diff --git a/plugins/gtf/src/GtfAdapter/GtfAdapter.test.ts b/plugins/gtf/src/GtfAdapter/GtfAdapter.test.ts index f687cabfcd..1454ab808e 100644 --- a/plugins/gtf/src/GtfAdapter/GtfAdapter.test.ts +++ b/plugins/gtf/src/GtfAdapter/GtfAdapter.test.ts @@ -20,12 +20,13 @@ describe('adapter can fetch features from volvox.sorted.gtf', () => { refName: 'ctgA', start: 0, end: 100000, + assemblyName: 'volvox', }) expect(await adapter.hasDataForRefName('ctgA')).toBe(true) expect(await adapter.hasDataForRefName('ctgB')).toBe(false) const featuresArray = await firstValueFrom(features.pipe(toArray())) // There are only 4 features in ctgB - expect(featuresArray.length).toBe(6) + expect(featuresArray.length).toBe(4) const featuresJsonArray = featuresArray.map(f => f.toJSON()) expect(featuresJsonArray).toMatchSnapshot() }) @@ -47,6 +48,7 @@ test('can instantiate new GtfAdapter and check for demo data', async () => { refName: 'GeneScaffold_1', start: 0, end: 1100000, + assemblyName: 'volvox', }) const featuresArray = await firstValueFrom(features.pipe(toArray())) const featuresJsonArray = featuresArray.map(f => f.toJSON()) diff --git a/plugins/gtf/src/GtfAdapter/GtfAdapter.ts b/plugins/gtf/src/GtfAdapter/GtfAdapter.ts index 137418960f..bdb34f62db 100644 --- a/plugins/gtf/src/GtfAdapter/GtfAdapter.ts +++ b/plugins/gtf/src/GtfAdapter/GtfAdapter.ts @@ -197,7 +197,7 @@ export default class GtfAdapter extends BaseFeatureDataAdapter { } else { observer.next( new SimpleFeature({ - id: `${this.id}-${feat.uniqueId}`, + id: feat.uniqueId, data: feat, }), ) @@ -211,7 +211,7 @@ export default class GtfAdapter extends BaseFeatureDataAdapter { const { uniqueId, strand } = subfeatures[0]! observer.next( new SimpleFeature({ - id: `${this.id}-${uniqueId}-parent`, + id: `${uniqueId}-parent`, data: { type: 'gene', subfeatures, diff --git a/plugins/gtf/src/GtfAdapter/__snapshots__/GtfAdapter.test.ts.snap b/plugins/gtf/src/GtfAdapter/__snapshots__/GtfAdapter.test.ts.snap index e55e0af386..57ab84612b 100644 --- a/plugins/gtf/src/GtfAdapter/__snapshots__/GtfAdapter.test.ts.snap +++ b/plugins/gtf/src/GtfAdapter/__snapshots__/GtfAdapter.test.ts.snap @@ -2,753 +2,6 @@ exports[`adapter can fetch features from volvox.sorted.gtf test getfeatures on gtf plain text adapter 1`] = ` [ - { - "_linehash": undefined, - "attributes": undefined, - "child_features": undefined, - "data": undefined, - "derived_features": undefined, - "end": 9000, - "featureType": undefined, - "frame": undefined, - "gene_id": "EDEN", - "gene_name": "EDEN", - "name": "EDEN.1", - "phase": 0, - "refName": "ctgA", - "score": undefined, - "seq_name": undefined, - "source": "example", - "start": 1049, - "strand": 1, - "subfeatures": [ - { - "_linehash": undefined, - "attributes": undefined, - "child_features": undefined, - "data": undefined, - "derived_features": undefined, - "end": 1500, - "featureType": undefined, - "frame": undefined, - "gene_id": "EDEN", - "gene_name": "EDEN", - "name": "EDEN.1", - "parentId": "test-ctgA-0", - "phase": 0, - "refName": "ctgA", - "score": undefined, - "seq_name": undefined, - "source": "example", - "start": 1049, - "strand": 1, - "transcript_id": "EDEN.1", - "type": "exon", - "uniqueId": "test-ctgA-0-0", - }, - { - "_linehash": undefined, - "attributes": undefined, - "child_features": undefined, - "data": undefined, - "derived_features": undefined, - "end": 