAA;QAC/B,CAAC;aAAM,IAAI,CAAC,KAAK,GAAG,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,EAAE,CAAC;YACxC,KAAK,GAAG,WAAW,CAAC,KAAK,EAAE,CAAC,CAAC,OAAO,CAAC,MAAM,CAAC,CAAA;YAC5C,MAAM,GAAG,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;YACrB,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC;gBACnB,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,EAAE,CAAA;YACpB,CAAC;YACD,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,IAAI,KAAK,CAAC,CAAC,CAAE,CAAA;QAC5B,CAAC;aAAM,IAAI,CAAC,KAAK,GAAG,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,EAAE,CAAC;YACxC,KAAK,GAAG,WAAW,CAAC,KAAK,EAAE,CAAC,CAAC,OAAO,CAAC,MAAM,CAAC,CAAA;YAC5C,MAAM,OAAO,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;YACzB,MAAM,GAAG,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;YACrB,MAAM,KAAK,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;YACvB,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC;gBACnB,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,EAAE,CAAA;YACpB,CAAC;YACD,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,EAAE,CAAC;gBAC5B,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,GAAG,EAAE,CAAA;YAC7B,CAAC;YACD,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;QACpC,CAAC;aAAM,IAAI,CAAC,KAAK,GAAG,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,EAAE,CAAC;YACxC,KAAK,GAAG,WAAW,CAAC,KAAK,EAAE,CAAC,CAAC,OAAO,CAAC,MAAM,CAAC,CAAA;YAC5C,MAAM,OAAO,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;YACzB,MAAM,GAAG,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;YACrB,MAAM,KAAK,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;YACvB,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC;gBACnB,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,EAAE,CAAA;YACpB,CAAC;YACD,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,EAAE,CAAC;gBAC5B,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,GAAG,EAAE,CAAA;YAC7B,CAAC;YACD,KAAK,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,IAAI,KAAK,CAAA;QACjC,CAAC;aAAM,IAAI,CAAC,KAAK,GAAG,SAAS,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,EAAE,CAAC;YAC1C,KAAK,GAAG,WAAW,CAAC,KAAK,EAAE,CAAC,CAAC,OAAO,CAAC,MAAM,CAAC,CAAA;YAC5C,MAAM,OAAO,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;YACzB,MAAM,OAAO,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;YACzB,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,OAAO,CAAC,EAAE,CAAC;gBAC5B,KAAK,CAAC,OAAO,CAAC,OAAO,CAAC,GAAG,EAAE,CAAA;gBAC3B,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;YAC7B,CAAC;YACD,KAAK,CAAC,OAAO,CAAC,OAAO,CAAC,IAAI,OAAO,CAAA;QACnC,CAAC;aAAM,IAAI,aAAa,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;YACpC,IAAI,OAAO,CAAC,MAAM,EAAE,CAAC;gBACnB,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;YACnC,CAAC;QACH,CAAC;IACH,CAAC;IAED,IAAI,KAAK,EAAE,CAAC;QACV,EAAE,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;IAChB,CAAC;IAED,OAAO,EAAE,CAAA;AACX,CAAC;AAED,MAAM,UAAU,KAAK,CACnB,IAAY,EACZ,IAA4C;IAE5C,MAAM,EAAE,GAAG,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;IAC/B,IAAI,EAAE,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACpB,MAAM,IAAI,KAAK,CAAC,qBAAqB,CAAC,CAAA;IACxC,CAAC;IACD,IAAI,EAAE,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QAClB,MAAM,IAAI,KAAK,CAAC,+BAA+B,CAAC,CAAA;IAClD,CAAC;IACD,OAAO,EAAE,CAAC,CAAC,CAAE,CAAA;AACf,CAAC"}
|
package/dist/types.d.ts
CHANGED
|
@@ -34,11 +34,13 @@ export interface InterProScanMatch {
|
|
|
34
34
|
name: string;
|
|
35
35
|
description: string;
|
|
36
36
|
accession: string;
|
|
37
|
+
featureType?: string;
|
|
37
38
|
};
|
|
38
39
|
};
|
|
39
40
|
locations: {
|
|
40
41
|
start: number;
|
|
41
42
|
end: number;
|
|
43
|
+
strand?: number;
|
|
42
44
|
}[];
|
|
43
45
|
}
|
|
44
46
|
export interface InterProScanResults {
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "msa-parsers",
|
|
3
|
-
"version": "5.
