Add ability to get promoter sequence and intron sequence for genes from the feature details panel

packages/core/BaseFeatureWidget/SequenceFeatureDetails.test.js

@@ -0,0 +1,103 @@
+import React from 'react'
+import { render } from '@testing-library/react'
+import fs from 'fs'
+import { SequencePanel } from './SequenceFeatureDetails'
+import DLGAP3 from './test_data/DLGAP3.json'
+import NCDN from './test_data/NCDN.json'
+
+test('test using the sequence feature panel', () => {
+  // produced from uniprot
+  // https://www.uniprot.org/uniprot/O95886.fasta
+  const pep = readFasta('./test_data/DLGAP3_pep.fa')
+
+  // produced with samtools faidx
+  // 'https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz'
+  // 1:35331037..35395251
+  const dna = readFasta('./test_data/DLGAP3_dna.fa')
+
+  // http://localhost:3000/?config=test_data%2Fconfig_demo.json&session=share-zMPjiv36k0&password=ddxCy
+  const feature = DLGAP3
+  const { getByTestId } = render(
+    <SequencePanel
+      sequence={{ seq: dna }}
+      mode="protein"
+      feature={feature.subfeatures[0]}
+    />,
+  )
+
+  const element = getByTestId('sequence_panel')
+
+  // http://m.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000116544;r=1:34865436-34929650
+  // with stop codon on the end
+  expect(element.textContent).toEqual(`${pep}*`)
+})
+
+const readFasta = filename => {
+  return fs
+    .readFileSync(require.resolve(filename), 'utf8')
+    .split('\n')
+    .slice(1)
+    .join('')
+}
+
+test('NCDN collapsed intron', () => {
+  // samtools faidx 'https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz' 1:36,023,400-36,032,380 > out.fa
+  const dna = readFasta('./test_data/NCDN_dna.fa')
+
+  // http://localhost:3000/?config=test_data%2Fconfig_demo.json&session=share-zMPjiv36k0&password=ddxCy
+  const feature = NCDN
+  const { getByTestId } = render(
+    <SequencePanel
+      sequence={{ seq: dna }}
+      mode="gene_collapsed_intron"
+      feature={feature.subfeatures[0]}
+    />,
+  )
+
+  const element = getByTestId('sequence_panel')
+
+  // UTR
+  expect(element.children[0].textContent).toEqual(
+    'AGTGGGCAACGCGGCGTGAGCAGCGGCCCGAGGCTCCCGGAGCATCGCGCTGGGAGAAGACTTCGCCGCTCGGGGCCGCAGCCTGGTGAGCTCAGCCCCCTTCGGGCCCTCCCCTGCATCCCAGCCGGGGCCTCTCCGAGCCGGCGCTGATCGATGCCGACACACCCCGGGGACCCTATCGCGACTCCATCGCGCCATATCGCGACACCATCGTGCCCTGTCGAGACTCCATTTTGTCACAGCCCTTTTCAATATATATCTTTTTTTTTTTTAATTTGCCCTGTCATCTTTGGGGGCTGTCTCCCATGTCGTGATTTTGACGTGATCTCTCCGTGACATCACCGCGCCATCGTGAAGTGTGATCTCATCGCCGCCCTGTCGTGACTTCATCA',
+  )
+  // first CDS
+  expect(element.children[2].textContent).toEqual(
+    'ATGTCGTGTTGTGACCTGGCTGCGGCGGGACAG',
+  )
+  // spliced intron
+  expect(element.children[3].textContent).toEqual('GTGGTGACCG...GTGTTCACAG')
+})
+
+test('NCDN updownstream', () => {
+  // produced from uniprot
+  // https://www.uniprot.org/uniprot/O95886.fasta
+  const upstream = readFasta('./test_data/NCDN_upstream_dna.fa')
+
+  // samtools faidx 'https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz' 1:36,023,400-36,032,380 > out.fa
+  const seq = readFasta('./test_data/NCDN_dna.fa')
+
+  // http://localhost:3000/?config=test_data%2Fconfig_demo.json&session=share-zMPjiv36k0&password=ddxCy
+  const feature = NCDN
+  const { getByTestId } = render(
+    <SequencePanel
+      sequence={{ seq, upstream }}
+      mode="gene_updownstream"
+      feature={feature.subfeatures[0]}
+    />,
+  )
+
+  const element = getByTestId('sequence_panel')
+
+  expect(element.children[0].textContent).toEqual(
+    'CTCACCCGGAGGAGGAGGAGGAAGAGGAAGAAGGTAGTGCGGGCTCCCCACCCGGACAGCTACCTCTCGCCTCAGCCTCCCTGGACAGCGACGGCGGCCGGAAACACCGCCTCCTCCCACCTCCCCGGGACCGACCCGGAAACACACTCTCCATGCTAACCAAGCCCTCCCGCCCCTCCCCCGGGAAGGGCAATGCCGGCCGCGAGACCAAGGGGGAGGAGGGGCAGTGCTGGGCGGGTAAAACTACGCACAAGCGAAGGAATCTGGGCCCCCAGCCTCTCGCCGCCCGCTCTCCAGAGGCAGTCTGCACCTTGCCTCCTTCGCTCGAGCCCCAGCCCCCAGACTCGGGCAATACCCACAAGCAAGATGGCGGCAACGGCGGCACCCCCTACTGCTTAGCACCCTGACTTGCCATTGGCCAGAGCCCGGAGTGAAGCAGCCGCGGATTCGTCAAGAGCGGTGCGGGGGTGGGGGTGGAGCTGCAGCAGCCTGGAGCCAGG',
+  )
+  expect(element.children[1].textContent).toEqual(
+    'AGTGGGCAACGCGGCGTGAGCAGCGGCCCGAGGCTCCCGGAGCATCGCGCTGGGAGAAGACTTCGCCGCTCGGGGCCGCAGCCTGGTGAGCTCAGCCCCCTTCGGGCCCTCCCCTGCATCCCAGCCGGGGCCTCTCCGAGCCGGCGCTGATCGATGCCGACACACCCCGGGGACCCTATCGCGACTCCATCGCGCCATATCGCGACACCATCGTGCCCTGTCGAGACTCCATTTTGTCACAGCCCTTTTCAATATATATCTTTTTTTTTTTTAATTTGCCCTGTCATCTTTGGGGGCTGTCTCCCATGTCGTGATTTTGACGTGATCTCTCCGTGACATCACCGCGCCATCGTGAAGTGTGATCTCATCGCCGCCCTGTCGTGACTTCATCA',
+  )
+
+  // 3rd is a blank element, so go to 4th, not strictly needed for 3rd to be
+  // blank but helps test
+  expect(element.children[3].textContent).toEqual(
+    'ATGTCGTGTTGTGACCTGGCTGCGGCGGGACAG',
+  )
+})