1200, - "featureType": undefined, - "frame": undefined, - "gene_id": "EDEN", - "gene_name": "EDEN", - "name": "EDEN.1", - "parentId": "test-ctgA-0", - "phase": 0, - "refName": "ctgA", - "score": undefined, - "seq_name": undefined, - "source": "example", - "start": 1049, - "strand": 1, - "transcript_id": "EDEN.1", - "type": "five_prime_UTR", - "uniqueId": "test-ctgA-0-1", - }, - { - "_linehash": undefined, - "attributes": undefined, - "child_features": undefined, - "data": undefined, - "derived_features": undefined, - "end": 1500, - "featureType": undefined, - "frame": undefined, - "gene_id": "EDEN", - "gene_name": "EDEN", - "name": "EDEN.1", - "parentId": "test-ctgA-0", - "phase": 0, - "refName": "ctgA", - "score": undefined, - "seq_name": undefined, - "source": "example", - "start": 1200, - "strand": 1, - "transcript_id": "EDEN.1", - "type": "CDS", - "uniqueId": "test-ctgA-0-2", - }, - { - "_linehash": undefined, - "attributes": undefined, - "child_features": undefined, - "data": undefined, - "derived_features": undefined, - "end": 3902, - "featureType": undefined, - "frame": undefined, - "gene_id": "EDEN", - "gene_name": "EDEN", - "name": "EDEN.1", - "parentId": "test-ctgA-0", - "phase": 0, - "refName": "ctgA", - "score": undefined, - "seq_name": undefined, - "source": "example", - "start": 2999, - "strand": 1, - "transcript_id": "EDEN.1", - "type": "CDS", - "uniqueId": "test-ctgA-0-3", - }, - { - "_linehash": undefined, - "attributes": undefined, - "child_features": undefined, - "data": undefined, - "derived_features": undefined, - "end": 3902, - "featureType": undefined, - "frame": undefined, - "gene_id": "EDEN", - "gene_name": "EDEN", - "name": "EDEN.1", - "parentId": "test-ctgA-0", - "phase": 0, - "refName": "ctgA", - "score": undefined, - "seq_name": undefined, - "source": "example", - "start": 2999, - "strand": 1, - "transcript_id": "EDEN.1", - "type": "exon", - "uniqueId": "test-ctgA-0-4", - }, - { - "_linehash": undefined, - "attributes": undefined, - "child_features": undefined, - "data": undefined, - "derived_features": undefined, - "end": 5500, - "featureType": undefined, - "frame": undefined, - "gene_id": "EDEN", - "gene_name": "EDEN", - "name": "EDEN.1", - "parentId": "test-ctgA-0", - "phase": 0, - "refName": "ctgA", - "score": undefined, - "seq_name": undefined, - "source": "example", - "start": 4999, - "strand": 1, - "transcript_id": "EDEN.1", - "type": "CDS", - "uniqueId": "test-ctgA-0-5", - }, - { - "_linehash": undefined, - "attributes": undefined, - "child_features": undefined, - "data": undefined, - "derived_features": undefined, - "end": 5500, - "featureType": undefined, - "frame": undefined, - "gene_id": "EDEN", - "gene_name": "EDEN", - "name": "EDEN.1", - "parentId": "test-ctgA-0", - "phase": 0, - "refName": "ctgA", - "score": undefined, - "seq_name": undefined, - "source": "example", - "start": 4999, - "strand": 1, - "transcript_id": "EDEN.1", - "type": "exon", - "uniqueId": "test-ctgA-0-6", - }, - { - "_linehash": undefined, - "attributes": undefined, - "child_features": undefined, - "data": undefined, - "derived_features": undefined, - "end": 7608, - "featureType": undefined, - "frame": undefined, - "gene_id": "EDEN", - "gene_name": "EDEN", - "name": "EDEN.1", - "parentId": "test-ctgA-0", - "phase": 