@apollo-annotation/shared 0.3.11 → 0.3.13

package/dist/GFF3/annotationFeatureToGFF3.test.js

@@ -1,38 +1,36 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
 /* eslint-disable prefer-destructuring */
 /* eslint-disable @typescript-eslint/no-floating-promises */
-const node_fs_1 = require("node:fs");
-const node_test_1 = require("node:test");
-const gff_1 = require("@gmod/gff");
-const chai_1 = require("chai");
-const annotationFeatureToGFF3_1 = require("./annotationFeatureToGFF3");
-const testUtil_1 = require("./testUtil");
-(0, node_test_1.describe)('Converts AnnotationFeatureSnapshot JSON to GFF3 when', () => {
-    for (const testCase of testUtil_1.testCases) {
+import { readFileSync } from 'node:fs';
+import { describe, it } from 'node:test';
+import { formatSync } from '@gmod/gff';
+import { assert, expect } from 'chai';
+import { annotationFeatureToGFF3 } from './annotationFeatureToGFF3.js';
+import { readAnnotationFeatureSnapshot, testCases } from './testUtil.js';
+describe('Converts AnnotationFeatureSnapshot JSON to GFF3 when', () => {
+    for (const testCase of testCases) {
         const { filenameStem, description } = testCase;
-        (0, node_test_1.it)(description, () => {
-            const annotationFeatures = JSON.parse((0, node_fs_1.readFileSync)(`test_data/${filenameStem}.json`, 'utf8'));
-            const expectedGFF3 = (0, node_fs_1.readFileSync)(`test_data/${filenameStem}.gff3`, 'utf8');
-            const gffFeatures = annotationFeatures.map((annotationFeature) => (0, annotationFeatureToGFF3_1.annotationFeatureToGFF3)(annotationFeature));
-            const gff3 = (0, gff_1.formatSync)(gffFeatures);
-            (0, chai_1.expect)(gff3).to.equal(expectedGFF3);
+        it(description, () => {
+            const annotationFeatures = JSON.parse(readFileSync(`test_data/${filenameStem}.json`, 'utf8'));
+            const expectedGFF3 = readFileSync(`test_data/${filenameStem}.gff3`, 'utf8');
+            const gffFeatures = annotationFeatures.map((annotationFeature) => annotationFeatureToGFF3(annotationFeature));
+            const gff3 = formatSync(gffFeatures);
+            expect(gff3).to.equal(expectedGFF3);
         });
     }
 });
-(0, node_test_1.describe)('annotationFeatureToGFF3', () => {
-    (0, node_test_1.it)('Test mandatory columns', () => {
-        const annotationFeature = (0, testUtil_1.readAnnotationFeatureSnapshot)('test_data/gene.json');
-        const [gff3Feature] = (0, annotationFeatureToGFF3_1.annotationFeatureToGFF3)(annotationFeature);
-        chai_1.assert.deepEqual(gff3Feature.seq_id, 'chr1');
-        chai_1.assert.deepEqual(gff3Feature.type, 'gene');
-        chai_1.assert.deepEqual(gff3Feature.start, 1000);
-        chai_1.assert.deepEqual(gff3Feature.end, 9000);
-        chai_1.assert.deepEqual(gff3Feature.strand, '+');
-        chai_1.assert.deepEqual(gff3Feature.score, 123);
-        chai_1.assert.deepEqual(gff3Feature.source, 'test_data');
+describe('annotationFeatureToGFF3', () => {
+    it('Test mandatory columns', () => {
+        const annotationFeature = readAnnotationFeatureSnapshot('test_data/gene.json');
+        const [gff3Feature] = annotationFeatureToGFF3(annotationFeature);
+        assert.deepEqual(gff3Feature.seq_id, 'chr1');
+        assert.deepEqual(gff3Feature.type, 'gene');
+        assert.deepEqual(gff3Feature.start, 1000);
+        assert.deepEqual(gff3Feature.end, 9000);
+        assert.deepEqual(gff3Feature.strand, '+');
+        assert.deepEqual(gff3Feature.score, 123);
+        assert.deepEqual(gff3Feature.source, 'test_data');
     });
-    (0, node_test_1.it)('Feature with no children and no gff_id has no ID attribute', () => {
+    it('Feature with no children and no gff_id has no ID attribute', () => {
         const annotationFeature = JSON.parse(`{
       "_id": "66d70e4ccc30b55b65e5f619",
       "refSeq": "chr1",
@@ -42,10 +40,10 @@ const testUtil_1 = require("./testUtil");
       "strand": 1,
       "attributes": {}
     }`);
-        const [gff3Feature] = (0, annotationFeatureToGFF3_1.annotationFeatureToGFF3)(annotationFeature);
-        chai_1.assert.isUndefined(gff3Feature.attributes?.ID);
+        const [gff3Feature] = annotationFeatureToGFF3(annotationFeature);
