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Add more functionality for loading synteny on the command line
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@cmdcolin
cmdcolin committed Mar 13, 2023
1 parent 39023c8 commit 4e61402
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Showing 11 changed files with 466 additions and 228 deletions.
4 changes: 4 additions & 0 deletions products/jbrowse-cli/README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -259,6 +259,10 @@ OPTIONS
-t, --trackType=trackType Type of track, by default inferred from track file
--bed1=bed1 Used only for mcscan anchors/simpleAnchors types
--bed2=bed2 Used only for mcscan anchors/simpleAnchors types
--category=category Optional Comma separated string of categories to group tracks
--config=config Any extra config settings to add to a track. i.e '{"defaultRendering":
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269 changes: 245 additions & 24 deletions products/jbrowse-cli/src/commands/add-track.test.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -9,22 +9,32 @@ import { setup, readConf, ctxDir } from '../testUtil'

const { writeFile, copyFile } = fs.promises

const baseDir = path.join(__dirname, '..', '..', 'test', 'data')
const simpleBam = path.join(baseDir, 'simple.bam')
const simpleBai = path.join(baseDir, 'simple.bai')
const simpleGff = path.join(baseDir, 'volvox.sort.gff3')
const simplePaf = path.join(baseDir, 'volvox_inv_indels.paf')
const simpleVcf = path.join(baseDir, 'volvox.filtered.vcf')
const simpleGtf = path.join(baseDir, 'volvox.sorted.gtf')
const simpleGffGz = path.join(baseDir, 'volvox.sort.gff3.gz')
const testConfig = path.join(baseDir, 'test_config.json')
const exists = (p: string) => fs.existsSync(p)

const base = path.join(__dirname, '..', '..', 'test', 'data')
const simpleBam = path.join(base, 'simple.bam')
const simpleBai = path.join(base, 'simple.bai')
const simpleGff = path.join(base, 'volvox.sort.gff3')
const simplePaf = path.join(base, 'volvox_inv_indels.paf')
const simplePafGz = path.join(base, 'volvox_inv_indels.paf.gz')
const simpleDelta = path.join(base, 'volvox_inv_indels.delta')
const simpleOut = path.join(base, 'volvox_inv_indels.out')
const simpleChain = path.join(base, 'volvox_inv_indels.chain')
const simpleMcScan = path.join(base, 'volvox_inv_indels.anchors')
const simpleMcScanGrape = path.join(base, 'grape.bed')
const simpleMcScanPeach = path.join(base, 'peach.bed')
const simpleMcScanSimple = path.join(base, 'volvox_inv_indels.anchors.simple')
const simpleVcf = path.join(base, 'volvox.filtered.vcf')
const simpleGtf = path.join(base, 'volvox.sorted.gtf')
const simpleGffGz = path.join(base, 'volvox.sort.gff3.gz')
const testConfig = path.join(base, 'test_config.json')

