@jbrowse/plugin-bed 1.7.9 → 2.0.0

package/src/BedAdapter/__snapshots__/BedAdapter.test.ts.snap

@@ -0,0 +1,437 @@
+// Jest Snapshot v1, https://goo.gl/fbAQLP
+
+exports[`adapter can fetch bed with header 1`] = `
+Array [
+  Object {
+    "end": 3009,
+    "refName": "contigA",
+    "start": 3000,
+    "strand": 0,
+    "uniqueId": "test-contigA-0",
+  },
+  Object {
+    "end": 3114,
+    "refName": "contigA",
+    "start": 3105,
+    "strand": 0,
+    "uniqueId": "test-contigA-1",
+  },
+  Object {
+    "end": 3161,
+    "refName": "contigA",
+    "start": 3152,
+    "strand": 0,
+    "uniqueId": "test-contigA-2",
+  },
+  Object {
+    "end": 3180,
+    "refName": "contigA",
+    "start": 3171,
+    "strand": 0,
+    "uniqueId": "test-contigA-3",
+  },
+  Object {
+    "end": 3183,
+    "refName": "contigA",
+    "start": 3174,
+    "strand": 0,
+    "uniqueId": "test-contigA-4",
+  },
+  Object {
+    "end": 3222,
+    "refName": "contigA",
+    "start": 3213,
+    "strand": 0,
+    "uniqueId": "test-contigA-5",
+  },
+  Object {
+    "end": 3474,
+    "refName": "contigA",
+    "start": 3465,
+    "strand": 0,
+    "uniqueId": "test-contigA-6",
+  },
+  Object {
+    "end": 3804,
+    "refName": "contigA",
+    "start": 3795,
+    "strand": 0,
+    "uniqueId": "test-contigA-7",
+  },
+  Object {
+    "end": 4044,
+    "refName": "contigA",
+    "start": 4035,
+    "strand": 0,
+    "uniqueId": "test-contigA-8",
+  },
+  Object {
+    "end": 4082,
+    "refName": "contigA",
+    "start": 4073,
+    "strand": 0,
+    "uniqueId": "test-contigA-9",
+  },
+]
+`;
+
+exports[`adapter can fetch features bed with autosql 1`] = `
+Array [
+  Object {
+    "Entrez_Gene_Id": "2782",
+    "Hugo_Symbol": "GNB1",
+    "Matched_Norm_Sample_Barcode": "TCGA-OR-A5KB-11A-11D-A30A-10",
+    "Reference_Allele": "T",
+    "Tumor_Sample_Barcode": "TCGA-OR-A5KB-01A-11D-A30A-10",
+    "Tumor_Seq_Allele1": "T",
+    "Tumor_Seq_Allele2": "G",
+    "Variant_Classification": "Splice_Region",
+    "Variant_Type": "SNP",
+    "alcohol_history": "--",
+    "alcohol_intensity": "--",
+    "bmi": "--",
+    "case_id": "09454ed6-64bc-4a35-af44-7c4344623d45",
+    "cigarettes_per_day": "--",
+    "days_to_death": "--",
+    "dbSNP_RS": "novel",
+    "dbSNP_Val_Status": "",
+    "end": 10,
+    "ethnicity": "not hispanic or latino",
+    "freq": "0.0108695652174",
+    "gender": "female",
+    "height": "--",
+    "name": "T>G",
+    "project_id": "TCGA-ACC",
+    "refName": "ctgA",
+    "reserved": "0,0,0",
+    "sampleCount": "1",
+    "score": 1,
+    "start": 1,
+    "strand": 0,
+    "subfeatures": Array [
+      Object {
+        "end": 2,
+        "parentId": "test-ctgA-0",
+        "start": 1,
+        "strand": 0,
+        "type": "three_prime_UTR",
+        "uniqueId": "test-ctgA-0-0",
+      },
+    ],
+    "type": "mRNA",
+    "uniqueId": "test-ctgA-0",
+    "weight": "--",
+    "years_smoked": "--",
+  },
+]
+`;
+
+exports[`adapter can fetch features from volvox.sort.bed simple bed3 1`] = `
+Array [
+  Object {
+    "end": 3009,
+    "refName": "contigA",
+    "start": 3000,
+    "strand": 0,
+    "uniqueId": "test-contigA-0",
+  },
+  Object {
+    "end": 3114,
+    "refName": "contigA",
+    "start": 3105,
+    "strand": 0,
+    "uniqueId": "test-contigA-1",