0, - "refName": "ctgA", - "score": undefined, - "seq_name": undefined, - "source": "example", - "start": 6999, - "strand": 1, - "transcript_id": "EDEN.1", - "type": "CDS", - "uniqueId": "test-ctgA-0-7", - }, - { - "_linehash": undefined, - "attributes": undefined, - "child_features": undefined, - "data": undefined, - "derived_features": undefined, - "end": 9000, - "featureType": undefined, - "frame": undefined, - "gene_id": "EDEN", - "gene_name": "EDEN", - "name": "EDEN.1", - "parentId": "test-ctgA-0", - "phase": 0, - "refName": "ctgA", - "score": undefined, - "seq_name": undefined, - "source": "example", - "start": 6999, - "strand": 1, - "transcript_id": "EDEN.1", - "type": "exon", - "uniqueId": "test-ctgA-0-8", - }, - { - "_linehash": undefined, - "attributes": undefined, - "child_features": undefined, - "data": undefined, - "derived_features": undefined, - "end": 9000, - "featureType": undefined, - "frame": undefined, - "gene_id": "EDEN", - "gene_name": "EDEN", - "name": "EDEN.1", - "parentId": "test-ctgA-0", - "phase": 0, - "refName": "ctgA", - "score": undefined, - "seq_name": undefined, - "source": "example", - "start": 7608, - "strand": 1, - "transcript_id": "EDEN.1", - "type": "three_prime_UTR", - "uniqueId": "test-ctgA-0-9", - }, - ], - "transcript_id": "EDEN.1", - "type": "transcript", - "uniqueId": "test-ctgA-0", - }, - { - "_linehash": undefined, - "attributes": undefined, - "child_features": undefined, - "data": undefined, - "derived_features": undefined, - "end": 9000, - "featureType": undefined, - "frame": undefined, - "gene_id": "EDEN", - "gene_name": "EDEN", - "name": "EDEN.2", - "phase": 0, - "refName": "ctgA", - "score": undefined, - "seq_name": undefined, - "source": "example", - "start": 1049, - "strand": 1, - "subfeatures": [ - { - "_linehash": undefined, - "attributes": undefined, - "child_features": undefined, - "data": undefined, - "derived_features": undefined, - "end": 1500, - "featureType": undefined, - "frame": undefined, - "gene_id": "EDEN", - "gene_name": "EDEN", - "name": "EDEN.2", - "parentId": "test-ctgA-1", - "phase": 0, - "refName": "ctgA", - "score": undefined, - "seq_name": undefined, - "source": "example", - "start": 1049, - "strand": 1, - "transcript_id": "EDEN.2", - "type": "exon", - "uniqueId": "test-ctgA-1-0", - }, - { - "_linehash": undefined, - "attributes": undefined, - "child_features": undefined, - "data": undefined, - "derived_features": undefined, - "end": 1200, - "featureType": undefined, - "frame": undefined, - "gene_id": "EDEN", - "gene_name": "EDEN", - "name": "EDEN.2", - "parentId": "test-ctgA-1", - "phase": 0, - "refName": "ctgA", - "score": undefined, - "seq_name": undefined, - "source": "example", - "start": 1049, - "strand": 1, - "transcript_id": "EDEN.2", - "type": "five_prime_UTR", - "uniqueId": "test-ctgA-1-1", - }, - { - "_linehash": undefined, - "attributes": undefined, - "child_features": undefined, - "data": undefined, - "derived_features": undefined, - "end": 1500, - "featureType": undefined, - "frame": undefined, - "gene_id": "EDEN", - "gene_name": "EDEN", - "name": "EDEN.2", - "parentId": "test-ctgA-1", - "phase": 0, - "refName": "ctgA", - "score": undefined, - "seq_name": undefined, - "source": "example", - "start": 1200, - "strand": 