+        assert.isUndefined(gff3Feature.attributes?.ID);
     });
-    (0, node_test_1.it)('Feature with children and no gff_id has internal _id as ID', () => {
+    it('Feature with children and no gff_id has internal _id as ID', () => {
         const annotationFeature = JSON.parse(`{
       "_id": "66d70e4ccc30b55b65e5f619",
       "refSeq": "chr1",
@@ -66,10 +64,10 @@ const testUtil_1 = require("./testUtil");
         }
       }
     }`);
-        const [gff3Feature] = (0, annotationFeatureToGFF3_1.annotationFeatureToGFF3)(annotationFeature);
-        chai_1.assert.deepEqual(gff3Feature.attributes?.ID, ['66d70e4ccc30b55b65e5f619']);
+        const [gff3Feature] = annotationFeatureToGFF3(annotationFeature);
+        assert.deepEqual(gff3Feature.attributes?.ID, ['66d70e4ccc30b55b65e5f619']);
     });
-    (0, node_test_1.it)('Convert multiple scores', () => {
+    it('Convert multiple scores', () => {
         const annotationFeature = JSON.parse(`{
       "_id": "66d70e4ccc30b55b65e5f619",
       "refSeq": "chr1",
@@ -82,10 +80,10 @@ const testUtil_1 = require("./testUtil");
         "gff_score": ["123", "345"]
       }
     }`);
-        const [gff3Feature] = (0, annotationFeatureToGFF3_1.annotationFeatureToGFF3)(annotationFeature);
-        chai_1.assert.deepEqual(gff3Feature.score, 123);
+        const [gff3Feature] = annotationFeatureToGFF3(annotationFeature);
+        assert.deepEqual(gff3Feature.score, 123);
     });
-    (0, node_test_1.it)('Convert invalid score', () => {
+    it('Convert invalid score', () => {
         const annotationFeature = JSON.parse(`{
       "_id": "66d70e4ccc30b55b65e5f619",
       "refSeq": "chr1",
@@ -98,73 +96,73 @@ const testUtil_1 = require("./testUtil");
         "gff_score": ["xyz"]
       }
     }`);
-        const [gff3Feature] = (0, annotationFeatureToGFF3_1.annotationFeatureToGFF3)(annotationFeature);
-        chai_1.assert.deepEqual(gff3Feature.score, null);
+        const [gff3Feature] = annotationFeatureToGFF3(annotationFeature);
+        assert.deepEqual(gff3Feature.score, null);
     });
-    (0, node_test_1.it)('Convert one gene test attributes', () => {
-        const annotationFeature = (0, testUtil_1.readAnnotationFeatureSnapshot)('test_data/gene.json');
-        const [gff3Feature] = (0, annotationFeatureToGFF3_1.annotationFeatureToGFF3)(annotationFeature);
-        chai_1.assert.deepEqual(gff3Feature.attributes?.Name, ['EDEN']);
-        chai_1.assert.deepEqual(gff3Feature.attributes?.testid, ['t001', 't003']);
-        chai_1.assert.deepEqual(gff3Feature.attributes?.ID, ['gene10001']);
-        chai_1.assert.deepEqual(gff3Feature.attributes?.Ontology_term, [
+    it('Convert one gene test attributes', () => {
+        const annotationFeature = readAnnotationFeatureSnapshot('test_data/gene.json');
+        const [gff3Feature] = annotationFeatureToGFF3(annotationFeature);
+        assert.deepEqual(gff3Feature.attributes?.Name, ['EDEN']);
+        assert.deepEqual(gff3Feature.attributes?.testid, ['t001', 't003']);
+        assert.deepEqual(gff3Feature.attributes?.ID, ['gene10001']);
+        assert.deepEqual(gff3Feature.attributes?.Ontology_term, [
             'GO1234',
             'GO4567',
             'SO1234',
         ]);
-        chai_1.assert.deepEqual(gff3Feature.attributes?.Alias, ['myalias']);
-        chai_1.assert.deepEqual(gff3Feature.attributes?.Target, ['mytarget']);
-        chai_1.assert.deepEqual(gff3Feature.attributes?.Gap, ['mygap']);
-        chai_1.assert.deepEqual(gff3Feature.attributes?.Derives_from, ['myderives']);
-        chai_1.assert.deepEqual(gff3Feature.attributes?.Note, ['mynote']);
-        chai_1.assert.deepEqual(gff3Feature.attributes?.Dbxref, ['mydbxref']);
-        chai_1.assert.deepEqual(gff3Feature.attributes?.Is_circular, ['true']);
+        assert.deepEqual(gff3Feature.attributes?.Alias, ['myalias']);
+        assert.deepEqual(gff3Feature.attributes?.Target, ['mytarget']);
+        assert.deepEqual(gff3Feature.attributes?.Gap, ['mygap']);
+        assert.deepEqual(gff3Feature.attributes?.Derives_from, ['myderives']);
+        assert.deepEqual(gff3Feature.attributes?.Note, ['mynote']);
+        assert.deepEqual(gff3Feature.attributes?.Dbxref, ['mydbxref']);