+  },
+  Object {
+    "end": 3161,
+    "refName": "contigA",
+    "start": 3152,
+    "strand": 0,
+    "uniqueId": "test-contigA-2",
+  },
+  Object {
+    "end": 3180,
+    "refName": "contigA",
+    "start": 3171,
+    "strand": 0,
+    "uniqueId": "test-contigA-3",
+  },
+  Object {
+    "end": 3183,
+    "refName": "contigA",
+    "start": 3174,
+    "strand": 0,
+    "uniqueId": "test-contigA-4",
+  },
+  Object {
+    "end": 3222,
+    "refName": "contigA",
+    "start": 3213,
+    "strand": 0,
+    "uniqueId": "test-contigA-5",
+  },
+  Object {
+    "end": 3474,
+    "refName": "contigA",
+    "start": 3465,
+    "strand": 0,
+    "uniqueId": "test-contigA-6",
+  },
+  Object {
+    "end": 3804,
+    "refName": "contigA",
+    "start": 3795,
+    "strand": 0,
+    "uniqueId": "test-contigA-7",
+  },
+  Object {
+    "end": 4044,
+    "refName": "contigA",
+    "start": 4035,
+    "strand": 0,
+    "uniqueId": "test-contigA-8",
+  },
+  Object {
+    "end": 4082,
+    "refName": "contigA",
+    "start": 4073,
+    "strand": 0,
+    "uniqueId": "test-contigA-9",
+  },
+]
+`;
+
+exports[`adapter can fetch features from volvox-bed12.bed 1`] = `
+Array [
+  Object {
+    "end": 9000,
+    "itemRgb": "0,0,0",
+    "name": "EDEN.1",
+    "refName": "ctgA",
+    "score": 1000,
+    "start": 1049,
+    "strand": 1,
+    "subfeatures": Array [
+      Object {
+        "end": 1200,
+        "parentId": "test-ctgA-0",
+        "start": 1049,
+        "strand": 1,
+        "type": "five_prime_UTR",
+        "uniqueId": "test-ctgA-0-0",
+      },
+      Object {
+        "end": 1500,
+        "parentId": "test-ctgA-0",
+        "start": 1200,
+        "strand": 1,
+        "type": "CDS",
+        "uniqueId": "test-ctgA-0-1",
+      },
+      Object {
+        "end": 3902,
+        "parentId": "test-ctgA-0",
+        "start": 2999,
+        "strand": 1,
+        "type": "CDS",
+        "uniqueId": "test-ctgA-0-2",
+      },
+      Object {
+        "end": 5500,
+        "parentId": "test-ctgA-0",
+        "start": 4999,
+        "strand": 1,
+        "type": "CDS",
+        "uniqueId": "test-ctgA-0-3",
+      },
+      Object {
+        "end": 7608,
+        "parentId": "test-ctgA-0",
+        "start": 6999,
+        "strand": 1,
+        "type": "CDS",
+        "uniqueId": "test-ctgA-0-4",
+      },
+      Object {
+        "end": 9000,
+        "parentId": "test-ctgA-0",
+        "start": 7608,
+        "strand": 1,
+        "type": "three_prime_UTR",
+        "uniqueId": "test-ctgA-0-5",
+      },
+    ],
+    "type": "mRNA",
+    "uniqueId": "test-ctgA-0",
+  },
+  Object {
+    "end": 9000,
+    "itemRgb": "0,0,0",
+    "name": "EDEN.2",
+    "refName": "ctgA",
+    "score": 1000,
+    "start": 1049,
+    "strand": 1,
+    "subfeatures": Array [
+      Object {
+        "end": 1200,
+        "parentId": "test-ctgA-1",
+        "start": 1049,
+        "strand": 1,
+        "type": "five_prime_UTR",
+        "uniqueId": "test-ctgA-1-0",
+      },
+      Object {
+        "end": 1500,
+        "parentId": "test-ctgA-1",
+        "start": 1200,
+        "strand": 1,
+        "type": "CDS",
+        "uniqueId": "test-ctgA-1-1",
+      },
+      Object {
+        "end": 5500,
+        "parentId": "test-ctgA-1",
+        "start": 4999,
+        "strand": 1,