1, - "transcript_id": "EDEN.2", - "type": "CDS", - "uniqueId": "test-ctgA-1-2", - }, - { - "_linehash": undefined, - "attributes": undefined, - "child_features": undefined, - "data": undefined, - "derived_features": undefined, - "end": 5500, - "featureType": undefined, - "frame": undefined, - "gene_id": "EDEN", - "gene_name": "EDEN", - "name": "EDEN.2", - "parentId": "test-ctgA-1", - "phase": 0, - "refName": "ctgA", - "score": undefined, - "seq_name": undefined, - "source": "example", - "start": 4999, - "strand": 1, - "transcript_id": "EDEN.2", - "type": "CDS", - "uniqueId": "test-ctgA-1-3", - }, - { - "_linehash": undefined, - "attributes": undefined, - "child_features": undefined, - "data": undefined, - "derived_features": undefined, - "end": 5500, - "featureType": undefined, - "frame": undefined, - "gene_id": "EDEN", - "gene_name": "EDEN", - "name": "EDEN.2", - "parentId": "test-ctgA-1", - "phase": 0, - "refName": "ctgA", - "score": undefined, - "seq_name": undefined, - "source": "example", - "start": 4999, - "strand": 1, - "transcript_id": "EDEN.2", - "type": "exon", - "uniqueId": "test-ctgA-1-4", - }, - { - "_linehash": undefined, - "attributes": undefined, - "child_features": undefined, - "data": undefined, - "derived_features": undefined, - "end": 7608, - "featureType": undefined, - "frame": undefined, - "gene_id": "EDEN", - "gene_name": "EDEN", - "name": "EDEN.2", - "parentId": "test-ctgA-1", - "phase": 0, - "refName": "ctgA", - "score": undefined, - "seq_name": undefined, - "source": "example", - "start": 6999, - "strand": 1, - "transcript_id": "EDEN.2", - "type": "CDS", - "uniqueId": "test-ctgA-1-5", - }, - { - "_linehash": undefined, - "attributes": undefined, - "child_features": undefined, - "data": undefined, - "derived_features": undefined, - "end": 9000, - "featureType": undefined, - "frame": undefined, - "gene_id": "EDEN", - "gene_name": "EDEN", - "name": "EDEN.2", - "parentId": "test-ctgA-1", - "phase": 0, - "refName": "ctgA", - "score": undefined, - "seq_name": undefined, - "source": "example", - "start": 6999, - "strand": 1, - "transcript_id": "EDEN.2", - "type": "exon", - "uniqueId": "test-ctgA-1-6", - }, - { - "_linehash": undefined, - "attributes": undefined, - "child_features": undefined, - "data": undefined, - "derived_features": undefined, - "end": 9000, - "featureType": undefined, - "frame": undefined, - "gene_id": "EDEN", - "gene_name": "EDEN", - "name": "EDEN.2", - "parentId": "test-ctgA-1", - "phase": 0, - "refName": "ctgA", - "score": undefined, - "seq_name": undefined, - "source": "example", - "start": 7608, - "strand": 1, - "transcript_id": "EDEN.2", - "type": "three_prime_UTR", - "uniqueId": "test-ctgA-1-7", - }, - ], - "transcript_id": "EDEN.2", - "type": "transcript", - "uniqueId": "test-ctgA-1", - }, - { - "_linehash": undefined, - "attributes": undefined, - "child_features": undefined, - "data": undefined, - "derived_features": undefined, - "end": 9000, - "featureType": undefined, - "frame": undefined, - "gene_id": "EDEN", - "gene_name": "EDEN", - "name": "EDEN.3", - "phase": 0, - "refName": "ctgA", - "score": undefined, - "seq_name": undefined, - "source": "example", - "start": 1299, - "strand": 1, - "subfeatures": [ - { - "_linehash": undefined, - "attributes": undefined, - "child_features": undefined, - "data": undefined, - "derived_features": undefined, - "end": 