+        assert.deepEqual(gff3Feature.attributes?.Is_circular, ['true']);
     });
-    (0, node_test_1.it)('Convert one gene test children', () => {
-        const annotationFeature = (0, testUtil_1.readAnnotationFeatureSnapshot)('test_data/gene.json');
-        const [gff3Feature] = (0, annotationFeatureToGFF3_1.annotationFeatureToGFF3)(annotationFeature);
+    it('Convert one gene test children', () => {
+        const annotationFeature = readAnnotationFeatureSnapshot('test_data/gene.json');
+        const [gff3Feature] = annotationFeatureToGFF3(annotationFeature);
         const [children] = gff3Feature.child_features;
         const [mrna] = children;
-        chai_1.assert.deepEqual(mrna.type, 'mRNA');
-        chai_1.assert.deepEqual(mrna.attributes?.Parent, ['gene10001']);
+        assert.deepEqual(mrna.type, 'mRNA');
+        assert.deepEqual(mrna.attributes?.Parent, ['gene10001']);
         const [cds] = mrna.child_features[2];
-        chai_1.assert.deepEqual(cds.type, 'CDS');
-        chai_1.assert.deepEqual(cds.attributes?.ID, ['cds10001']);
-        chai_1.assert.deepEqual(cds.attributes?.Parent, ['mRNA10001']);
+        assert.deepEqual(cds.type, 'CDS');
+        assert.deepEqual(cds.attributes?.ID, ['cds10001']);
+        assert.deepEqual(cds.attributes?.Parent, ['mRNA10001']);
     });
-    (0, node_test_1.it)('Convert CDSs', () => {
-        const annotationFeature = (0, testUtil_1.readAnnotationFeatureSnapshot)('test_data/gene.json');
-        const [gff3Feature] = (0, annotationFeatureToGFF3_1.annotationFeatureToGFF3)(annotationFeature);
+    it('Convert CDSs', () => {
+        const annotationFeature = readAnnotationFeatureSnapshot('test_data/gene.json');
+        const [gff3Feature] = annotationFeatureToGFF3(annotationFeature);
         const [children] = gff3Feature.child_features;
         const [mrna] = children;
         const cds10001 = mrna.child_features.filter((child) => {
             const id = child[0].attributes?.ID;
             return id !== undefined && id[0] === 'cds10001';
         });
-        chai_1.assert.deepEqual(cds10001.length, 2);
+        assert.deepEqual(cds10001.length, 2);
         const cds1_1 = cds10001[0][0];
-        chai_1.assert.deepEqual(cds1_1.attributes?.ID, ['cds10001']);
-        chai_1.assert.deepEqual(cds1_1.start, 1201);
-        chai_1.assert.deepEqual(cds1_1.end, 1500);
-        chai_1.assert.deepEqual(cds1_1.phase, '0');
+        assert.deepEqual(cds1_1.attributes?.ID, ['cds10001']);
+        assert.deepEqual(cds1_1.start, 1201);
+        assert.deepEqual(cds1_1.end, 1500);
+        assert.deepEqual(cds1_1.phase, '0');
         const cds1_2 = cds10001[1][0];
-        chai_1.assert.deepEqual(cds1_2.attributes?.ID, ['cds10001']);
-        chai_1.assert.deepEqual(cds1_2.start, 5000);
-        chai_1.assert.deepEqual(cds1_2.end, 5100);
-        chai_1.assert.deepEqual(cds1_2.phase, '0');
-        chai_1.assert.deepEqual(cds1_1.child_features[0][0].attributes?.ID, [
+        assert.deepEqual(cds1_2.attributes?.ID, ['cds10001']);
+        assert.deepEqual(cds1_2.start, 5000);
+        assert.deepEqual(cds1_2.end, 5100);
+        assert.deepEqual(cds1_2.phase, '0');
+        assert.deepEqual(cds1_1.child_features[0][0].attributes?.ID, [
             'cds_region10001',
         ]);
-        chai_1.assert.deepEqual(cds1_1.child_features[0][0].start, 1351);
-        chai_1.assert.deepEqual(cds1_1.child_features[0][0].end, 1400);
-        chai_1.assert.deepEqual(cds1_1.child_features[0][0].phase, null);
+        assert.deepEqual(cds1_1.child_features[0][0].start, 1351);
+        assert.deepEqual(cds1_1.child_features[0][0].end, 1400);
+        assert.deepEqual(cds1_1.child_features[0][0].phase, null);
         const cds10004 = mrna.child_features.filter((child) => {
             const id = child[0].attributes?.ID;
             return id !== undefined && id[0] === 'cds10004';
         });
-        chai_1.assert.deepEqual(cds10004.length, 2);
+        assert.deepEqual(cds10004.length, 2);
         const cds4_1 = cds10004[0][0];
-        chai_1.assert.deepEqual(cds4_1.attributes?.ID, ['cds10004']);
+        assert.deepEqual(cds4_1.attributes?.ID, ['cds10004']);
     });
 });
 //# sourceMappingURL=annotationFeatureToGFF3.test.js.map

