@apollo-annotation/shared 0.3.9 → 0.3.11

package/dist/GFF3/gff3ToAnnotationFeature.test.js

@@ -1,6 +1,5 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.readAnnotationFeatureSnapshot = readAnnotationFeatureSnapshot;
 const tslib_1 = require("tslib");
 /* eslint-disable @typescript-eslint/no-floating-promises */
 const node_fs_1 = require("node:fs");
@@ -9,74 +8,8 @@ const gff_1 = require("@gmod/gff");
 const chai_1 = require("chai");
 const chai_exclude_1 = tslib_1.__importDefault(require("chai-exclude"));
 const gff3ToAnnotationFeature_1 = require("./gff3ToAnnotationFeature");
+const testUtil_1 = require("./testUtil");
 (0, chai_1.use)(chai_exclude_1.default);
-const testCases = [
-    [
-        'a feature with no children',
-        'ctgA	example	remark	1000	2000	.	.	.	Name=Remark:hga;Alias=hga\n',
-        {
-            _id: '66c51f3e002c683eaf98a223',
-            refSeq: 'ctgA',
-            type: 'remark',
-            min: 999,
-            max: 2000,
-            attributes: {
-                gff_source: ['example'],
-                gff_name: ['Remark:hga'],
-                gff_alias: ['hga'],
-            },
-        },
-    ],
-    [
-        'a feature with two children',
-        `ctgA	est	EST_match	1050	3202	.	+	.	ID=Match1;Name=agt830.5;Target=agt830.5 1 654
-ctgA	est	match_part	1050	1500	.	+	.	Parent=Match1;Name=agt830.5;Target=agt830.5 1 451
-ctgA	est	match_part	3000	3202	.	+	.	Parent=Match1;Name=agt830.5;Target=agt830.5 452 654
-`,
-        {
-            _id: '66cf9fbb4e947fa2c27d3d6a',
-            refSeq: 'ctgA',
-            type: 'EST_match',
-            min: 1049,
-            max: 3202,
-            strand: 1,
-            children: {
-                '66cf9fbb4e947fa2c27d3d68': {
-                    _id: '66cf9fbb4e947fa2c27d3d68',
-                    refSeq: 'ctgA',
-                    type: 'match_part',
-                    min: 1049,
-                    max: 1500,
-                    strand: 1,
-                    attributes: {
-                        gff_source: ['est'],
-                        gff_name: ['agt830.5'],
-                        gff_target: ['agt830.5 1 451'],
-                    },
-                },
-                '66cf9fbb4e947fa2c27d3d69': {
-                    _id: '66cf9fbb4e947fa2c27d3d69',
-                    refSeq: 'ctgA',
-                    type: 'match_part',
-                    min: 2999,
-                    max: 3202,
-                    strand: 1,
-                    attributes: {
-                        gff_source: ['est'],
-                        gff_name: ['agt830.5'],
-                        gff_target: ['agt830.5 452 654'],
-                    },
-                },
-            },
-            attributes: {
-                gff_source: ['est'],
-                gff_id: ['Match1'],
-                gff_name: ['agt830.5'],
-                gff_target: ['agt830.5 1 654'],
-            },
-        },
-    ],
-];
 function childrenToArray(feature) {
     const { children } = feature;
     if (!children) {
@@ -88,6 +21,21 @@ function childrenToArray(feature) {
 function compareFeatures(feature1, feature2) {
     chai_1.assert.deepEqualExcludingEvery(childrenToArray(feature1), childrenToArray(feature2), '_id');
 }
+(0, node_test_1.describe)('Converts GFF3 to AnnotationFeatureSnapshot JSON when', () => {
+    for (const testCase of testUtil_1.testCases) {
+        const { filenameStem, description } = testCase;
+        (0, node_test_1.it)(description, () => {
+            const fileText = (0, node_fs_1.readFileSync)(`test_data/${filenameStem}.gff3`, 'utf8');
+            const gffFeatures = (0, gff_1.parseStringSync)(fileText, { parseSequences: false });
+            const annotationFeatures = gffFeatures.map((gff3Feature) => (0, gff3ToAnnotationFeature_1.gff3ToAnnotationFeature)(gff3Feature));
+            const annotationFeaturesExpected = JSON.parse((0, node_fs_1.readFileSync)(`test_data/${filenameStem}.json`, 'utf8'));
+            for (const [i, annotationFeatureExpected,] of annotationFeaturesExpected.entries()) {
+                const annotationFeature = annotationFeatures[i];
+                compareFeatures(annotationFeature, annotationFeatureExpected);
+            }
+        });
+    }
+});
 function readFeatureFile(fn) {
     const lines = (0, node_fs_1.readFileSync)(fn).toString().split('\n');
     const feature = [];
@@ -99,20 +47,11 @@ function readFeatureFile(fn) {
     const inGff = (0, gff_1.parseStringSync)(feature.join('\n'));
     return inGff;
 }
-function readAnnotationFeatureSnapshot(fn) {
-    const lines = (0, node_fs_1.readFileSync)(fn).toString();
-    return JSON.parse(lines);
-}
 const [ex1, , ex2, , ex3, , ex4] = readFeatureFile('test_data/gene_representations.gff3');
 (0, node_test_1.describe)('gff3ToAnnotationFeature examples', () => {
