@apollo-annotation/shared 0.3.8 → 0.3.10
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/Changes/AddAssemblyAndFeaturesFromFileChange.d.ts +3 -0
- package/dist/Changes/AddAssemblyAndFeaturesFromFileChange.js +5 -4
- package/dist/Changes/AddAssemblyAndFeaturesFromFileChange.js.map +1 -1
- package/dist/Changes/AddFeatureChange.js +23 -4
- package/dist/Changes/AddFeatureChange.js.map +1 -1
- package/dist/Changes/AddFeaturesFromFileChange.d.ts +3 -0
- package/dist/Changes/AddFeaturesFromFileChange.js +5 -2
- package/dist/Changes/AddFeaturesFromFileChange.js.map +1 -1
- package/dist/Changes/AddRefSeqAliasesChange.js +1 -4
- package/dist/Changes/AddRefSeqAliasesChange.js.map +1 -1
- package/dist/Changes/FromFileBaseChange.d.ts +2 -0
- package/dist/Changes/FromFileBaseChange.js +26 -11
- package/dist/Changes/FromFileBaseChange.js.map +1 -1
- package/dist/Checks/CDSCheck.js +5 -4
- package/dist/Checks/CDSCheck.js.map +1 -1
- package/dist/Checks/TranscriptCheck.js +12 -12
- package/dist/Checks/TranscriptCheck.js.map +1 -1
- package/dist/Checks/util.d.ts +2 -0
- package/dist/Checks/util.js +15 -0
- package/dist/Checks/util.js.map +1 -0
- package/dist/GFF3/annotationFeatureToGFF3.js +3 -1
- package/dist/GFF3/annotationFeatureToGFF3.js.map +1 -1
- package/dist/GFF3/annotationFeatureToGFF3.test.js +19 -5
- package/dist/GFF3/annotationFeatureToGFF3.test.js.map +1 -1
- package/dist/GFF3/gff3ToAnnotationFeature.d.ts +1 -1
- package/dist/GFF3/gff3ToAnnotationFeature.js +9 -12
- package/dist/GFF3/gff3ToAnnotationFeature.js.map +1 -1
- package/dist/GFF3/gff3ToAnnotationFeature.test.d.ts +1 -2
- package/dist/GFF3/gff3ToAnnotationFeature.test.js +25 -98
- package/dist/GFF3/gff3ToAnnotationFeature.test.js.map +1 -1
- package/dist/GFF3/testUtil.d.ts +6 -0
- package/dist/GFF3/testUtil.js +24 -0
- package/dist/GFF3/testUtil.js.map +1 -0
- package/dist/tsconfig.tsbuildinfo +1 -1
- package/package.json +6 -6
- package/src/Changes/AddAssemblyAndFeaturesFromFileChange.ts +6 -5
- package/src/Changes/AddFeatureChange.ts +26 -4
- package/src/Changes/AddFeaturesFromFileChange.ts +6 -1
- package/src/Changes/AddRefSeqAliasesChange.ts +1 -5
- package/src/Changes/FromFileBaseChange.ts +28 -16
- package/src/Checks/CDSCheck.ts +6 -4
- package/src/Checks/TranscriptCheck.ts +11 -12
- package/src/Checks/util.ts +13 -0
- package/src/GFF3/annotationFeatureToGFF3.test.ts +24 -2
- package/src/GFF3/annotationFeatureToGFF3.ts +4 -1
- package/src/GFF3/gff3ToAnnotationFeature.test.ts +26 -97
- package/src/GFF3/gff3ToAnnotationFeature.ts +7 -16
- package/src/GFF3/testUtil.ts +25 -0
- package/test_data/gene_with_two_cds.gff3 +6 -0
- package/test_data/gene_with_two_cds.json +69 -0
- package/test_data/single_feature_no_children.gff3 +1 -0
- package/test_data/single_feature_no_children.json +14 -0
- package/test_data/single_feature_two_children.gff3 +3 -0
- package/test_data/single_feature_two_children.json +44 -0
- package/test_data/two_cds.gff3 +0 -9
- package/test_data/two_cds.json +0 -67
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@@ -2,13 +2,27 @@
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Object.defineProperty(exports, "__esModule", { value: true });
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/* eslint-disable prefer-destructuring */
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/* eslint-disable @typescript-eslint/no-floating-promises */
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const node_fs_1 = require("node:fs");
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const node_test_1 = require("node:test");
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const gff_1 = require("@gmod/gff");
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const chai_1 = require("chai");
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const annotationFeatureToGFF3_1 = require("./annotationFeatureToGFF3");
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const
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const testUtil_1 = require("./testUtil");
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(0, node_test_1.describe)('Converts AnnotationFeatureSnapshot JSON to GFF3 when', () => {
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for (const testCase of testUtil_1.testCases) {
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const { filenameStem, description } = testCase;
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(0, node_test_1.it)(description, () => {
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const annotationFeatures = JSON.parse((0, node_fs_1.readFileSync)(`test_data/${filenameStem}.json`, 'utf8'));
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const expectedGFF3 = (0, node_fs_1.readFileSync)(`test_data/${filenameStem}.gff3`, 'utf8');
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const gffFeatures = annotationFeatures.map((annotationFeature) => (0, annotationFeatureToGFF3_1.annotationFeatureToGFF3)(annotationFeature));
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const gff3 = (0, gff_1.formatSync)(gffFeatures);
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(0, chai_1.expect)(gff3).to.equal(expectedGFF3);
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});
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}
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});
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(0, node_test_1.describe)('annotationFeatureToGFF3', () => {
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(0, node_test_1.it)('Test mandatory columns', () => {
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const annotationFeature = (0,