package/dist/GFF3/annotationFeatureToGFF3.test.js.map

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package/dist/GFF3/gff3ToAnnotationFeature.d.ts

@@ -1,3 +1,4 @@
-import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
-import { type GFF3Feature } from '@gmod/gff';
+import type { AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
+import type { GFF3Feature } from '@gmod/gff';
 export declare function gff3ToAnnotationFeature(gff3Feature: GFF3Feature, refSeq?: string): AnnotationFeatureSnapshot;
+//# sourceMappingURL=gff3ToAnnotationFeature.d.ts.map

package/dist/GFF3/gff3ToAnnotationFeature.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"gff3ToAnnotationFeature.d.ts","sourceRoot":"","sources":["../../src/GFF3/gff3ToAnnotationFeature.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,yBAAyB,EAAE,MAAM,wBAAwB,CAAA;AACvE,OAAO,KAAK,EAAE,WAAW,EAA2B,MAAM,WAAW,CAAA;AAMrE,wBAAgB,uBAAuB,CACrC,WAAW,EAAE,WAAW,EACxB,MAAM,CAAC,EAAE,MAAM,GACd,yBAAyB,CAgD3B"}

package/dist/GFF3/gff3ToAnnotationFeature.js

@@ -1,19 +1,12 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.gff3ToAnnotationFeature = gff3ToAnnotationFeature;
-const tslib_1 = require("tslib");
-const util_1 = require("@jbrowse/core/util");
-const bson_objectid_1 = tslib_1.__importDefault(require("bson-objectid"));
-const gffReservedKeys_1 = require("./gffReservedKeys");
-function gff3ToAnnotationFeature(gff3Feature, refSeq) {
+import { doesIntersect2 } from '@jbrowse/core/util';
+import ObjectID from 'bson-objectid';
+import { gffToInternal, isGFFReservedAttribute } from './gffReservedKeys.js';
+export function gff3ToAnnotationFeature(gff3Feature, refSeq) {
     const [firstFeature] = gff3Feature;
-    const { end, seq_id: refName, start, strand, type } = firstFeature;
+    const { end, seq_id: refName, start, strand } = firstFeature;
     if (!refName) {
         throw new Error(`feature does not have seq_id: ${JSON.stringify(firstFeature)}`);
     }
-    if (!type) {
-        throw new Error(`feature does not have type: ${JSON.stringify(firstFeature)}`);
-    }
     if (start === null) {
         throw new Error(`feature does not have start: ${JSON.stringify(firstFeature)}`);
     }
@@ -24,9 +17,9 @@ function gff3ToAnnotationFeature(gff3Feature, refSeq) {
     const convertedChildren = convertChildren(gff3Feature, refSeq);
     const convertedAttributes = convertFeatureAttributes(gff3Feature);
     const feature = {
-        _id: new bson_objectid_1.default().toHexString(),
+        _id: new ObjectID().toHexString(),
         refSeq: refSeq ?? refName,
-        type,
+        type: getFeatureType(gff3Feature),
         min,
         max,
     };
@@ -50,9 +43,6 @@ function gff3ToAnnotationFeature(gff3Feature, refSeq) {
     return feature;
 }
 function getFeatureMinMax(gff3Feature) {
-    if (gff3Feature.length > 1 && !gff3Feature.every((f) => f.type === 'CDS')) {
-        throw new Error('GFF3 features has multiple locations but is not a CDS');
-    }
     const mins = gff3Feature.map((f) => f.start).filter((m) => m !== null);
     const maxes = gff3Feature.map((f) => f.end).filter((m) => m !== null);
     const min = Math.min(...mins);
@@ -93,7 +83,7 @@ function convertFeatureAttributes(gff3Feature) {
                 if (key === 'Parent') {
                     continue;
                 }
-                const newKey = (0, gffReservedKeys_1.isGFFReservedAttribute)(key) ? gffReservedKeys_1.gffToInternal[key] : key;
+                const newKey = isGFFReservedAttribute(key) ? gffToInternal[key] : key;
                 const existingVal = convertedAttributes[newKey];