     (0, node_test_1.it)('Convert one CDS', () => {
         const actual = (0, gff3ToAnnotationFeature_1.gff3ToAnnotationFeature)(readFeatureFile('test_data/one_cds.gff3')[0]);
-        const expected = readAnnotationFeatureSnapshot('test_data/one_cds.json');
-        compareFeatures(actual, expected);
-    });
-    (0, node_test_1.it)('Convert two CDSs', () => {
-        const actual = (0, gff3ToAnnotationFeature_1.gff3ToAnnotationFeature)(readFeatureFile('test_data/two_cds.gff3')[0]);
-        const expected = readAnnotationFeatureSnapshot('test_data/two_cds.json');
+        const expected = (0, testUtil_1.readAnnotationFeatureSnapshot)('test_data/one_cds.json');
         compareFeatures(actual, expected);
     });
     (0, node_test_1.it)('Convert example 1', () => {
@@ -120,14 +59,14 @@ const [ex1, , ex2, , ex3, , ex4] = readFeatureFile('test_data/gene_representatio
         const txt = JSON.stringify(actual, null, 2);
         chai_1.assert.equal(txt.match(/"type": "CDS"/g)?.length, 4);
         chai_1.assert.equal(txt.match(/"type": "TF_binding_site"/g)?.length, 1);
-        const expected = readAnnotationFeatureSnapshot('test_data/example01.json');
+        const expected = (0, testUtil_1.readAnnotationFeatureSnapshot)('test_data/example01.json');
         compareFeatures(actual, expected);
     });
     (0, node_test_1.it)('Convert example 2', () => {
         const actual = (0, gff3ToAnnotationFeature_1.gff3ToAnnotationFeature)(ex2);
         const txt = JSON.stringify(actual, null, 2);
         chai_1.assert.equal(txt.match(/"type": "CDS"/g)?.length, 4);
-        const expected = readAnnotationFeatureSnapshot('test_data/example02.json');
+        const expected = (0, testUtil_1.readAnnotationFeatureSnapshot)('test_data/example02.json');
         compareFeatures(actual, expected);
     });
     (0, node_test_1.it)('Convert example 3', () => {
@@ -149,7 +88,7 @@ const [ex1, , ex2, , ex3, , ex4] = readFeatureFile('test_data/gene_representatio
         const txt = JSON.stringify(actual, null, 2);
         chai_1.assert.equal(txt.match(/"type": "CDS"/g)?.length, 4);
         chai_1.assert.equal(txt.match(/prime_UTR/g), null);
-        const expected = readAnnotationFeatureSnapshot('test_data/example04.json');
+        const expected = (0, testUtil_1.readAnnotationFeatureSnapshot)('test_data/example04.json');
         compareFeatures(actual, expected);
     });
     (0, node_test_1.it)('Convert braker gff', () => {
@@ -164,34 +103,22 @@ const [ex1, , ex2, , ex3, , ex4] = readFeatureFile('test_data/gene_representatio
     (0, node_test_1.it)('Convert mRNA with CDS but without exon', () => {
         const [gffFeature] = readFeatureFile('test_data/cds_without_exon.gff');
         const actual = (0, gff3ToAnnotationFeature_1.gff3ToAnnotationFeature)(gffFeature);
-        const expected = readAnnotationFeatureSnapshot('test_data/cds_without_exon.json');
+        const expected = (0, testUtil_1.readAnnotationFeatureSnapshot)('test_data/cds_without_exon.json');
         compareFeatures(actual, expected);
     });
     (0, node_test_1.it)('Convert mRNA with CDS but without exon and spliced UTR', () => {
         const [gffFeature] = readFeatureFile('test_data/cds_without_exon_spliced_utr.gff');
         const actual = (0, gff3ToAnnotationFeature_1.gff3ToAnnotationFeature)(gffFeature);
-        const expected = readAnnotationFeatureSnapshot('test_data/cds_without_exon_spliced_utr.json');
+        const expected = (0, testUtil_1.readAnnotationFeatureSnapshot)('test_data/cds_without_exon_spliced_utr.json');
         compareFeatures(actual, expected);
     });
     (0, node_test_1.it)('Convert mRNA with one CDS, without exons non-adjacent UTR', () => {
         const [gffFeature] = readFeatureFile('test_data/onecds_without_exon_spliced_utr.gff');
         const actual = (0, gff3ToAnnotationFeature_1.gff3ToAnnotationFeature)(gffFeature);
-        const expected = readAnnotationFeatureSnapshot('test_data/onecds_without_exon_spliced_utr.json');
+        const expected = (0, testUtil_1.readAnnotationFeatureSnapshot)('test_data/onecds_without_exon_spliced_utr.json');
         compareFeatures(actual, expected);
     });
 });
-(0, node_test_1.describe)('gff3ToAnnotationFeature', () => {
-    for (const testCase of testCases) {
-        const [description, featureLine, convertedFeature] = testCase;
-        (0, node_test_1.it)(`converts ${description}`, () => {
-            const gff3Feature = (0, gff_1.parseStringSync)(featureLine, {
-                parseSequences: false,
-            });
-            const feature = (0, gff3ToAnnotationFeature_1.gff3ToAnnotationFeature)(gff3Feature[0]);
-            compareFeatures(convertedFeature, feature);
-        });
-    }
-});
 (0, node_test_1.describe)('Source and score', () => {
     (0, node_test_1.it)('Convert score and source', () => {
         const gffFeature = [