|
|
3
|
+
"version": "5.5.0",
|
|
4
4
|
"license": "MIT",
|
|
5
5
|
"type": "module",
|
|
6
6
|
"repository": {
|
|
@@ -28,7 +28,7 @@
|
|
|
28
28
|
},
|
|
29
29
|
"devDependencies": {
|
|
30
30
|
"typescript": "^6.0.3",
|
|
31
|
-
"vitest": "^4.1.
|
|
31
|
+
"vitest": "^4.1.9"
|
|
32
32
|
},
|
|
33
33
|
"scripts": {
|
|
34
34
|
"clean": "rimraf dist",
|
|
@@ -33,6 +33,7 @@ describe('gffToInterProResults', () => {
|
|
|
33
33
|
accession: 'PF00001',
|
|
34
34
|
name: '7tm_1',
|
|
35
35
|
description: 'GPCR family',
|
|
36
|
+
featureType: 'protein_match',
|
|
36
37
|
})
|
|
37
38
|
expect(result.seq1?.matches[0]?.locations).toEqual([{ start: 10, end: 50 }])
|
|
38
39
|
expect(result.seq1?.xref).toEqual([{ id: 'seq1' }])
|
|
@@ -136,6 +137,68 @@ describe('gffToInterProResults', () => {
|
|
|
136
137
|
])
|
|
137
138
|
})
|
|
138
139
|
|
|
140
|
+
test('gives gene-level features a direction but leaves exons/domains as blocks', () => {
|
|
141
|
+
const records: GFFRecord[] = [
|
|
142
|
+
{
|
|
143
|
+
seq_id: 'seq1',
|
|
144
|
+
source: 'x',
|
|
145
|
+
type: 'gene',
|
|
146
|
+
start: 5,
|
|
147
|
+
end: 50,
|
|
148
|
+
score: 0,
|
|
149
|
+
strand: '+',
|
|
150
|
+
phase: '.',
|
|
151
|
+
Name: 'GENEA',
|
|
152
|
+
},
|
|
153
|
+
{
|
|
154
|
+
seq_id: 'seq1',
|
|
155
|
+
source: 'x',
|
|
156
|
+
type: 'mRNA',
|
|
157
|
+
start: 60,
|
|
158
|
+
end: 90,
|
|
159
|
+
score: 0,
|
|
160
|
+
strand: '-',
|
|
161
|
+
phase: '.',
|
|
162
|
+
Name: 'GENEB',
|
|
163
|
+
},
|
|
164
|
+
{
|
|
165
|
+
seq_id: 'seq1',
|
|
166
|
+
source: 'x',
|
|
167
|
+
type: 'exon',
|
|
168
|
+
start: 5,
|
|
169
|
+
end: 20,
|
|
170
|
+
score: 0,
|
|
171
|
+
strand: '+',
|
|
172
|
+
phase: '.',
|
|
173
|
+
Name: 'exon-1',
|
|
174
|
+
},
|
|
175
|
+
{
|
|
176
|
+
seq_id: 'seq1',
|
|
177
|
+
source: 'x',
|
|
178
|
+
type: 'protein_match',
|
|
179
|
+
start: 5,
|
|
180
|
+
end: 20,
|
|
181
|
+
score: 0,
|
|
182
|
+
strand: '+',
|
|
183
|
+
phase: '.',
|
|
184
|
+
Name: 'PF00001',
|
|
185
|
+
},
|
|
186
|
+
]
|
|
187
|
+
const result = gffToInterProResults(records)
|
|
188
|
+
const byAccession = Object.fromEntries(
|
|
189
|
+
result.seq1!.matches.map(m => [
|
|
190
|
+
m.signature.entry!.accession,
|
|
191
|
+
m.locations[0]!.strand,
|
|
192
|
+
]),
|
|
193
|
+
)
|
|
194
|
+
expect(byAccession).toEqual({
|
|
195
|
+
GENEA: 1, // + gene -> arrow right
|
|
196
|
+
GENEB: -1, // - gene -> arrow left
|
|
197
|
+
'exon-1': undefined, // exon stays a block even though it is stranded
|
|
198
|
+
PF00001: undefined, // protein domain stays a block
|
|
199
|
+
})
|
|
200
|
+
})
|
|
201
|
+
|
|
139
202
|
test('uses ID as fallback for Name', () => {
|
|
140
203
|
const records: GFFRecord[] = [
|
|
141
204
|
{
|
package/src/gff/gffToInterPro.ts
CHANGED
|
@@ -14,6 +14,32 @@ import type {
|
|
|
14
14
|
* - start/end: domain positions (1-based)
|
|
15
15
|
* - Attributes: Name (accession), signature_desc (name), Dbxref, etc.