function initctx(ctx: { dir: string }) {
return copyFile(testConfig, path.join(ctx.dir, 'config.json'))
}
function init2bit(ctx: { dir: string }) {
return copyFile(
path.join(baseDir, 'simple.2bit'),
path.join(base, 'simple.2bit'),
path.join(ctx.dir, 'simple.2bit'),
)
}
Expand Down Expand Up @@ -93,8 +103,8 @@ describe('add-track', () => {
.do(initctx)
.command(['add-track', simpleBam, '--load', 'copy'])
.it('adds a bam track with bai', async ctx => {
expect(fs.existsSync(path.join(ctx.dir, 'simple.bam'))).toBeTruthy()
expect(fs.existsSync(path.join(ctx.dir, 'simple.bam.bai'))).toBeTruthy()
expect(exists(path.join(ctx.dir, 'simple.bam'))).toBeTruthy()
expect(exists(path.join(ctx.dir, 'simple.bam.bai'))).toBeTruthy()
expect(readConf(ctx).tracks).toEqual([
{
type: 'AlignmentsTrack',
Expand Down Expand Up @@ -137,8 +147,8 @@ describe('add-track', () => {
simpleBam + '.csi',
])
.it('adds a bam track with csi', async ctx => {
expect(fs.existsSync(ctxDir(ctx, 'simple.bam'))).toBeTruthy()
expect(fs.existsSync(ctxDir(ctx, 'simple.bam.csi'))).toBeTruthy()
expect(exists(ctxDir(ctx, 'simple.bam'))).toBeTruthy()
expect(exists(ctxDir(ctx, 'simple.bam.csi'))).toBeTruthy()
expect(readConf(ctx).tracks).toEqual([
{
type: 'AlignmentsTrack',
Expand Down Expand Up @@ -256,8 +266,8 @@ describe('add-track', () => {
simpleBai,
])
.it('adds a bam track with indexFile for bai', async ctx => {
expect(fs.existsSync(ctxDir(ctx, 'simple.bam'))).toBeTruthy()
expect(fs.existsSync(ctxDir(ctx, 'simple.bai'))).toBeTruthy()
expect(exists(ctxDir(ctx, 'simple.bam'))).toBeTruthy()
expect(exists(ctxDir(ctx, 'simple.bai'))).toBeTruthy()
expect(readConf(ctx).tracks).toEqual([
{
type: 'AlignmentsTrack',
Expand Down Expand Up @@ -515,7 +525,7 @@ describe('add-track', () => {
.do(initctx)
.command(['add-track', simpleGff, '--load', 'copy'])
.it('adds a plaintext gff', async ctx => {
expect(fs.existsSync(ctxDir(ctx, 'volvox.sort.gff3'))).toBeTruthy()
expect(exists(ctxDir(ctx, 'volvox.sort.gff3'))).toBeTruthy()
expect(readConf(ctx).tracks).toEqual([
{
type: 'FeatureTrack',
Expand All @@ -537,7 +547,7 @@ describe('add-track', () => {
.do(initctx)
.command(['add-track', simpleVcf, '--load', 'copy'])
.it('adds a plaintext vcf', async ctx => {
expect(fs.existsSync(ctxDir(ctx, 'volvox.filtered.vcf'))).toBeTruthy()
expect(exists(ctxDir(ctx, 'volvox.filtered.vcf'))).toBeTruthy()
expect(readConf(ctx).tracks).toEqual([
{
type: 'VariantTrack',
Expand All @@ -559,7 +569,7 @@ describe('add-track', () => {
.do(initctx)
.command(['add-track', simpleGtf, '--load', 'copy'])
.it('adds a plaintext gtf', async ctx => {
expect(fs.existsSync(ctxDir(ctx, 'volvox.sorted.gtf'))).toBeTruthy()
expect(exists(ctxDir(ctx, 'volvox.sorted.gtf'))).toBeTruthy()
expect(readConf(ctx).tracks).toEqual([
{
type: 'FeatureTrack',
Expand Down Expand Up @@ -588,8 +598,8 @@ describe('add-track', () => {
simpleGffGz + '.csi',
])
.it('adds a tabix gff with csi', async ctx => {
expect(fs.existsSync(ctxDir(ctx, 'volvox.sort.gff3.gz'))).toBeTruthy()
expect(fs.existsSync(ctxDir(ctx, 'volvox.sort.gff3.gz.csi'))).toBeTruthy()
expect(exists(ctxDir(ctx, 'volvox.sort.gff3.gz'))).toBeTruthy()
expect(exists(ctxDir(ctx, 'volvox.sort.gff3.gz.csi'))).toBeTruthy()
expect(readConf(ctx).tracks).toEqual([
{
type: 'FeatureTrack',
Expand All @@ -614,6 +624,36 @@ describe('add-track', () => {
])
})

setup
.do(initctx)
.command([
'add-track',
simplePafGz,
'--assemblyNames',
'volvox_random_inv,volvox',
'--load',
'copy',
])
.it('adds a paf gz file', async ctx => {
expect(exists(ctxDir(ctx, 'volvox_inv_indels.paf.gz'))).toBeTruthy()
expect(readConf(ctx).tracks).toEqual([
{
type: 'SyntenyTrack',
trackId: 'volvox_inv_indels.paf',
name: 'volvox_inv_indels.paf',
adapter: {
type: 'PAFAdapter',
pafLocation: {
uri: 'volvox_inv_indels.paf.gz',
locationType: 'UriLocation',
},
assemblyNames: ['volvox_random_inv', 'volvox'],
},
assemblyNames: ['volvox_random_inv', 'volvox'],
},
])
})

setup
.do(initctx)
.command([
Expand All @@ -625,7 +665,7 @@ describe('add-track', () => {
'copy',
])
.it('adds a paf file', async ctx => {
expect(fs.existsSync(ctxDir(ctx, 'volvox_inv_indels.paf'))).toBeTruthy()
expect(exists(ctxDir(ctx, 'volvox_inv_indels.paf'))).toBeTruthy()
expect(readConf(ctx).tracks).toEqual([
{
type: 'SyntenyTrack',
Expand All @@ -644,12 +684,193 @@ describe('add-track', () => {
])
})

setup
.do(initctx)
.command([
'add-track',
simpleDelta,
'--assemblyNames',
'volvox_random_inv,volvox',
'--load',
'copy',
])
.it('adds a delta file', async ctx => {
expect(exists(ctxDir(ctx, 'volvox_inv_indels.delta'))).toBeTruthy()
expect(readConf(ctx).tracks).toEqual([
{
type: 'SyntenyTrack',
trackId: 'volvox_inv_indels',
name: 'volvox_inv_indels',
adapter: {
type: 'DeltaAdapter',
assemblyNames: ['volvox_random_inv', 'volvox'],
deltaLocation: {
uri: 'volvox_inv_indels.delta',
locationType: 'UriLocation',
},
},
assemblyNames: ['volvox_random_inv', 'volvox'],
},
])
})