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const annotationFeature = (0, testUtil_1.readAnnotationFeatureSnapshot)('test_data/gene.json');
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const [gff3Feature] = (0, annotationFeatureToGFF3_1.annotationFeatureToGFF3)(annotationFeature);
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chai_1.assert.deepEqual(gff3Feature.seq_id, 'chr1');
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chai_1.assert.deepEqual(gff3Feature.type, 'gene');
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@@ -88,7 +102,7 @@ const gff3ToAnnotationFeature_test_1 = require("./gff3ToAnnotationFeature.test")
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chai_1.assert.deepEqual(gff3Feature.score, null);
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});
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(0, node_test_1.it)('Convert one gene test attributes', () => {
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const annotationFeature = (0,
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const annotationFeature = (0, testUtil_1.readAnnotationFeatureSnapshot)('test_data/gene.json');
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const [gff3Feature] = (0, annotationFeatureToGFF3_1.annotationFeatureToGFF3)(annotationFeature);
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chai_1.assert.deepEqual(gff3Feature.attributes?.Name, ['EDEN']);
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chai_1.assert.deepEqual(gff3Feature.attributes?.testid, ['t001', 't003']);
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@@ -107,7 +121,7 @@ const gff3ToAnnotationFeature_test_1 = require("./gff3ToAnnotationFeature.test")
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chai_1.assert.deepEqual(gff3Feature.attributes?.Is_circular, ['true']);
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});
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(0, node_test_1.it)('Convert one gene test children', () => {
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const annotationFeature = (0,
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const annotationFeature = (0, testUtil_1.readAnnotationFeatureSnapshot)('test_data/gene.json');
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const [gff3Feature] = (0, annotationFeatureToGFF3_1.annotationFeatureToGFF3)(annotationFeature);
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const [children] = gff3Feature.child_features;
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const [mrna] = children;
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@@ -119,7 +133,7 @@ const gff3ToAnnotationFeature_test_1 = require("./gff3ToAnnotationFeature.test")
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chai_1.assert.deepEqual(cds.attributes?.Parent, ['mRNA10001']);
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});
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(0, node_test_1.it)('Convert CDSs', () => {
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const annotationFeature = (0,
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const annotationFeature = (0, testUtil_1.readAnnotationFeatureSnapshot)('test_data/gene.json');
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const [gff3Feature] = (0, annotationFeatureToGFF3_1.annotationFeatureToGFF3)(annotationFeature);
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const [children] = gff3Feature.child_features;
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const [mrna] = children;
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@@ -1 +1 @@
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-
{"version":3,"file":"annotationFeatureToGFF3.test.js","sourceRoot":"","sources":["../../src/GFF3/annotationFeatureToGFF3.test.ts"],"names":[],"mappings":";;AAAA,yCAAyC;AACzC,4DAA4D;AAC5D,yCAAwC;AAGxC,+
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{"version":3,"file":"annotationFeatureToGFF3.test.js","sourceRoot":"","sources":["../../src/GFF3/annotationFeatureToGFF3.test.ts"],"names":[],"mappings":";;AAAA,yCAAyC;AACzC,4DAA4D;AAC5D,qCAAsC;AACtC,yCAAwC;AAGxC,mCAAsC;AACtC,+BAAqC;AAErC,uEAAmE;AACnE,yCAAqE;AAErE,IAAA,oBAAQ,EAAC,sDAAsD,EAAE,GAAG,EAAE;IACpE,KAAK,MAAM,QAAQ,IAAI,oBAAS,EAAE,CAAC;QACjC,MAAM,EAAE,YAAY,EAAE,WAAW,EAAE,GAAG,QAAQ,CAAA;QAC9C,IAAA,cAAE,EAAC,WAAW,EAAE,GAAG,EAAE;YACnB,MAAM,kBAAkB,GAAG,IAAI,CAAC,KAAK,CACnC,IAAA,sBAAY,EAAC,aAAa,YAAY,OAAO,EAAE,MAAM,CAAC,CACxB,CAAA;YAChC,MAAM,YAAY,GAAG,IAAA,sBAAY,EAC/B,aAAa,YAAY,OAAO,EAChC,MAAM,CACP,CAAA;YACD,MAAM,WAAW,GAAG,kBAAkB,CAAC,GAAG,CAAC,CAAC,iBAAiB,EAAE,EAAE,CAC/D,IAAA,iDAAuB,EAAC,iBAAiB,CAAC,CAC3C,CAAA;YACD,MAAM,IAAI,GAAG,IAAA,gBAAU,EAAC,WAAW,CAAC,CAAA;YACpC,IAAA,aAAM,EAAC,IAAI,CAAC,CAAC,EAAE,CAAC,KAAK,CAAC,YAAY,CAAC,CAAA;QACrC,CAAC,CAAC,CAAA;IACJ,CAAC;AACH,CAAC,CAAC,CAAA;AAEF,IAAA,oBAAQ,EAAC,yBAAyB,EAAE,GAAG,EAAE;IACvC,IAAA,cAAE,EAAC,wBAAwB,EAAE,GAAG,EAAE;QAChC,MAAM,iBAAiB,GAAG,IAAA,wCAA6B,EACrD,qBAAqB,CACtB,CAAA;QACD,MAAM,CAAC,WAAW,CAAC,GAAG,IAAA,iDAAuB,EAAC,iBAAiB,CAAC,CAAA;QAEhE,aAAM,CAAC,SAAS,CAAC,WAAW,CAAC,MAAM,EAAE,MAAM,CAAC,CAAA;QAC5C,aAAM,CAAC,SAAS,CAAC,WAAW,CAAC,IAAI,EAAE,MAAM,CAAC,CAAA;QAC1C,aAAM,CAAC,SAAS,CAAC,WAAW,CAAC,KAAK,EAAE,IAAI,CAAC,CAAA;QACzC,aAAM,CAAC,SAAS,CAAC,WAAW,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;QACvC,aAAM,CAAC,SAAS,CAAC,WAAW,CAAC,MAAM,EAAE,GAAG,CAAC,CAAA;QACzC,aAAM,CAAC,SAAS,CAAC,WAAW,CAAC,KAAK,EAAE,GAAG,CAAC,CAAA;QACxC,aAAM,CAAC,SAAS,CAAC,WAAW,CAAC,MAAM,EAAE,WAAW,CAAC,CAAA;IACnD,CAAC,CAAC,CAAA;IACF,IAAA,cAAE,EAAC,4DAA4D,EAAE,GAAG,EAAE;QACpE,MAAM,iBAAiB,GAAG,IAAI,CAAC,KAAK,CAAC;;;;;;;;MAQnC,CAA8B,CAAA;QAChC,MAAM,CAAC,WAAW,CAAC,GAAG,IAAA,iDAAuB,EAAC,iBAAiB,CAAC,CAAA;QAChE,aAAM,CAAC,WAAW,CAAC,WAAW,CAAC,UAAU,EAAE,EAAE,CAAC,CAAA;IAChD,CAAC,CAAC,CAAA;IACF,IAAA,cAAE,EAAC,4DAA4D,EAAE,GAAG,EAAE;QACpE,MAAM,iBAAiB,GAAG,IAAI,CAAC,KAAK,CAAC;;;;;;;;;;;;;;;;;;;MAmBnC,CAA8B,CAAA;QAChC,MAAM,CAAC,WAAW,CAAC,GAAG,IAAA,iDAAuB,EAAC,iBAAiB,CAAC,CAAA;QAChE,aAAM,CAAC,SAAS,CAAC,WAAW,CAAC,UAAU,EAAE,EAAE,EAAE,CAAC,0BAA0B,CAAC,CAAC,CAAA;IAC5E,CAAC,CAAC,CAAA;IACF,IAAA,cAAE,EAAC,yBAAyB,EAAE,GAAG,EAAE;QACjC,MAAM,iBAAiB,GAAG,IAAI,CAAC,KAAK,CAAC;;;;;;;;;;;MAWnC,CAA8B,CAAA;QAChC,MAAM,CAAC,WAAW,CAAC,GAAG,IAAA,iDAAuB,EAAC,iBAAiB,CAAC,CAAA;QAChE,aAAM,CAAC,SAAS,CAAC,WAAW,CAAC,KAAK,EAAE,GAAG,CAAC,CAAA;IAC1C,CAAC,CAAC,CAAA;IACF,IAAA,cAAE,EAAC,uBAAuB,EAAE,GAAG,EAAE;QAC/B,MAAM,iBAAiB,GAAG,IAAI,CAAC,KAAK,CAAC;;;;;;;;;;;MAWnC,CAA8B,CAAA;QAChC,MAAM,CAAC,WAAW,CAAC,GAAG,IAAA,iDAAuB,EAAC,iBAAiB,CAAC,CAAA;QAChE,aAAM,CAAC,SAAS,CAAC,WAAW,CAAC,KAAK,EAAE,IAAI,CAAC,CAAA;IAC3C,CAAC,CAAC,CAAA;IACF,IAAA,cAAE,EAAC,kCAAkC,EAAE,GAAG,EAAE;QAC1C,MAAM,iBAAiB,GAAG,IAAA,wCAA6B,EACrD,qBAAqB,CACtB,CAAA;QACD,MAAM,CAAC,WAAW,CAAC,GAAG,IAAA,iDAAuB,EAAC,iBAAiB,CAAC,CAAA;QAEhE,aAAM,CAAC,SAAS,CAAC,WAAW,CAAC,UAAU,EAAE,IAAI,EAAE,CAAC,MAAM,CAAC,CAAC,CAAA;QACxD,aAAM,CAAC,SAAS,CAAC,WAAW,CAAC,UAAU,EAAE,MAAM,EAAE,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC,CAAA;QAClE,aAAM,CAAC,SAAS,CAAC,WAAW,CAAC,UAAU,EAAE,EAAE,EAAE,CAAC,WAAW,CAAC,CAAC,CAAA;QAC3D,aAAM,CAAC,SAAS,CAAC,WAAW,CAAC,UAAU,EAAE,aAAa,EAAE;YACtD,QAAQ;YACR,QAAQ;YACR,QAAQ;SACT,CAAC,CAAA;QACF,aAAM,CAAC,SAAS,CAAC,WAAW,CAAC,UAAU,EAAE,KAAK,EAAE,CAAC,SAAS,CAAC,CAAC,CAAA;QAC5D,aAAM,CAAC,SAAS,CAAC,WAAW,CAAC,UAAU,EAAE,MAAM,EAAE,CAAC,UAAU,CAAC,CAAC,CAAA;QAC9D,aAAM,CAAC,SAAS,CAAC,WAAW,CAAC,UAAU,EAAE,GAAG,EAAE,CAAC,OAAO,CAAC,CAAC,CAAA;QACxD,aAAM,CAAC,SAAS,CAAC,WAAW,CAAC,UAAU,EAAE,YAAY,EAAE,CAAC,WAAW,CAAC,CAAC,CAAA;QACrE,aAAM,CAAC,SAAS,CAAC,WAAW,CAAC,UAAU,EAAE,IAAI,EAAE,CAAC,QAAQ,CAAC,CAAC,CAAA;QAC1D,aAAM,CAAC,SAAS,CAAC,WAAW,CAAC,UAAU,EAAE,MAAM,EAAE,CAAC,UAAU,CAAC,CAAC,CAAA;QAC9D,aAAM,CAAC,SAAS,CAAC,WAAW,CAAC,UAAU,EAAE,WAAW,EAAE,CAAC,MAAM,CAAC,CAAC,CAAA;IACjE,CAAC,CAAC,CAAA;IACF,IAAA,cAAE,EAAC,gCAAgC,EAAE,GAAG,EAAE;QACxC,MAAM,iBAAiB,GAAG,IAAA,wCAA6B,EACrD,qBAAqB,CACtB,CAAA;QACD,MAAM,CAAC,WAAW,CAAC,GAAG,IAAA,iDAAuB,EAAC,iBAAiB,CAAC,CAAA;QAChE,MAAM,CAAC,QAAQ,CAAC,GAAG,WAAW,CAAC,cAAc,CAAA;QAC7C,MAAM,CAAC,IAAI,CAAC,GAAG,QAAQ,CAAA;QACvB,aAAM,CAAC,SAAS,CAAC,IAAI,CAAC,IAAI,EAAE,MAAM,CAAC,CAAA;QACnC,aAAM,CAAC,SAAS,CAAC,IAAI,CAAC,UAAU,EAAE,MAAM,EAAE,CAAC,WAAW,CAAC,CAAC,CAAA;QAExD,MAAM,CAAC,GAAG,CAAC,GAAG,IAAI,CAAC,cAAc,CAAC,CAAC,CAAC,CAAA;QACpC,aAAM,CAAC,SAAS,CAAC,GAAG,CAAC,IAAI,EAAE,KAAK,CAAC,CAAA;QACjC,aAAM,CAAC,SAAS,CAAC,GAAG,CAAC,UAAU,EAAE,EAAE,EAAE,CAAC,UAAU,CAAC,CAAC,CAAA;QAClD,aAAM,CAAC,SAAS,CAAC,GAAG,CAAC,UAAU,EAAE,MAAM,EAAE,CAAC,WAAW,CAAC,CAAC,CAAA;IACzD,CAAC,CAAC,CAAA;IACF,IAAA,cAAE,EAAC,cAAc,EAAE,GAAG,EAAE;QACtB,MAAM,iBAAiB,GAAG,IAAA,wCAA6B,EACrD,qBAAqB,CACtB,CAAA;QACD,MAAM,CAAC,WAAW,CAAC,GAAG,IAAA,iDAAuB,EAAC,iBAAiB,CAAC,CAAA;QAChE,MAAM,CAAC,QAAQ,CAAC,GAAG,WAAW,CAAC,cAAc,CAAA;QAC7C,MAAM,CAAC,IAAI,CAAC,GAAG,QAAQ,CAAA;QACvB,MAAM,QAAQ,GAAG,IAAI,CAAC,cAAc,CAAC,MAAM,CAAC,CAAC,KAAK,EAAE,EAAE;YACpD,MAAM,EAAE,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC,UAAU,EAAE,EAAE,CAAA;YAClC,OAAO,EAAE,KAAK,SAAS,IAAI,EAAE,CAAC,CAAC,CAAC,KAAK,UAAU,CAAA;QACjD,CAAC,CAAC,CAAA;QACF,aAAM,CAAC,SAAS,CAAC,QAAQ,CAAC,MAAM,EAAE,CAAC,CAAC,CAAA;QAEpC,MAAM,MAAM,GAAG,QAAQ,CAA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import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
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import { type GFF3Feature } from '@gmod/gff';
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export declare function gff3ToAnnotationFeature(gff3Feature: GFF3Feature, refSeq?: string
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export declare function gff3ToAnnotationFeature(gff3Feature: GFF3Feature, refSeq?: string): AnnotationFeatureSnapshot;
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const bson_objectid_1 = tslib_1.__importDefault(require("bson-objectid"));
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const gffReservedKeys_1 = require("./gffReservedKeys");
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function gff3ToAnnotationFeature(gff3Feature, refSeq
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|
8
|
+
function gff3ToAnnotationFeature(gff3Feature, refSeq) {
|
|
9
9
|
const [firstFeature] = gff3Feature;
|
|
10
10
|
const { end, seq_id: refName, start, strand, type } = firstFeature;
|
|
11
11
|
if (!refName) {
|
|
@@ -21,7 +21,7 @@ function gff3ToAnnotationFeature(gff3Feature, refSeq, featureIds) {
|
|
|
21
21
|
throw new Error(`feature does not have end: ${JSON.stringify(firstFeature)}`);
|
|
22
22
|
}
|
|
23
23
|
const [min, max] = getFeatureMinMax(gff3Feature);
|
|
24
|
-
const convertedChildren = convertChildren(gff3Feature, refSeq
|
|
24
|
+
const convertedChildren = convertChildren(gff3Feature, refSeq);
|
|
25
25
|
const convertedAttributes = convertFeatureAttributes(gff3Feature);
|
|
26
26
|
const feature = {
|
|
27
27
|
_id: new bson_objectid_1.default().toHexString(),
|
|
@@ -47,9 +47,6 @@ function gff3ToAnnotationFeature(gff3Feature, refSeq, featureIds) {
|
|
|
47
47
|
if (convertedAttributes) {
|
|
48
48
|
feature.attributes = convertedAttributes;
|
|
49
49
|
}
|
|
50
|
-
if (featureIds) {
|
|
51
|
-
featureIds.push(feature._id);
|
|
52
|
-
}
|
|
53
50
|
return feature;
|
|
54
51
|
}
|
|
55
52
|
function getFeatureMinMax(gff3Feature) {
|
|
@@ -93,7 +90,7 @@ function convertFeatureAttributes(gff3Feature) {
|
|
|
93
90
|
if (attributesCollections.length > 0) {
|
|
94
91
|