|
|
16
16
|
*/
|
|
17
|
+
// Feature types that read as a directional "gene" and get an arrowhead in the
|
|
18
|
+
// overlay. Exon/CDS/UTR/domain features deliberately stay rectangular blocks —
|
|
19
|
+
// turning every exon into an arrow is misleading, since exons are segments of a
|
|
20
|
+
// single transcript, not independently-oriented genes.
|
|
21
|
+
const GENE_LEVEL_TYPES = new Set([
|
|
22
|
+
'gene',
|
|
23
|
+
'pseudogene',
|
|
24
|
+
'mRNA',
|
|
25
|
+
'transcript',
|
|
26
|
+
'primary_transcript',
|
|
27
|
+
'ncRNA',
|
|
28
|
+
'tRNA',
|
|
29
|
+
'rRNA',
|
|
30
|
+
'snRNA',
|
|
31
|
+
'snoRNA',
|
|
32
|
+
'miRNA',
|
|
33
|
+
'lnc_RNA',
|
|
34
|
+
])
|
|
35
|
+
|
|
36
|
+
// +1/-1 for a stranded gene-level feature, undefined otherwise (which the
|
|
37
|
+
// renderer draws as a plain block).
|
|
38
|
+
function geneStrand({ type, strand }: GFFRecord): number | undefined {
|
|
39
|
+
const directional = strand === '+' ? 1 : strand === '-' ? -1 : undefined
|
|
40
|
+
return GENE_LEVEL_TYPES.has(type) ? directional : undefined
|
|
41
|
+
}
|
|
42
|
+
|
|
17
43
|
export function gffToInterProResults(
|
|
18
44
|
gffRecords: GFFRecord[],
|
|
19
45
|
): Record<string, InterProScanResults> {
|
|
@@ -33,11 +59,16 @@ export function gffToInterProResults(
|
|
|
33
59
|
for (const [seqId, records] of bySequence) {
|
|
34
60
|
const matchesByAccession = new Map<
|
|
35
61
|
string,
|
|
36
|
-
{ start: number; end: number }[]
|
|
62
|
+
{ start: number; end: number; strand?: number }[]
|
|
37
63
|
>()
|
|
38
64
|
const matchInfo = new Map<
|
|
39
65
|
string,
|
|
40
|
-
{
|
|
66
|
+
{
|
|
67
|
+
name: string
|
|
68
|
+
description: string
|
|
69
|
+
accession: string
|
|
70
|
+
featureType: string
|
|
71
|
+
}
|
|
41
72
|
>()
|
|
42
73
|
|
|
43
74
|
for (const record of records) {
|
|
@@ -56,16 +87,24 @@ export function gffToInterProResults(
|
|
|
56
87
|
name
|
|
57
88
|
|
|
58
89
|
if (!matchInfo.has(accession)) {
|
|
59
|
-
matchInfo.set(accession, {
|
|
90
|
+
matchInfo.set(accession, {
|
|
91
|
+
name,
|
|
92
|
+
description,
|
|
93
|
+
accession,
|
|
94
|
+
featureType: record.type,
|
|
95
|
+
})
|
|
60
96
|
}
|
|
61
97
|
|
|
98
|
+
const location = {
|
|
99
|
+
start: record.start,
|
|
100
|
+
end: record.end,
|
|
101
|
+
strand: geneStrand(record),
|
|
102
|
+
}
|
|
62
103
|
const locations = matchesByAccession.get(accession)
|
|
63
104
|
if (locations) {
|
|
64
|
-
locations.push(
|
|
105
|
+
locations.push(location)
|
|
65
106
|
} else {
|
|
66
|
-
matchesByAccession.set(accession, [
|
|
67
|
-