setup
.do(initctx)
.command([
'add-track',
simpleOut,
'--assemblyNames',
'volvox_random_inv,volvox',
'--load',
'copy',
])
.it('adds a mashmap file', async ctx => {
expect(exists(ctxDir(ctx, 'volvox_inv_indels.out'))).toBeTruthy()
expect(readConf(ctx).tracks).toEqual([
{
type: 'SyntenyTrack',
trackId: 'volvox_inv_indels',
name: 'volvox_inv_indels',
adapter: {
type: 'MashMapAdapter',
assemblyNames: ['volvox_random_inv', 'volvox'],
outLocation: {
uri: 'volvox_inv_indels.out',
locationType: 'UriLocation',
},
},
assemblyNames: ['volvox_random_inv', 'volvox'],
},
])
})

setup
.do(initctx)
.command([
'add-track',
simpleMcScanSimple,
'--assemblyNames',
'volvox_random_inv,volvox',
'--bed1',
simpleMcScanGrape,
'--bed2',
simpleMcScanPeach,
'--load',
'copy',
])
.it('adds a mcscan simpleanchors file', async ctx => {
expect(
exists(ctxDir(ctx, 'volvox_inv_indels.anchors.simple')),
).toBeTruthy()
expect(exists(ctxDir(ctx, 'grape.bed'))).toBeTruthy()
expect(exists(ctxDir(ctx, 'peach.bed'))).toBeTruthy()
expect(readConf(ctx).tracks).toEqual([
{
type: 'SyntenyTrack',
trackId: 'volvox_inv_indels.anchors',
name: 'volvox_inv_indels.anchors',
adapter: {
type: 'MCScanSimpleAnchorsAdapter',
assemblyNames: ['volvox_random_inv', 'volvox'],
mcscanSimpleAnchorsLocation: {
uri: 'volvox_inv_indels.anchors.simple',
locationType: 'UriLocation',
},
bed1Location: {
uri: 'grape.bed',
locationType: 'UriLocation',
},
bed2Location: {
uri: 'peach.bed',
locationType: 'UriLocation',
},
},
assemblyNames: ['volvox_random_inv', 'volvox'],
},
])
})

setup
.do(initctx)
.command([
'add-track',
simpleMcScan,
'--assemblyNames',
'volvox_random_inv,volvox',
'--bed1',
simpleMcScanGrape,
'--bed2',
simpleMcScanPeach,
'--load',
'copy',
])
.it('adds a mcscan anchors file', async ctx => {
expect(exists(ctxDir(ctx, 'volvox_inv_indels.anchors'))).toBeTruthy()
expect(exists(ctxDir(ctx, 'grape.bed'))).toBeTruthy()
expect(exists(ctxDir(ctx, 'peach.bed'))).toBeTruthy()

expect(readConf(ctx).tracks).toEqual([
{
type: 'SyntenyTrack',
trackId: 'volvox_inv_indels',
name: 'volvox_inv_indels',
adapter: {
type: 'MCScanAnchorsAdapter',
assemblyNames: ['volvox_random_inv', 'volvox'],
mcscanAnchorsLocation: {
uri: 'volvox_inv_indels.anchors',
locationType: 'UriLocation',
},
bed1Location: {
uri: 'grape.bed',
locationType: 'UriLocation',
},
bed2Location: {
uri: 'peach.bed',
locationType: 'UriLocation',
},
},
assemblyNames: ['volvox_random_inv', 'volvox'],
},
])
})

setup
.do(initctx)
.command([
'add-track',
simpleChain,
'--assemblyNames',
'volvox_random_inv,volvox',
'--load',
'copy',
])
.it('adds a liftover chain file', async ctx => {
expect(exists(ctxDir(ctx, 'volvox_inv_indels.chain'))).toBeTruthy()
expect(readConf(ctx).tracks).toEqual([
{
type: 'SyntenyTrack',
trackId: 'volvox_inv_indels',
name: 'volvox_inv_indels',
adapter: {
type: 'ChainAdapter',
assemblyNames: ['volvox_random_inv', 'volvox'],
chainLocation: {
uri: 'volvox_inv_indels.chain',
locationType: 'UriLocation',
},
},
assemblyNames: ['volvox_random_inv', 'volvox'],
},
])
})

setup
.do(initctx)
.command(['add-track', simpleGffGz, '--load', 'copy'])
.it('adds a tabix gff', async ctx => {
expect(fs.existsSync(ctxDir(ctx, 'volvox.sort.gff3.gz'))).toBeTruthy()
expect(fs.existsSync(ctxDir(ctx, 'volvox.sort.gff3.gz.tbi'))).toBeTruthy()
expect(exists(ctxDir(ctx, 'volvox.sort.gff3.gz'))).toBeTruthy()
expect(exists(ctxDir(ctx, 'volvox.sort.gff3.gz.tbi'))).toBeTruthy()
expect(readConf(ctx).tracks).toEqual([
{
type: 'FeatureTrack',
Expand Down
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