for (const attributesCollection of attributesCollections) {
|
|
95
92
|
for (const [key, val] of Object.entries(attributesCollection)) {
|
|
96
|
-
if (
|
|
93
|
+
if (key === 'Parent') {
|
|
97
94
|
continue;
|
|
98
95
|
}
|
|
99
96
|
const newKey = (0, gffReservedKeys_1.isGFFReservedAttribute)(key) ? gffReservedKeys_1.gffToInternal[key] : key;
|
|
@@ -150,12 +147,12 @@ function convertChildren(gff3Feature, refSeq, featureIds) {
|
|
|
150
147
|
cdsFeatures.push(childFeature);
|
|
151
148
|
}
|
|
152
149
|
else {
|
|
153
|
-
const child = gff3ToAnnotationFeature(childFeature, refSeq
|
|
150
|
+
const child = gff3ToAnnotationFeature(childFeature, refSeq);
|
|
154
151
|
convertedChildren[child._id] = child;
|
|
155
152
|
}
|
|
156
153
|
}
|
|
157
154
|
if (cdsFeatures.length > 0) {
|
|
158
|
-
const processedCDS = processCDS(cdsFeatures, refSeq
|
|
155
|
+
const processedCDS = processCDS(cdsFeatures, refSeq);
|
|
159
156
|
for (const cds of processedCDS) {
|
|
160
157
|
convertedChildren[cds._id] = cds;
|
|
161
158
|
}
|
|
@@ -311,13 +308,13 @@ function mergeAnnotationFeatures(features) {
|
|
|
311
308
|
* should be represented in our internal structure
|
|
312
309
|
* @param cdsFeatures -
|
|
313
310
|
*/
|
|
314
|
-
function processCDS(cdsFeatures, refSeq
|
|
311
|
+
function processCDS(cdsFeatures, refSeq) {
|
|
315
312
|
const locationCounts = cdsFeatures.map((cds) => cds.length);
|
|
316
313
|
// If any CDS have multiple locations, assume it really is multiple CDS
|
|
317
314
|
// (e.g. the mRNA has multiple alternative translational start sites)
|
|
318
315
|
// and process normally.
|
|
319
316
|
if (locationCounts.some((count) => count > 1)) {
|
|
320
|
-
return cdsFeatures.map((cds) => gff3ToAnnotationFeature(cds, refSeq
|
|
317
|
+
return cdsFeatures.map((cds) => gff3ToAnnotationFeature(cds, refSeq));
|
|
321
318
|
}
|
|
322
319
|
// If all CDS have a single location, we guess that this GFF3 represented CDS
|
|
323
320
|
// as multiple features instead of a single feature with multiple locations.
|
|
@@ -338,7 +335,7 @@ function processCDS(cdsFeatures, refSeq, featureIds) {
|
|
|
338
335
|
});
|
|
339
336
|
// If no overlaps, assume it's a single CDS feature
|
|
340
337
|
if (!overlapping) {
|
|
341
|
-
return [gff3ToAnnotationFeature(sortedCDSLocations, refSeq
|
|
338
|
+
return [gff3ToAnnotationFeature(sortedCDSLocations, refSeq)];
|
|
342
339
|
}
|
|
343
340
|
// Some CDS locations overlap, the best we can do is use the original order to
|
|
344
341
|
// guess how to group the locations into features
|
|
@@ -360,6 +357,6 @@ function processCDS(cdsFeatures, refSeq, featureIds) {
|
|
|
360
357
|
lastGroup.push(location);
|
|
361
358
|
}
|
|
362
359
|
}
|
|
363
|
-
return groupedLocations.map((group) => gff3ToAnnotationFeature(group, refSeq
|
|
360
|
+
return groupedLocations.map((group) => gff3ToAnnotationFeature(group, refSeq));
|
|
364
361
|
}
|
|
365
362
|
//# sourceMappingURL=gff3ToAnnotationFeature.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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+
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@@ -1,2 +1 @@
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1
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-
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2
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-
export declare function readAnnotationFeatureSnapshot(fn: string): AnnotationFeatureSnapshot;
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1
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+
export {};
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@@ -1,82 +1,15 @@
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1
1
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"use strict";
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2
2
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Object.defineProperty(exports, "__esModule", { value: true });
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3
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-
exports.readAnnotationFeatureSnapshot = readAnnotationFeatureSnapshot;
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4
3
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const tslib_1 = require("tslib");
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5
4
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/* eslint-disable @typescript-eslint/no-floating-promises */
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6
5
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const node_fs_1 = require("node:fs");
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7
6
|
const node_test_1 = require("node:test");
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8
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-
const gff_1 =
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7
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+
const gff_1 = require("@gmod/gff");
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9
8
|
const chai_1 = require("chai");
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10
9
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const chai_exclude_1 = tslib_1.__importDefault(require("chai-exclude"));
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11
10
|
const gff3ToAnnotationFeature_1 = require("./gff3ToAnnotationFeature");
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11
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+
const testUtil_1 = require("./testUtil");
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12
12
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(0, chai_1.use)(chai_exclude_1.default);