{ start: record.start, end: record.end },
|
|
68
|
-
])
|
|
107
|
+
matchesByAccession.set(accession, [location])
|
|
69
108
|
}
|
|
70
109
|
}
|
|
71
110
|
|
package/src/gff/parseGFF.ts
CHANGED
|
@@ -23,9 +23,17 @@ function parseAttributes(col9?: string): Record<string, string | undefined> {
|
|
|
23
23
|
const eq = f.indexOf('=')
|
|
24
24
|
const key = (eq === -1 ? f : f.slice(0, eq)).trim()
|
|
25
25
|
const val = eq === -1 ? undefined : f.slice(eq + 1)
|
|
26
|
+
// split on comma (the GFF3 multi-value separator) BEFORE decoding, so a
|
|
27
|
+
// literal comma encoded as %2C survives the split and isn't mistaken
|
|
28
|
+
// for a separator
|
|
26
29
|
return [
|
|
27
30
|
key,
|
|
28
|
-
val
|
|
31
|
+
val
|
|
32
|
+
? val
|
|
33
|
+
.split(',')
|
|
34
|
+
.map(v => safeDecode(v).trim())
|
|
35
|
+
.join(' ')
|
|
36
|
+
: undefined,
|
|
29
37
|
]
|
|
30
38
|
})
|
|
31
39
|
.filter(([key]) => key !== ''),
|
package/src/msa/FastaMSA.ts
CHANGED
|
@@ -6,6 +6,10 @@ export default class FastaMSA extends BaseMSA {
|
|
|
6
6
|
colonNormalized: Record<string, string>
|
|
7
7
|
}
|
|
8
8
|
|
|
9
|
+
// explicit insertion-ordered ids: object key order reorders integer-like
|
|
10
|
+
// keys (e.g. a numeric ">123" defline) to the front, scrambling row order
|
|
11
|
+
private orderedNames: string[] = []
|
|
12
|
+
|
|
9
13
|
constructor(text: string) {
|
|
10
14
|
super()
|
|
11
15
|
const seqdata: Record<string, string> = {}
|
|
@@ -23,6 +27,7 @@ export default class FastaMSA extends BaseMSA {
|
|
|
23
27
|
const id = spaceIdx === -1 ? defLine : defLine.slice(0, spaceIdx)
|
|
24
28
|
if (id) {
|
|
25
29
|
seqdata[id] = entry.slice(newlineIdx + 1).replaceAll(/\s/g, '')
|
|
30
|
+
this.orderedNames.push(id)
|
|
26
31
|
if (id.includes(':')) {
|
|
27
32
|
colonNormalized[id.replaceAll(':', '_')] = id
|
|
28
33
|
}
|
|
@@ -36,7 +41,7 @@ export default class FastaMSA extends BaseMSA {
|
|
|
36
41
|
}
|
|
37
42
|
|
|
38
43
|
getNames() {
|
|
39
|
-
return
|
|
44
|
+
return this.orderedNames
|
|
40
45
|
}
|
|
41
46
|
|
|
42
47
|
getRow(name: string) {
|
|
@@ -48,7 +53,7 @@ export default class FastaMSA extends BaseMSA {
|
|
|
48
53
|
}
|
|
49
54
|
|
|
50
55
|
getWidth() {
|
|
51
|
-
const name =
|
|
52
|
-
return this.getRow(name).length
|
|
56
|
+
const name = this.orderedNames[0]
|
|
57
|
+
return name === undefined ? 0 : this.getRow(name).length
|
|
53
58
|
}
|
|
54
59
|
}
|
package/src/msa/StockholmMSA.ts
CHANGED
|
@@ -14,7 +14,11 @@ export default class StockholmMSA extends BaseMSA {
|
|
|
14
14
|
super()
|
|
15
15
|
const res = parseAll(text)
|
|
16
16