package/dist/GFF3/gff3ToAnnotationFeature.test.js.map

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package/dist/GFF3/testUtil.d.ts

@@ -0,0 +1,6 @@
+import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
+export declare function readAnnotationFeatureSnapshot(fn: string): AnnotationFeatureSnapshot;
+export declare const testCases: {
+    filenameStem: string;
+    description: string;
+}[];

package/dist/GFF3/testUtil.js

@@ -0,0 +1,24 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.testCases = void 0;
+exports.readAnnotationFeatureSnapshot = readAnnotationFeatureSnapshot;
+const node_fs_1 = require("node:fs");
+function readAnnotationFeatureSnapshot(fn) {
+    const lines = (0, node_fs_1.readFileSync)(fn).toString();
+    return JSON.parse(lines);
+}
+exports.testCases = [
+    {
+        filenameStem: 'single_feature_no_children',
+        description: 'there is a single feature with no children',
+    },
+    {
+        filenameStem: 'single_feature_two_children',
+        description: 'there is a single feature with two children',
+    },
+    {
+        filenameStem: 'gene_with_two_cds',
+        description: 'Gene with two CDS',
+    },
+];
+//# sourceMappingURL=testUtil.js.map

package/dist/GFF3/testUtil.js.map

@@ -0,0 +1 @@
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