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13
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-
const testCases = [
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14
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-
[
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15
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-
'a feature with no children',
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16
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-
'ctgA example remark 1000 2000 . . . Name=Remark:hga;Alias=hga\n',
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17
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-
{
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18
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-
_id: '66c51f3e002c683eaf98a223',
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19
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refSeq: 'ctgA',
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20
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type: 'remark',
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21
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min: 999,
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22
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-
max: 2000,
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23
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-
attributes: {
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24
|
-
gff_source: ['example'],
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25
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-
gff_name: ['Remark:hga'],
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26
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-
gff_alias: ['hga'],
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27
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-
},
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28
|
-
},
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29
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-
],
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30
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-
[
|
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31
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-
'a feature with two children',
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32
|
-
`ctgA est EST_match 1050 3202 . + . ID=Match1;Name=agt830.5;Target=agt830.5 1 654
|
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33
|
-
ctgA est match_part 1050 1500 . + . Parent=Match1;Name=agt830.5;Target=agt830.5 1 451
|
|
34
|
-
ctgA est match_part 3000 3202 . + . Parent=Match1;Name=agt830.5;Target=agt830.5 452 654
|
|
35
|
-
`,
|
|
36
|
-
{
|
|
37
|
-
_id: '66cf9fbb4e947fa2c27d3d6a',
|
|
38
|
-
refSeq: 'ctgA',
|
|
39
|
-
type: 'EST_match',
|
|
40
|
-
min: 1049,
|
|
41
|
-
max: 3202,
|
|
42
|
-
strand: 1,
|
|
43
|
-
children: {
|
|
44
|
-
'66cf9fbb4e947fa2c27d3d68': {
|
|
45
|
-
_id: '66cf9fbb4e947fa2c27d3d68',
|
|
46
|
-
refSeq: 'ctgA',
|
|
47
|
-
type: 'match_part',
|
|
48
|
-
min: 1049,
|
|
49
|
-
max: 1500,
|
|
50
|
-
strand: 1,
|
|
51
|
-
attributes: {
|
|
52
|
-
gff_source: ['est'],
|
|
53
|
-
gff_name: ['agt830.5'],
|
|
54
|
-
gff_target: ['agt830.5 1 451'],
|
|
55
|
-
},
|
|
56
|
-
},
|
|
57
|
-
'66cf9fbb4e947fa2c27d3d69': {
|
|
58
|
-
_id: '66cf9fbb4e947fa2c27d3d69',
|
|
59
|
-
refSeq: 'ctgA',
|
|
60
|
-
type: 'match_part',
|
|
61
|
-
min: 2999,
|
|
62
|
-
max: 3202,
|
|
63
|
-
strand: 1,
|
|
64
|
-
attributes: {
|
|
65
|
-
gff_source: ['est'],
|
|
66
|
-
gff_name: ['agt830.5'],
|
|
67
|
-
gff_target: ['agt830.5 452 654'],
|
|
68
|
-
},
|
|
69
|
-
},
|
|
70
|
-
},
|
|
71
|
-
attributes: {
|
|
72
|
-
gff_source: ['est'],
|
|
73
|
-
gff_id: ['Match1'],
|
|
74
|
-
gff_name: ['agt830.5'],
|
|
75
|
-
gff_target: ['agt830.5 1 654'],
|
|
76
|
-
},
|
|
77
|
-
},
|
|
78
|
-
],
|
|
79
|
-
];
|
|
80
13
|
function childrenToArray(feature) {
|
|
81
14
|
const { children } = feature;
|
|
82
15
|
if (!children) {
|
|
@@ -88,6 +21,21 @@ function childrenToArray(feature) {
|
|
|
88
21
|
function compareFeatures(feature1, feature2) {
|
|
89
22
|
chai_1.assert.deepEqualExcludingEvery(childrenToArray(feature1), childrenToArray(feature2), '_id');
|
|
90
23
|
}
|
|
24
|
+
(0, node_test_1.describe)('Converts GFF3 to AnnotationFeatureSnapshot JSON when', () => {
|
|
25
|
+
for (const testCase of testUtil_1.testCases) {
|
|
26
|
+
const { filenameStem, description } = testCase;
|
|
27
|
+
(0, node_test_1.it)(description, () => {
|
|
28
|
+
const fileText = (0, node_fs_1.readFileSync)(`test_data/${filenameStem}.gff3`, 'utf8');
|
|
29
|
+
const gffFeatures = (0, gff_1.parseStringSync)(fileText, { parseSequences: false });
|
|
30
|
+
const annotationFeatures = gffFeatures.map((gff3Feature) => (0, gff3ToAnnotationFeature_1.gff3ToAnnotationFeature)(gff3Feature));
|
|
31
|
+
const annotationFeaturesExpected = JSON.parse((0, node_fs_1.readFileSync)(`test_data/${filenameStem}.json`, 'utf8'));
|
|
32
|
+
for (const [i, annotationFeatureExpected,] of annotationFeaturesExpected.entries()) {
|
|
33
|
+
const annotationFeature = annotationFeatures[i];
|
|
34
|
+
compareFeatures(annotationFeature, annotationFeatureExpected);
|
|
35
|
+
}
|
|
36
|
+
});
|
|
37
|
+
}
|
|
38
|
+
});
|
|
91
39
|
function readFeatureFile(fn) {
|
|
92
40
|
const lines = (0, node_fs_1.readFileSync)(fn).toString().split('\n');
|
|
93
41
|
const feature = [];
|
|
@@ -96,23 +44,14 @@ function readFeatureFile(fn) {
|
|
|
96
44
|
feature.push(line);
|
|
97
45
|
}
|
|
98
46
|
}
|
|
99
|
-
const inGff = gff_1.