                 if (existingVal) {
                     // if (JSON.stringify(existingVal) === JSON.stringify(val)) {
@@ -113,12 +103,30 @@ function convertFeatureAttributes(gff3Feature) {
     }
     return;
 }
+function getFeatureType(gff3Feature) {
+    const [firstFeature] = gff3Feature;
+    if (gff3Feature.length === 1 || firstFeature.type === 'CDS') {
+        const { type } = firstFeature;
+        if (!type) {
+            throw new Error(`feature does not have type: ${JSON.stringify(firstFeature)}`);
+        }
+        return type;
+    }
+    return 'apollo_feature_container';
+}
 function convertChildren(gff3Feature, refSeq, featureIds) {
     const convertedChildren = {};
     const locationsWithChildren = gff3Feature.filter((feature) => feature.child_features.length > 0);
     if (locationsWithChildren.length > 1) {
         throw new Error('Features with multiple locations may not have children');
     }
+    if (gff3Feature.length > 1 && gff3Feature[0].type !== 'CDS') {
+        for (const gff3FeatureLocation of gff3Feature) {
+            const annotationFeature = gff3ToAnnotationFeature([gff3FeatureLocation], refSeq);
+            convertedChildren[annotationFeature._id] = annotationFeature;
+        }
+        return convertedChildren;
+    }
     if (locationsWithChildren.length === 0) {
         return;
     }
@@ -182,7 +190,7 @@ function inferMissingExons(cdsFeatures, existingExons, utrFeatures, refSeq, feat
                 strand = -1;
             }
             utrExons.push({
-                _id: new bson_objectid_1.default().toHexString(),
+                _id: new ObjectID().toHexString(),
                 refSeq,
                 type: 'exon',
                 min: utr.start - 1,
@@ -231,7 +239,7 @@ function inferMissingExons(cdsFeatures, existingExons, utrFeatures, refSeq, feat
                     strand = -1;
                 }
                 const newExon = {
-                    _id: new bson_objectid_1.default().toHexString(),
+                    _id: new ObjectID().toHexString(),
                     refSeq,
                     type: 'exon',
                     min: cds.start - 1,
@@ -331,7 +339,7 @@ function processCDS(cdsFeatures, refSeq) {
             return false;
         }
         // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
-        return (0, util_1.doesIntersect2)(loc.start, loc.end, nextLoc.start, nextLoc.end);
+        return doesIntersect2(loc.start, loc.end, nextLoc.start, nextLoc.end);
     });
     // If no overlaps, assume it's a single CDS feature
     if (!overlapping) {
@@ -347,7 +355,7 @@ function processCDS(cdsFeatures, refSeq) {
             groupedLocations.push([location]);
             continue;
         }
-        const overlaps = lastGroup.some((lastGroupLoc) => (0, util_1.doesIntersect2)(
+        const overlaps = lastGroup.some((lastGroupLoc) => doesIntersect2(
         /* eslint-disable @typescript-eslint/no-non-null-assertion */
         lastGroupLoc.start, lastGroupLoc.end, location.start, location.end));
         if (overlaps) {

package/dist/GFF3/gff3ToAnnotationFeature.js.map

@@ -1 +1 @@
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package/dist/GFF3/gff3ToAnnotationFeature.test.d.ts

@@ -1 +1,2 @@
 export {};
+//# sourceMappingURL=gff3ToAnnotationFeature.test.d.ts.map

package/dist/GFF3/gff3ToAnnotationFeature.test.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"gff3ToAnnotationFeature.test.d.ts","sourceRoot":"","sources":["../../src/GFF3/gff3ToAnnotationFeature.test.ts"],"names":[],"mappings":""}