1500, - "featureType": undefined, - "frame": undefined, - "gene_id": "EDEN", - "gene_name": "EDEN", - "name": "EDEN.3", - "parentId": "test-ctgA-2", - "phase": 0, - "refName": "ctgA", - "score": undefined, - "seq_name": undefined, - "source": "example", - "start": 1299, - "strand": 1, - "transcript_id": "EDEN.3", - "type": "exon", - "uniqueId": "test-ctgA-2-0", - }, - { - "_linehash": undefined, - "attributes": undefined, - "child_features": undefined, - "data": undefined, - "derived_features": undefined, - "end": 1500, - "featureType": undefined, - "frame": undefined, - "gene_id": "EDEN", - "gene_name": "EDEN", - "name": "EDEN.3", - "parentId": "test-ctgA-2", - "phase": 1, - "refName": "ctgA", - "score": undefined, - "seq_name": undefined, - "source": "example", - "start": 1299, - "strand": 1, - "transcript_id": "EDEN.3", - "type": "five_prime_UTR", - "uniqueId": "test-ctgA-2-1", - }, - { - "_linehash": undefined, - "attributes": undefined, - "child_features": undefined, - "data": undefined, - "derived_features": undefined, - "end": 3902, - "featureType": undefined, - "frame": undefined, - "gene_id": "EDEN", - "gene_name": "EDEN", - "name": "EDEN.3", - "parentId": "test-ctgA-2", - "phase": 0, - "refName": "ctgA", - "score": undefined, - "seq_name": undefined, - "source": "example", - "start": 2999, - "strand": 1, - "transcript_id": "EDEN.3", - "type": "exon", - "uniqueId": "test-ctgA-2-2", - }, - { - "_linehash": undefined, - "attributes": undefined, - "child_features": undefined, - "data": undefined, - "derived_features": undefined, - "end": 3300, - "featureType": undefined, - "frame": undefined, - "gene_id": "EDEN", - "gene_name": "EDEN", - "name": "EDEN.3", - "parentId": "test-ctgA-2", - "phase": 1, - "refName": "ctgA", - "score": undefined, - "seq_name": undefined, - "source": "example", - "start": 2999, - "strand": 1, - "transcript_id": "EDEN.3", - "type": "five_prime_UTR", - "uniqueId": "test-ctgA-2-3", - }, - { - "_linehash": undefined, - "attributes": undefined, - "child_features": undefined, - "data": undefined, - "derived_features": undefined, - "end": 3902, - "featureType": undefined, - "frame": undefined, - "gene_id": "EDEN", - "gene_name": "EDEN", - "name": "EDEN.3", - "parentId": "test-ctgA-2", - "phase": 0, - "refName": "ctgA", - "score": undefined, - "seq_name": undefined, - "source": "example", - "start": 3300, - "strand": 1, - "transcript_id": "EDEN.3", - "type": "CDS", - "uniqueId": "test-ctgA-2-4", - }, - { - "_linehash": undefined, - "attributes": undefined, - "child_features": undefined, - "data": undefined, - "derived_features": undefined, - "end": 5500, - "featureType": undefined, - "frame": undefined, - "gene_id": "EDEN", - "gene_name": "EDEN", - "name": "EDEN.3", - "parentId": "test-ctgA-2", - "phase": 1, - "refName": "ctgA", - "score": undefined, - "seq_name": undefined, - "source": "example", - "start": 4999, - "strand": 1, - "transcript_id": "EDEN.3", - "type": "CDS", - "uniqueId": "test-ctgA-2-5", - }, - { - "_linehash": undefined, - "attributes": undefined, - "child_features": undefined, - "data": undefined, - "derived_features": undefined, - "end": 5500, - "featureType": undefined, - "frame": undefined, - "gene_id": "EDEN", - "gene_name": "EDEN", - "name": "EDEN.3", - "parentId": "test-ctgA-2", - "phase": 0, - "refName": "ctgA", - "score": undefined, - "seq_name": undefined, - "source": "example", - "start": 