|
|
47
|
+
const inGff = (0, gff_1.parseStringSync)(feature.join('\n'));
|
|
100
48
|
return inGff;
|
|
101
49
|
}
|
|
102
|
-
function readAnnotationFeatureSnapshot(fn) {
|
|
103
|
-
const lines = (0, node_fs_1.readFileSync)(fn).toString();
|
|
104
|
-
return JSON.parse(lines);
|
|
105
|
-
}
|
|
106
50
|
const [ex1, , ex2, , ex3, , ex4] = readFeatureFile('test_data/gene_representations.gff3');
|
|
107
51
|
(0, node_test_1.describe)('gff3ToAnnotationFeature examples', () => {
|
|
108
52
|
(0, node_test_1.it)('Convert one CDS', () => {
|
|
109
53
|
const actual = (0, gff3ToAnnotationFeature_1.gff3ToAnnotationFeature)(readFeatureFile('test_data/one_cds.gff3')[0]);
|
|
110
|
-
const expected = readAnnotationFeatureSnapshot('test_data/one_cds.json');
|
|
111
|
-
compareFeatures(actual, expected);
|
|
112
|
-
});
|
|
113
|
-
(0, node_test_1.it)('Convert two CDSs', () => {
|
|
114
|
-
const actual = (0, gff3ToAnnotationFeature_1.gff3ToAnnotationFeature)(readFeatureFile('test_data/two_cds.gff3')[0]);
|
|
115
|
-
const expected = readAnnotationFeatureSnapshot('test_data/two_cds.json');
|
|
54
|
+
const expected = (0, testUtil_1.readAnnotationFeatureSnapshot)('test_data/one_cds.json');
|
|
116
55
|
compareFeatures(actual, expected);
|
|
117
56
|
});
|
|
118
57
|
(0, node_test_1.it)('Convert example 1', () => {
|
|
@@ -120,14 +59,14 @@ const [ex1, , ex2, , ex3, , ex4] = readFeatureFile('test_data/gene_representatio
|
|
|
120
59
|
const txt = JSON.stringify(actual, null, 2);
|
|
121
60
|
chai_1.assert.equal(txt.match(/"type": "CDS"/g)?.length, 4);
|
|
122
61
|
chai_1.assert.equal(txt.match(/"type": "TF_binding_site"/g)?.length, 1);
|
|
123
|
-
const expected = readAnnotationFeatureSnapshot('test_data/example01.json');
|
|
62
|
+
const expected = (0, testUtil_1.readAnnotationFeatureSnapshot)('test_data/example01.json');
|
|
124
63
|
compareFeatures(actual, expected);
|
|
125
64
|
});
|
|
126
65
|
(0, node_test_1.it)('Convert example 2', () => {
|
|
127
66
|
const actual = (0, gff3ToAnnotationFeature_1.gff3ToAnnotationFeature)(ex2);
|
|
128
67
|
const txt = JSON.stringify(actual, null, 2);
|
|
129
68
|
chai_1.assert.equal(txt.match(/"type": "CDS"/g)?.length, 4);
|
|
130
|
-
const expected = readAnnotationFeatureSnapshot('test_data/example02.json');
|
|
69
|
+
const expected = (0, testUtil_1.readAnnotationFeatureSnapshot)('test_data/example02.json');
|
|
131
70
|
compareFeatures(actual, expected);
|
|
132
71
|
});
|
|
133
72
|
(0, node_test_1.it)('Convert example 3', () => {
|
|
@@ -149,7 +88,7 @@ const [ex1, , ex2, , ex3, , ex4] = readFeatureFile('test_data/gene_representatio
|
|
|
149
88
|
const txt = JSON.stringify(actual, null, 2);
|
|
150
89
|
chai_1.assert.equal(txt.match(/"type": "CDS"/g)?.length, 4);
|
|
151
90
|
chai_1.assert.equal(txt.match(/prime_UTR/g), null);
|
|
152
|
-
const expected = readAnnotationFeatureSnapshot('test_data/example04.json');
|
|
91
|
+
const expected = (0, testUtil_1.readAnnotationFeatureSnapshot)('test_data/example04.json');
|
|
153
92
|
compareFeatures(actual, expected);
|
|
154
93
|
});
|
|
155
94
|
(0, node_test_1.it)('Convert braker gff', () => {
|
|
@@ -164,34 +103,22 @@ const [ex1, , ex2, , ex3, , ex4] = readFeatureFile('test_data/gene_representatio
|
|
|
164
103
|
(0, node_test_1.it)('Convert mRNA with CDS but without exon', () => {
|
|
165
104
|
const [gffFeature] = readFeatureFile('test_data/cds_without_exon.gff');
|
|
166
105
|
const actual = (0, gff3ToAnnotationFeature_1.gff3ToAnnotationFeature)(gffFeature);
|
|
167
|
-
const expected = readAnnotationFeatureSnapshot('test_data/cds_without_exon.json');
|
|
106
|
+
const expected = (0, testUtil_1.readAnnotationFeatureSnapshot)('test_data/cds_without_exon.json');
|
|
168
107
|
compareFeatures(actual, expected);
|
|
169
108
|
});
|
|
170
109
|
(0, node_test_1.it)('Convert mRNA with CDS but without exon and spliced UTR', () => {
|
|
171
110
|
const [gffFeature] = readFeatureFile('test_data/cds_without_exon_spliced_utr.gff');
|
|
172
111
|
const actual = (0, gff3ToAnnotationFeature_1.gff3ToAnnotationFeature)(gffFeature);
|
|
173
|
-
const expected = readAnnotationFeatureSnapshot('test_data/cds_without_exon_spliced_utr.json');
|
|
112
|
+
const expected = (0, testUtil_1.readAnnotationFeatureSnapshot)('test_data/cds_without_exon_spliced_utr.json');
|
|
174
113
|
compareFeatures(actual, expected);
|
|
175
114
|
});
|
|
176
115
|
(0, node_test_1.it)('Convert mRNA with one CDS, without exons non-adjacent UTR', () => {
|
|
177
116
|
const [gffFeature] = readFeatureFile('test_data/onecds_without_exon_spliced_utr.gff');
|
|
178
117
|