|
this.data = res
|
|
17
|
-
|
|
17
|
+
const aln = res[currentAlignment] ?? res[0]
|
|
18
|
+
if (!aln) {
|
|
19
|
+
throw new Error('No alignments found in Stockholm file')
|
|
20
|
+
}
|
|
21
|
+
this.MSA = aln
|
|
18
22
|
}
|
|
19
23
|
|
|
20
24
|
getMSA() {
|
|
@@ -26,8 +30,8 @@ export default class StockholmMSA extends BaseMSA {
|
|
|
26
30
|
}
|
|
27
31
|
|
|
28
32
|
getWidth() {
|
|
29
|
-
const name = Object.keys(this.MSA.seqdata)[0]
|
|
30
|
-
return this.getRow(name).length
|
|
33
|
+
const name = Object.keys(this.MSA.seqdata)[0]
|
|
34
|
+
return name === undefined ? 0 : this.getRow(name).length
|
|
31
35
|
}
|
|
32
36
|
|
|
33
37
|
get alignmentNames() {
|
package/src/msa/index.test.ts
CHANGED
|
@@ -18,6 +18,20 @@ GHIKL`
|
|
|
18
18
|
expect(msa.getNames()).toEqual(['seq1', 'seq2'])
|
|
19
19
|
})
|
|
20
20
|
|
|
21
|
+
test('preserves row order for numeric FASTA ids', () => {
|
|
22
|
+
// object key order would hoist integer-like keys ('10' before '2'),
|
|
23
|
+
// scrambling the alignment; getNames must keep file order
|
|
24
|
+
const fasta = `>3
|
|
25
|
+
ACDEF
|
|
26
|
+
>1
|
|
27
|
+
GHIKL
|
|
28
|
+
>2
|
|
29
|
+
MNPQR`
|
|
30
|
+
const msa = parseMSA(fasta)
|
|
31
|
+
|
|
32
|
+
expect(msa.getNames()).toEqual(['3', '1', '2'])
|
|
33
|
+
})
|
|
34
|
+
|
|
21
35
|
test('parses A3M format', () => {
|
|
22
36
|
const a3m = `>seq1
|
|
23
37
|
ACDEFghiKLMNPQ
|
|
@@ -24,6 +24,21 @@ function createStockholm(): StockholmData {
|
|
|
24
24
|
}
|
|
25
25
|
}
|
|
26
26
|
|
|
27
|
+
// records before a "# STOCKHOLM 1.0" header are an error in strict mode,
|
|
28
|
+
// otherwise they implicitly start a new alignment
|
|
29
|
+
function ensureStock(
|
|
30
|
+
stock: StockholmData | null,
|
|
31
|
+
strict: boolean,
|
|
32
|
+
): StockholmData {
|
|
33
|
+
if (stock) {
|
|
34
|
+
return stock
|
|
35
|
+
}
|
|
36
|
+
if (strict) {
|
|
37
|
+
throw new Error('No format header: # STOCKHOLM 1.0')
|
|
38
|
+
}
|
|
39
|
+
return createStockholm()
|
|
40
|
+
}
|
|
41
|
+
|
|
27
42
|
const formatStartRegex = /^# STOCKHOLM 1.0/
|
|
28
43
|
const formatEndRegex = /^\/\/\s*$/
|
|
29
44
|
const gfRegex = /^#=GF\s+(\S+)\s+(.*?)\s*$/
|
|
@@ -57,36 +72,21 @@ export function parseAll(
|
|
|
57
72
|
}
|
|
58
73
|
stock = null
|
|
59
74
|
} else if ((match = gfRegex.exec(line))) {
|
|
60
|
-
|
|
61
|
-
if (options.strict) {
|
|
62
|
-
throw new Error('No format header: # STOCKHOLM 1.0')
|
|
63
|
-
}
|
|
64
|
-
stock = createStockholm()
|
|
65
|
-
}
|
|
75
|
+
stock = ensureStock(stock, !!options.strict)
|
|
66
76
|
const tag = match[1]!