4999, - "strand": 1, - "transcript_id": "EDEN.3", - "type": "exon", - "uniqueId": "test-ctgA-2-6", - }, - { - "_linehash": undefined, - "attributes": undefined, - "child_features": undefined, - "data": undefined, - "derived_features": undefined, - "end": 7600, - "featureType": undefined, - "frame": undefined, - "gene_id": "EDEN", - "gene_name": "EDEN", - "name": "EDEN.3", - "parentId": "test-ctgA-2", - "phase": 1, - "refName": "ctgA", - "score": undefined, - "seq_name": undefined, - "source": "example", - "start": 6999, - "strand": 1, - "transcript_id": "EDEN.3", - "type": "CDS", - "uniqueId": "test-ctgA-2-7", - }, - { - "_linehash": undefined, - "attributes": undefined, - "child_features": undefined, - "data": undefined, - "derived_features": undefined, - "end": 9000, - "featureType": undefined, - "frame": undefined, - "gene_id": "EDEN", - "gene_name": "EDEN", - "name": "EDEN.3", - "parentId": "test-ctgA-2", - "phase": 0, - "refName": "ctgA", - "score": undefined, - "seq_name": undefined, - "source": "example", - "start": 6999, - "strand": 1, - "transcript_id": "EDEN.3", - "type": "exon", - "uniqueId": "test-ctgA-2-8", - }, - { - "_linehash": undefined, - "attributes": undefined, - "child_features": undefined, - "data": undefined, - "derived_features": undefined, - "end": 9000, - "featureType": undefined, - "frame": undefined, - "gene_id": "EDEN", - "gene_name": "EDEN", - "name": "EDEN.3", - "parentId": "test-ctgA-2", - "phase": 1, - "refName": "ctgA", - "score": undefined, - "seq_name": undefined, - "source": "example", - "start": 7600, - "strand": 1, - "transcript_id": "EDEN.3", - "type": "three_prime_UTR", - "uniqueId": "test-ctgA-2-9", - }, - ], - "transcript_id": "EDEN.3", - "type": "transcript", - "uniqueId": "test-ctgA-2", - }, { "_linehash": undefined, "attributes": undefined, @@ -1082,6 +335,767 @@ exports[`adapter can fetch features from volvox.sorted.gtf test getfeatures on g "type": "transcript", "uniqueId": "test-ctgA-5", }, + { + "end": 9000, + "name": "EDEN", + "refName": "ctgA", + "start": 1049, + "strand": 1, + "subfeatures": [ + { + "_linehash": undefined, + "attributes": undefined, + "child_features": undefined, + "data": undefined, + "derived_features": undefined, + "end": 9000, + "featureType": undefined, + "frame": undefined, + "gene_id": "EDEN", + "gene_name": "EDEN", + "name": "EDEN.1", + "parentId": "test-ctgA-0-parent", + "phase": 0, + "refName": "ctgA", + "score": undefined, + "seq_name": undefined, + "source": "example", + "start": 1049, + "strand": 1, + "subfeatures": [ + { + "_linehash": undefined, + "attributes": undefined, + "child_features": undefined, + "data": undefined, + "derived_features": undefined, + "end": 1500, + "featureType": undefined, + "frame": undefined, + "gene_id": "EDEN", + "gene_name": "EDEN", + "name": "EDEN.1", + "parentId": "test-ctgA-0", + "phase": 0, + "refName": "ctgA", + "score": undefined, + "seq_name": undefined, + "source": "example", + "start": 1049, + "strand": 1, + "transcript_id": "EDEN.1", + "type": "exon", + "uniqueId": "test-ctgA-0-0", + }, + { + "_linehash": undefined, + "attributes": undefined, + "child_features": undefined, + "data": undefined, + "derived_features": undefined, + "end": 1200, + "featureType": 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