const actual = (0, gff3ToAnnotationFeature_1.gff3ToAnnotationFeature)(gffFeature);
|
|
179
|
-
const expected = readAnnotationFeatureSnapshot('test_data/onecds_without_exon_spliced_utr.json');
|
|
118
|
+
const expected = (0, testUtil_1.readAnnotationFeatureSnapshot)('test_data/onecds_without_exon_spliced_utr.json');
|
|
180
119
|
compareFeatures(actual, expected);
|
|
181
120
|
});
|
|
182
121
|
});
|
|
183
|
-
(0, node_test_1.describe)('gff3ToAnnotationFeature', () => {
|
|
184
|
-
for (const testCase of testCases) {
|
|
185
|
-
const [description, featureLine, convertedFeature] = testCase;
|
|
186
|
-
(0, node_test_1.it)(`converts ${description}`, () => {
|
|
187
|
-
const gff3Feature = gff_1.default.parseStringSync(featureLine, {
|
|
188
|
-
parseSequences: false,
|
|
189
|
-
});
|
|
190
|
-
const feature = (0, gff3ToAnnotationFeature_1.gff3ToAnnotationFeature)(gff3Feature[0]);
|
|
191
|
-
compareFeatures(convertedFeature, feature);
|
|
192
|
-
});
|
|
193
|
-
}
|
|
194
|
-
});
|
|
195
122
|
(0, node_test_1.describe)('Source and score', () => {
|
|
196
123
|
(0, node_test_1.it)('Convert score and source', () => {
|
|
197
124
|
const gffFeature = [
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"gff3ToAnnotationFeature.test.js","sourceRoot":"","sources":["../../src/GFF3/gff3ToAnnotationFeature.test.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"gff3ToAnnotationFeature.test.js","sourceRoot":"","sources":["../../src/GFF3/gff3ToAnnotationFeature.test.ts"],"names":[],"mappings":";;;AAAA,4DAA4D;AAC5D,qCAAsC;AACtC,yCAAwC;AAGxC,mCAA6D;AAC7D,+BAAkC;AAClC,wEAAsC;AAEtC,uEAAmE;AACnE,yCAAqE;AAErE,IAAA,UAAG,EAAC,sBAAW,CAAC,CAAA;AAOhB,SAAS,eAAe,CACtB,OAAkC;IAElC,MAAM,EAAE,QAAQ,EAAE,GAAG,OAAO,CAAA;IAC5B,IAAI,CAAC,QAAQ,EAAE,CAAC;QACd,OAAO,OAAqD,CAAA;IAC9D,CAAC;IACD,MAAM,aAAa,GAAG,MAAM,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAC,GAAG,CAAC,CAAC,KAAK,EAAE,EAAE,CAC1D,eAAe,CAAC,KAAK,CAAC,CACvB,CAAA;IACD,OAAO,EAAE,GAAG,OAAO,EAAE,QAAQ,EAAE,aAAa,EAAE,CAAA;AAChD,CAAC;AAED,SAAS,eAAe,CACtB,QAAmC,EACnC,QAAmC;IAEnC,aAAM,CAAC,uBAAuB,CAC5B,eAAe,CAAC,QAAQ,CAAC,EACzB,eAAe,CAAC,QAAQ,CAAC,EACzB,KAAK,CACN,CAAA;AACH,CAAC;AAED,IAAA,oBAAQ,EAAC,sDAAsD,EAAE,GAAG,EAAE;IACpE,KAAK,MAAM,QAAQ,IAAI,oBAAS,EAAE,CAAC;QACjC,MAAM,EAAE,YAAY,EAAE,WAAW,EAAE,GAAG,QAAQ,CAAA;QAC9C,IAAA,cAAE,EAAC,WAAW,EAAE,GAAG,EAAE;YACnB,MAAM,QAAQ,GAAG,IAAA,sBAAY,EAAC,aAAa,YAAY,OAAO,EAAE,MAAM,CAAC,CAAA;YACvE,MAAM,WAAW,GAAG,IAAA,qBAAe,EAAC,QAAQ,EAAE,EAAE,cAAc,EAAE,KAAK,EAAE,CAAC,CAAA;YACxE,MAAM,kBAAkB,GAAG,WAAW,CAAC,GAAG,CAAC,CAAC,WAAW,EAAE,EAAE,CACzD,IAAA,iDAAuB,EAAC,WAAW,CAAC,CACrC,CAAA;YACD,MAAM,0BAA0B,GAAG,IAAI,CAAC,KAAK,CAC3C,IAAA,sBAAY,EAAC,aAAa,YAAY,OAAO,EAAE,MAAM,CAAC,CACxB,CAAA;YAChC,KAAK,MAAM,CACT,CAAC,EACD,yBAAyB,EAC1B,IAAI,0BAA0B,CAAC,OAAO,EAAE,EAAE,CAAC;gBAC1C,MAAM,iBAAiB,GAAG,kBAAkB,CAAC,CAAC,CAAC,CAAA;gBAC/C,eAAe,CAAC,iBAAiB,EAAE,yBAAyB,CAAC,CAAA;YAC/D,CAAC;QACH,CAAC,CAAC,CAAA;IACJ,CAAC;AACH,CAAC,CAAC,CAAA;AAEF,SAAS,eAAe,CAAC,EAAU;IACjC,MAAM,KAAK,GAAG,IAAA,sBAAY,EAAC,EAAE,CAAC,CAAC,QAAQ,EAAE,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;IACrD,MAAM,OAAO,GAAa,EAAE,CAAA;IAC5B,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE,CAAC;QACzB,IAAI,CAAC,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE,CAAC;YAC1B,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QACpB,CAAC;IACH,CAAC;IACD,MAAM,KAAK,GAAG,IAAA,qBAAe,EAAC,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAkB,CAAA;IAClE,OAAO,KAAK,CAAA;AACd,CAAC;AAED,MAAM,CAAC,GAAG,EAAE,AAAD,EAAG,GAAG,EAAE,AAAD,EAAG,GAAG,EAAE,AAAD,EAAG,GAAG,CAAC,GAAG,eAAe,CAChD,qCAAqC,CACtC,CAAA;AAED,IAAA,oBAAQ,EAAC,kCAAkC,EAAE,GAAG,EAAE;IAChD,IAAA,cAAE,EAAC,iBAAiB,EAAE,GAAG,EAAE;QACzB,MAAM,MAAM,GAAG,IAAA,iDAAuB,EACpC,eAAe,CAAC,wBAAwB,CAAC,CAAC,CAAC,CAAC,CAC7C,CAAA;QACD,MAAM,QAAQ,GAAG,IAAA,wCAA6B,EAAC,wBAAwB,CAAC,CAAA;QACxE,eAAe,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAA;IACnC,CAAC,CAAC,CAAA;IACF,IAAA,cAAE,EAAC,mBAAmB,EAAE,GAAG,EAAE;QAC3B,MAAM,MAAM,GAAG,IAAA,iDAAuB,EAAC,GAAG,CAAC,CAAA;QAC3C,MAAM,GAAG,GAAG,IAAI,CAAC,SAAS,CAAC,MAAM,EAAE,IAAI,EAAE,CAAC,CAAC,CAAA;QAE3C,aAAM,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,gBAAgB,CAAC,EAAE,MAAM,EAAE,CAAC,CAAC,CAAA;QACpD,aAAM,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,4BAA4B,CAAC,EAAE,MAAM,EAAE,CAAC,CAAC,CAAA;QAEhE,MAAM,QAAQ,GAAG,IAAA,wCAA6B,EAAC,0BAA0B,CAAC,CAAA;QAC1E,eAAe,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAA;IACnC,CAAC,CAAC,CAAA;IACF,IAAA,cAAE,EAAC,mBAAmB,EAAE,GAAG,EAAE;QAC3B,MAAM,MAAM,GAAG,IAAA,iDAAuB,EAAC,GAAG,CAAC,CAAA;QAC3C,MAAM,GAAG,GAAG,IAAI,CAAC,SAAS,CAAC,MAAM,EAAE,IAAI,EAAE,CAAC,CAAC,CAAA;QAC3C,aAAM,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,gBAAgB,CAAC,EAAE,MAAM,EAAE,CAAC,CAAC,CAAA;QACpD,MAAM,QAAQ,GAAG,IAAA,wCAA6B,EAAC,0BAA0B,CAAC,CAAA;QAC1E,eAAe,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAA;IACnC,CAAC,CAAC,CAAA;IACF,IAAA,cAAE,EAAC,mBAAmB,EAAE,GAAG,EAAE;QAC3B,gFAAgF;QAChF,oFAAoF;QACpF,qGAAqG;QACrG,qBAAqB;QACrB,MAAM,MAAM,GAAG,IAAA,iDAAuB,EAAC,GAAG,CAAC,CAAA;QAC3C,MAAM,GAAG,GAAG,IAAI,CAAC,SAAS,CAAC,MAAM,EAAE,IAAI,EAAE,CAAC,CAAC,CAAA;QAC3C,aAAM,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,gBAAgB,CAAC,EAAE,MAAM,EAAE,CAAC,CAAC,CAAA;QAEpD,6EAA6E;QAC7E,oCAAoC;IACtC,CAAC,CAAC,CAAA;IACF,IAAA,cAAE,EAAC,mBAAmB,EAAE,GAAG,EAAE;QAC3B,MAAM,EAAE,GAAG,IAAI,CAAC,SAAS,CAAC,GAAG,EAAE,IAAI,EAAE,CAAC,CAAC,CAAA;QACvC,aAAM,CAAC,KAAK,CAAC,EAAE,CAAC,KAAK,CAAC,2BAA2B,CAAC,EAAE,MAAM,EAAE,CAAC,CAAC,CAAA;QAC9D,aAAM,CAAC,KAAK,CAAC,EAAE,CAAC,KAAK,CAAC,4BAA4B,CAAC,EAAE,MAAM,EAAE,CAAC,CAAC,CAAA;QAE/D,MAAM,MAAM,GAAG,IAAA,iDAAuB,EAAC,GAAG,CAAC,CAAA;QAC3C,MAAM,GAAG,GAAG,IAAI,CAAC,SAAS,CAAC,MAAM,EAAE,IAAI,EAAE,CAAC,CAAC,CAAA;QAC3C,aAAM,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,gBAAgB,CAAC,EAAE,MAAM,EAAE,CAAC,CAAC,CAAA;QACpD,aAAM,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,YAAY,CAAC,EAAE,IAAI,CAAC,CAAA;QAE3C,MAAM,QAAQ,GAAG,IAAA,wCAA6B,EAAC,0BAA0B,CAAC,CAAA;QAC1E,eAAe,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAA;IACnC,CAAC,CAAC,CAAA;IACF,IAAA,cAAE,EAAC,oBAAoB,EAAE,GAAG,EAAE;QAC5B,MAAM,CAAC,UAAU,CAAC,GAAG,eAAe,CAAC,sBAAsB,CAAC,CAAA;QAC5D,MAAM,MAAM,GAAG,IAAA,iDAAuB,EAAC,UAAU,CAAC,CAAA;QAClD,MAAM,GAAG,GAAG,IAAI,CAAC,SAAS,CAAC,MAAM,EAAE,IAAI,EAAE,CAAC,CAAC,CAAA;QAC3C,aAAM,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,SAAS,CAAC,EAAE,IAAI,CAAC,CAAA;QACxC,aAAM,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,SAAS,CAAC,EAAE,IAAI,CAAC,CAAA;IAC1C,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA;AAEF,IAAA,oBAAQ,EAAC,mBAAmB,EAAE,GAAG,EAAE;IACjC,IAAA,cAAE,EAAC,wCAAwC,EAAE,GAAG,EAAE;QAChD,MAAM,CAAC,UAAU,CAAC,GAAG,eAAe,CAAC,gCAAgC,CAAC,CAAA;QACtE,MAAM,MAAM,GAAG,IAAA,iDAAuB,EAAC,UAAU,CAAC,CAAA;QAClD,MAAM,QAAQ,GAAG,IAAA,wCAA6B,EAC5C,iCAAiC,CAClC,CAAA;QACD,eAAe,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAA;IACnC,CAAC,CAAC,CAAA;IACF,IAAA,cAAE,EAAC,wDAAwD,EAAE,GAAG,EAAE;QAChE,MAAM,CAAC,UAAU,CAAC,GAAG,eAAe,CAClC,4CAA4C,CAC7C,CAAA;QACD,MAAM,MAAM,GAAG,IAAA,iDAAuB,EAAC,UAAU,CAAC,CAAA;QAClD,MAAM,QAAQ,GAAG,IAAA,wCAA6B,EAC5C,6CAA6C,CAC9C,CAAA;QACD,eAAe,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAA;IACnC,CAAC,CAAC,CAAA;IACF,IAAA,cAAE,EAAC,2DAA2D,EAAE,GAAG,EAAE;QACnE,MAAM,CAAC,UAAU,CAAC,GAAG,eAAe,CAClC,+CAA+C,CAChD,CAAA;QACD,MAAM,MAAM,GAAG,IAAA,iDAAuB,EAAC,UAAU,CAAC,CAAA;QAClD,MAAM,QAAQ,GAAG,IAAA,wCAA6B,EAC5C,gDAAgD,CACjD,CAAA;QACD,eAAe,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAA;IACnC,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA;AAEF,IAAA,oBAAQ,EAAC,kBAAkB,EAAE,GAAG,EAAE;IAChC,IAAA,cAAE,EAAC,0BAA0B,EAAE,GAAG,EAAE;QAClC,MAAM,UAAU,GAAgB;YAC9B;gBACE,MAAM,EAAE,MAAM;gBACd,MAAM,EAAE,UAAU;gBAClB,IAAI,EAAE,MAAM;gBACZ,KAAK,EAAE,IAAI;gBACX,GAAG,EAAE,IAAI;gBACT,KAAK,EAAE,CAAC;gBACR,MAAM,EAAE,GAAG;gBACX,KAAK,EAAE,IAAI;gBACX,UAAU,EAAE;oBACV,EAAE,EAAE,CAAC,WAAW,CAAC;oBACjB,IAAI,EAAE,CAAC,MAAM,CAAC;oBACd,MAAM,EAAE,CAAC,MAAM,CAAC;iBACjB;gBACD,cAAc,EAAE,EAAE;gBAClB,gBAAgB,EAAE,EAAE;aACrB;SACF,CAAA;QACD,MAAM,MAAM,GAAG,IAAA,iDAAuB,EAAC,UAAU,CAAC,CAAA;QAClD,aAAM,CAAC,eAAe,CAAC,MAAM,CAAC,UAAU,EAAE,UAAU,EAAE,EAAE,CAAC,CAAC,CAAC,EAAE,UAAU,CAAC,CAAA;QACxE,aAAM,CAAC,eAAe,CAAC,MAAM,CAAC,UAAU,EAAE,SAAS,EAAE,EAAE,CAAC,CAAC,CAAC,EAAE,GAAG,CAAC,CAAA;IAClE,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA"}
|
|
@@ -0,0 +1,24 @@
|
|
|
1
|
+
"use strict";
|
|
2
|
+
Object.defineProperty(exports, "__esModule", { value: true });
|
|
3
|
+
exports.testCases = void 0;
|
|
4
|
+
exports.readAnnotationFeatureSnapshot = readAnnotationFeatureSnapshot;
|
|
5
|
+
const node_fs_1 = require("node:fs");
|
|
6
|
+
function readAnnotationFeatureSnapshot(fn) {
|
|
7
|
+
const lines = (0, node_fs_1.readFileSync)(fn).toString();
|
|
8
|
+
return JSON.parse(lines);
|
|
9
|
+
}
|
|
10
|
+
exports.testCases = [
|
|
11
|
+
{
|
|
12
|
+
filenameStem: 'single_feature_no_children',
|
|
13
|
+
description: 'there is a single feature with no children',
|
|
14
|
+
},
|
|
15
|
+
{
|
|
16
|
+
filenameStem: 'single_feature_two_children',
|
|
17
|
+
description: 'there is a single feature with two children',
|
|
18
|
+
},
|
|
19
|
+
{
|
|
20
|
+
filenameStem: 'gene_with_two_cds',
|
|
21
|
+
description: 'Gene with two CDS',
|
|
22
|
+
},
|
|
23
|
+
];
|
|
24
|
+
//# sourceMappingURL=testUtil.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
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|