msa-parsers 5.4.1 → 5.6.0
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/msa/BaseMSA.js.map +1 -1
- package/dist/msa/index.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/msa/BaseMSA.ts +1 -2
- package/src/msa/index.ts +1 -5
- 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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+
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|
package/dist/msa/BaseMSA.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"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,
|
|
1
|
+
{"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,SAC6D,CAAA;IACtE,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"}
|
package/dist/msa/index.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
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;
|
|
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;AAOzD,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/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": "5.6.0",
|
|
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": "^4.1.10"
|
|
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/msa/BaseMSA.ts
CHANGED
|
@@ -21,8 +21,7 @@ export default abstract class BaseMSA {
|
|
|
21
21
|
|
|
22
22
|
getRowData(_name: string) {
|
|
23
23
|
return undefined as
|
|
24
|
-
|
|
25
|
-
| undefined
|
|
24
|
+
{ name?: string; accession?: string; dbxref?: string } | undefined
|
|
26
25
|
}
|
|
27
26
|
|
|
28
27
|
getStructures(): Record<string, unknown> {
|
package/src/msa/index.ts
CHANGED
|
@@ -8,11 +8,7 @@ export { parseEmfTree } from 'emf-js'
|
|
|
8
8
|
export { default as parseNewick } from './parseNewick.ts'
|
|
9
9
|
|
|
10
10
|
export type MSAParserType =
|
|
11
|
-
|
|
|
12
|
-
| A3mMSA
|
|
13
|
-
| FastaMSA
|
|
14
|
-
| EmfMSA
|
|
15
|
-
| ClustalMSA
|
|
11
|
+
StockholmMSA | A3mMSA | FastaMSA | EmfMSA | ClustalMSA
|
|
16
12
|
|
|
17
13
|
export type MSAFormat = 'stockholm' | 'a3m' | 'fasta' | 'emf' | 'clustal'
|
|
18
14
|
|
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 {
|