+        "type": "CDS",
+        "uniqueId": "test-ctgA-1-2",
+      },
+      Object {
+        "end": 7608,
+        "parentId": "test-ctgA-1",
+        "start": 6999,
+        "strand": 1,
+        "type": "CDS",
+        "uniqueId": "test-ctgA-1-3",
+      },
+      Object {
+        "end": 9000,
+        "parentId": "test-ctgA-1",
+        "start": 7608,
+        "strand": 1,
+        "type": "three_prime_UTR",
+        "uniqueId": "test-ctgA-1-4",
+      },
+    ],
+    "type": "mRNA",
+    "uniqueId": "test-ctgA-1",
+  },
+  Object {
+    "end": 9000,
+    "itemRgb": "0,0,0",
+    "name": "EDEN.3",
+    "refName": "ctgA",
+    "score": 1000,
+    "start": 1299,
+    "strand": 1,
+    "subfeatures": Array [
+      Object {
+        "end": 1500,
+        "parentId": "test-ctgA-2",
+        "start": 1299,
+        "strand": 1,
+        "type": "five_prime_UTR",
+        "uniqueId": "test-ctgA-2-0",
+      },
+      Object {
+        "end": 3300,
+        "parentId": "test-ctgA-2",
+        "start": 2999,
+        "strand": 1,
+        "type": "five_prime_UTR",
+        "uniqueId": "test-ctgA-2-1",
+      },
+      Object {
+        "end": 3902,
+        "parentId": "test-ctgA-2",
+        "start": 3300,
+        "strand": 1,
+        "type": "CDS",
+        "uniqueId": "test-ctgA-2-2",
+      },
+      Object {
+        "end": 5500,
+        "parentId": "test-ctgA-2",
+        "start": 4999,
+        "strand": 1,
+        "type": "CDS",
+        "uniqueId": "test-ctgA-2-3",
+      },
+      Object {
+        "end": 7600,
+        "parentId": "test-ctgA-2",
+        "start": 6999,
+        "strand": 1,
+        "type": "CDS",
+        "uniqueId": "test-ctgA-2-4",
+      },
+      Object {
+        "end": 9000,
+        "parentId": "test-ctgA-2",
+        "start": 7600,
+        "strand": 1,
+        "type": "three_prime_UTR",
+        "uniqueId": "test-ctgA-2-5",
+      },
+    ],
+    "type": "mRNA",
+    "uniqueId": "test-ctgA-2",
+  },
+  Object {
+    "end": 23000,
+    "itemRgb": "0,0,0",
+    "name": "rna-Apple3",
+    "refName": "ctgA",
+    "score": 1000,
+    "start": 17399,
+    "strand": 1,
+    "subfeatures": Array [
+      Object {
+        "end": 17999,
+        "parentId": "test-ctgA-3",
+        "start": 17399,
+        "strand": 1,
+        "type": "five_prime_UTR",
+        "uniqueId": "test-ctgA-3-0",
+      },
+      Object {
+        "end": 18800,
+        "parentId": "test-ctgA-3",
+        "start": 17999,
+        "strand": 1,
+        "type": "CDS",
+        "uniqueId": "test-ctgA-3-1",
+      },
+      Object {
+        "end": 19500,
+        "parentId": "test-ctgA-3",
+        "start": 18999,
+        "strand": 1,
+        "type": "CDS",
+        "uniqueId": "test-ctgA-3-2",
+      },
+      Object {
+        "end": 21200,
+        "parentId": "test-ctgA-3",
+        "start": 20999,
+        "strand": 1,
+        "type": "CDS",
+        "uniqueId": "test-ctgA-3-3",
+      },
+      Object {
+        "end": 23000,
+        "parentId": "test-ctgA-3",
+        "start": 21200,
+        "strand": 1,
+        "type": "three_prime_UTR",
+        "uniqueId": "test-ctgA-3-4",
+      },
+    ],
+    "type": "mRNA",
+    "uniqueId": "test-ctgA-3",
+  },
+]
+`;
+
+exports[`adapter can use gwas header 1`] = `Array []`;