|
|
67
77
|
if (!stock.gf[tag]) {
|
|
68
78
|
stock.gf[tag] = []
|
|
69
79
|
}
|
|
70
80
|
stock.gf[tag].push(match[2]!)
|
|
71
81
|
} else if ((match = gcRegex.exec(line))) {
|
|
72
|
-
|
|
73
|
-
if (options.strict) {
|
|
74
|
-
throw new Error('No format header: # STOCKHOLM 1.0')
|
|
75
|
-
}
|
|
76
|
-
stock = createStockholm()
|
|
77
|
-
}
|
|
82
|
+
stock = ensureStock(stock, !!options.strict)
|
|
78
83
|
const tag = match[1]!
|
|
79
84
|
if (!stock.gc[tag]) {
|
|
80
85
|
stock.gc[tag] = ''
|
|
81
86
|
}
|
|
82
87
|
stock.gc[tag] += match[2]!
|
|
83
88
|
} else if ((match = gsRegex.exec(line))) {
|
|
84
|
-
|
|
85
|
-
if (options.strict) {
|
|
86
|
-
throw new Error('No format header: # STOCKHOLM 1.0')
|
|
87
|
-
}
|
|
88
|
-
stock = createStockholm()
|
|
89
|
-
}
|
|
89
|
+
stock = ensureStock(stock, !!options.strict)
|
|
90
90
|
const seqname = match[1]!
|
|
91
91
|
const tag = match[2]!
|
|
92
92
|
const value = match[3]!
|
|
@@ -98,12 +98,7 @@ export function parseAll(
|
|
|
98
98
|
}
|
|
99
99
|
stock.gs[tag][seqname].push(value)
|
|
100
100
|
} else if ((match = grRegex.exec(line))) {
|
|
101
|
-
|
|
102
|
-
if (options.strict) {
|
|
103
|
-
throw new Error('No format header: # STOCKHOLM 1.0')
|
|
104
|
-
}
|
|
105
|
-
stock = createStockholm()
|
|
106
|
-
}
|
|
101
|
+
stock = ensureStock(stock, !!options.strict)
|
|
107
102
|
const seqname = match[1]!
|
|
108
103
|
const tag = match[2]!
|
|
109
104
|
const value = match[3]!
|
|
@@ -115,12 +110,7 @@ export function parseAll(
|
|
|
115
110
|
}
|
|
116
111
|
stock.gr[tag][seqname] += value
|
|
117
112
|
} else if ((match = lineRegex.exec(line))) {
|
|
118
|
-
|
|
119
|
-
if (options.strict) {
|
|
120
|
-
throw new Error('No format header: # STOCKHOLM 1.0')
|
|
121
|
-
}
|
|
122
|
-
stock = createStockholm()
|
|
123
|
-
}
|
|
113
|
+
stock = ensureStock(stock, !!options.strict)
|
|
124
114
|
const seqname = match[1]!
|
|
125
115
|
const seqdata = match[2]!
|
|
126
116
|
if (!stock.seqdata[seqname]) {
|
package/src/types.ts
CHANGED
|
@@ -38,9 +38,13 @@ export interface InterProScanMatch {
|
|
|
38
38
|
name: string
|
|
39
39
|
description: string
|
|
40
40
|
accession: string
|
|
41
|
+
// original GFF feature type (exon, CDS, gene, ...) when sourced from GFF;
|
|
42
|
+
// lets the viewer treat ordinal segments (exons) differently from
|
|
43
|
+
// categorical domains
|
|
44
|
+
featureType?: string
|
|
41
45
|
}
|
|
42
46
|
}
|
|
43
|
-
locations: { start: number; end: number }[]
|
|
47
|
+
locations: { start: number; end: number; strand?: number }[]
|
|
44
48
|
}
|
|
45
49
|
|
|
46
50
|
export interface InterProScanResults {
|