package/src/BedAdapter/configSchema.ts

@@ -0,0 +1,45 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration'
+
+export default ConfigurationSchema(
+  'BedAdapter',
+  {
+    bedLocation: {
+      type: 'fileLocation',
+      defaultValue: { uri: '/path/to/my.bed.gz', locationType: 'UriLocation' },
+    },
+
+    columnNames: {
+      type: 'stringArray',
+      description: 'List of column names',
+      defaultValue: [],
+    },
+
+    scoreColumn: {
+      type: 'string',
+      description: 'The column to use as a "score" attribute',
+      defaultValue: '',
+    },
+
+    autoSql: {
+      type: 'string',
+      description: 'The autoSql definition for the data fields in the file',
+      defaultValue: '',
+    },
+    colRef: {
+      type: 'number',
+      description: 'The column to use as a "refName" attribute',
+      defaultValue: 0,
+    },
+    colStart: {
+      type: 'number',
+      description: 'The column to use as a "start" attribute',
+      defaultValue: 1,
+    },
+    colEnd: {
+      type: 'number',
+      description: 'The column to use as a "end" attribute',
+      defaultValue: 2,
+    },
+  },
+  { explicitlyTyped: true },
+)

package/src/BedAdapter/index.ts

@@ -0,0 +1 @@
+export { default as configSchema } from './configSchema'

package/src/BedAdapter/test_data/gwas.bed

@@ -0,0 +1,20 @@
+#chrom	pos	rsid	ref	alt	neg_log_pvalue	beta	stderr_beta	alt_allele_freq
+1	721290	rs12565286	G	C	0.275233	.	.	.
+1	752566	rs3094315	G	A	0.0315638	.	.	.
+1	775659	rs2905035	A	G	0.183626	.	.	.
+1	777122	rs2980319	A	T	0.207258	.	.	.
+1	779322	rs4040617	A	G	0.0326393	.	.	.
+1	780785	rs2977612	T	A	0.0225965	.	.	.
+1	785050	rs2905062	G	A	0.0346572	.	.	.
+1	785989	rs2980300	T	C	0.00638744	.	.	.
+1	798959	rs11240777	G	A	0.49853	.	.	.
+1	990380	.	C	A,G,T	0.136915	.	.	.
+1	998501	rs3813193	G	C	0.450384	.	.	.
+1	1003629	rs4075116	C	T	0.881074	.	.	.
+1	1005806	rs3934834	C	T	0.756218	.	.	.
+1	1017170	rs3766193	C	G	0.336111	.	.	.
+1	1017197	rs3766192	C	T	0.381743	.	.	.
+1	1017587	rs3766191	C	T	0.775467	.	.	.
+1	1018562	rs9442371	C	T	0.233364	.	.	.
+1	1018704	rs9442372	A	G	0.248721	.	.	.
+1	1021346	rs10907177	A	G	0.842846	.	.	.

package/src/BedAdapter/test_data/volvox-autosql.bed

@@ -0,0 +1 @@
+ctgA	1	10	T>G	1	.	1815756	1815757	0,0,0	1	1	0	1	0.0108695652174	GNB1	2782	Splice_Region	SNP	T	T	G	novel		--	--	--	--	--	--	--	--	female	TCGA-ACC	not hispanic or latino	TCGA-OR-A5KB-01A-11D-A30A-10	TCGA-OR-A5KB-11A-11D-A30A-10	09454ed6-64bc-4a35-af44-7c4344623d45

package/src/BedAdapter/test_data/volvox-bed12.bed

@@ -0,0 +1,4 @@
+ctgA	1049	9000	EDEN.1	1000	+	1200	7608	0,0,0	4	451,903,501,2001	0,1950,3950,5950	EDEN	EDEN	-	-	-
+ctgA	1049	9000	EDEN.2	1000	+	1200	7608	0,0,0	3	451,501,2001	0,3950,5950	EDEN	EDEN	-	-	-
+ctgA	1299	9000	EDEN.3	1000	+	3300	7600	0,0,0	4	201,903,501,2001	0,1700,3700,5700	EDEN	EDEN	-	-	-
+ctgA	17399	23000	rna-Apple3	1000	+	17999	21200	0,0,0	3	1401,501,2001	0,1600,3600	rna-Apple3	rna-Apple3	-	-	-

package/src/BedAdapter/test_data/volvox.sort.bed

@@ -0,0 +1,109 @@
+contigA	3000	3009
+contigA	3105	3114
+contigA	3152	3161
+contigA	3171	3180
+contigA	3174	3183
+contigA	3213	3222
+contigA	3465	3474
+contigA	3795	3804
+contigA	4035	4044
+contigA	4073	4082
+contigA	4074	4083
+contigA	4166	4175
+contigA	4179	4188
+contigA	4204	4213
+contigA	4248	4257
+contigA	4260	4269
+contigA	4577	4586
+contigA	4828	4837
+contigA	4901	4910
+contigA	5006	5015
+contigA	5051	5060
+contigA	5201	5210
+contigA	5260	5269
+contigA	5281	5290
+contigA	5349	5358
+contigA	5353	5362
+contigA	5423	5432
+contigA	5457	5466
+contigA	5548	5557
+contigA	5626	5635
+contigA	5835	5844
+contigA	5909	5918
+contigA	5927	5936
+contigA	5969	5978
+contigA	6070	6079
+contigA	6185	6194
+contigA	6285	6294
+contigA	6363	6372
+contigA	6559	6568
+contigA	6834	6843
+contigA	6908	6917
+contigA	6918	6927
+contigA	7141	7150
+contigA	7173	7182
+contigA	7569	7578
+contigA	7619	7628
+contigA	7654	7663
+contigA	7671	7680
+contigA	7707	7716
+contigA	7739	7748
+contigA	8077	8086
+contigA	8128	8137
+contigA	8132	8141
+contigA	8210	8219
+contigA	8267	8276
+contigA	8328	8337
+contigA	8524	8533
+contigA	8659	8668
+contigA	8660	8669
+contigA	8742	8751
+contigA	8811	8820
+contigA	8816	8825
+contigA	8964	8973
+contigA	9048	9057
+contigA	9054	9063
+contigA	9136	9145
+contigA	9243	9252
+contigA	9320	9329
+contigA	9366	9375
+contigA	9525	9534
+contigA	9580	9589
+contigA	9610	9619
+contigA	9744	9753
+contigA	9753	9762
+contigA	9759	9768
+contigA	9807	9816
+contigA	9853	9862
+contigA	9884	9893
+contigA	9920	9929
+contigA	10043	10052
+contigA	10216	10225
+contigA	10217	10226
+contigA	10252	10261
+contigA	10384	10393
+contigA	10498	10507
+contigA	10585	10594
+contigA	10684	10693
+contigA	10781	10790
+contigA	10875	10884
+contigA	11004	11013
+contigA	11095	11104
+contigA	11182	11191
+contigA	11207	11216
+contigA	11241	11250
+contigA	11335	11344
+contigA	11340	11349
+contigA	11535	11544
+contigA	11543	11552
+contigA	11549	11558
+contigA	11653	11662
+contigA	11675	11684
+contigA	11689	11698
+contigA	11774	11783
+contigA	11832	11841
+contigA	12386	12395
+contigA	12408	12417
+contigA	12441	12450
+contigA	12530	12539
+contigA	12738	12747