Create the jbrowse pif command

GMOD · Dec 11, 2023 · 87209ca · 87209ca
1 parent 1f3ca2d
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diff --git a/products/jbrowse-cli/README.md b/products/jbrowse-cli/README.md
@@ -53,8 +53,8 @@ It is likely preferable in most cases to install the tools globally with
 - [`jbrowse add-track-json TRACK`](#jbrowse-add-track-json-track)
 - [`jbrowse admin-server`](#jbrowse-admin-server)
 - [`jbrowse create LOCALPATH`](#jbrowse-create-localpath)
-- [`jbrowse create-pif FILE`](#jbrowse-create-pif-file)
 - [`jbrowse help [COMMANDS]`](#jbrowse-help-commands)
+- [`jbrowse make-pif FILE`](#jbrowse-make-pif-file)
 - [`jbrowse remove-track TRACK`](#jbrowse-remove-track-track)
 - [`jbrowse set-default-session`](#jbrowse-set-default-session)
 - [`jbrowse sort-gff FILE`](#jbrowse-sort-gff-file)
@@ -458,56 +458,56 @@ EXAMPLES
 _See code:
 [src/commands/create.ts](https://github.com/GMOD/jbrowse-components/blob/v2.9.0/products/jbrowse-cli/src/commands/create.ts)_
 
-## `jbrowse create-pif FILE`
+## `jbrowse help [COMMANDS]`
 
-creates pairwise indexed PAF (PIF), with bgzip and tabix
+Display help for jbrowse.
 
 ```
 USAGE
-  $ jbrowse create-pif FILE [--out <value>] [--csi <value>] [-h]
+  $ jbrowse help [COMMANDS] [-n]
 
 ARGUMENTS
-  FILE  PAF file as input
+  COMMANDS  Command to show help for.
 
 FLAGS
-  -h, --help         Show CLI help.
-      --csi=<value>  Create a CSI index for the PIF file instead of TBI
-      --out=<value>  Where to write the output file. If unspecified, will be ${file}.pif.gz
+  -n, --nested-commands  Include all nested commands in the output.
 
 DESCRIPTION
-  creates pairwise indexed PAF (PIF), with bgzip and tabix
-
-EXAMPLES
-  $ jbrowse create-pif input.paf # creates input.pif.gz in same directory
-
-
-
-  $ jbrowse create-pif input.paf --out output.pif.gz # specify output file, creates output.pif.gz.tbi also
+  Display help for jbrowse.
 ```
 
 _See code:
-[src/commands/create-pif.ts](https://github.com/GMOD/jbrowse-components/blob/v2.9.0/products/jbrowse-cli/src/commands/create-pif.ts)_
+[@oclif/plugin-help](https://github.com/oclif/plugin-help/blob/v5.2.20/src/commands/help.ts)_
 
-## `jbrowse help [COMMANDS]`
+## `jbrowse make-pif FILE`
 
-Display help for jbrowse.
+creates pairwise indexed PAF (PIF), with bgzip and tabix
 
 ```
 USAGE
-  $ jbrowse help [COMMANDS] [-n]
+  $ jbrowse make-pif FILE [--out <value>] [--csi] [-h]
 
 ARGUMENTS
-  COMMANDS  Command to show help for.
+  FILE  PAF file as input
 
 FLAGS
-  -n, --nested-commands  Include all nested commands in the output.
+  -h, --help         Show CLI help.
+      --csi          Create a CSI index for the PIF file instead of TBI
+      --out=<value>  Where to write the output file. will write ${file}.pif.gz and ${file}.pif.gz.tbi
 
 DESCRIPTION
-  Display help for jbrowse.
+  creates pairwise indexed PAF (PIF), with bgzip and tabix
+
+EXAMPLES
+  $ jbrowse pif input.paf # creates input.pif.gz in same directory
+
+
+
+  $ jbrowse pif input.paf --out output.pif.gz # specify output file, creates output.pif.gz.tbi also
 ```
 
 _See code:
-[@oclif/plugin-help](https://github.com/oclif/plugin-help/blob/v5.2.20/src/commands/help.ts)_
+[src/commands/make-pif.ts](https://github.com/GMOD/jbrowse-components/blob/v2.9.0/products/jbrowse-cli/src/commands/make-pif.ts)_
 
 ## `jbrowse remove-track TRACK`
 

diff --git a/products/jbrowse-cli/out.paf b/products/jbrowse-cli/out.paf
@@ -0,0 +1,7 @@
+ctgA	45141	1	45141	+	ctgA	50001	1	50001	45135	50000	60	tp:A:P	cm:i:8494	s1:i:44546	s2:i:0	dv:f:0	rl:i:0
+ctgB	6079	2	6079	+	ctgB	6079	2	6079	6077	6077	2	tp:A:P	cm:i:1213	s1:i:6077	s2:i:6027	dv:f:0	rl:i:0
+ctgB	6079	52	6079	+	ctgB	6079	2	6029	6027	6027	0	tp:A:S	cm:i:1203	s1:i:6027	dv:f:0.0001	rl:i:0
+ctgB	6079	2	6029	+	ctgB	6079	52	6079	6027	6027	0	tp:A:S	cm:i:1203	s1:i:6027	dv:f:0	rl:i:0
+ctgB	6079	102	6079	+	ctgB	6079	2	5979	5977	5977	0	tp:A:S	cm:i:1193	s1:i:5977	dv:f:0.0001	rl:i:0
+ctgB	6079	2	5979	+	ctgB	6079	102	6079	5977	5977	0	tp:A:S	cm:i:1193	s1:i:5977	dv:f:0	rl:i:0
+ctgB	6079	2	5929	+	ctgB	6079	152	6079	5927	5927	0	tp:A:S	cm:i:1183	s1:i:5927	dv:f:0	rl:i:0
diff --git a/products/jbrowse-cli/out.pif.gz b/products/jbrowse-cli/out.pif.gz
diff --git a/products/jbrowse-cli/out.pif.gz.tbi b/products/jbrowse-cli/out.pif.gz.tbi
diff --git a/...rowse-cli/src/commands/create-pif.test.ts → ...jbrowse-cli/src/commands/make-pif.test.ts b/...rowse-cli/src/commands/create-pif.test.ts → ...jbrowse-cli/src/commands/make-pif.test.ts
@@ -12,12 +12,16 @@ const simplePaf = path.join(base, 'volvox_inv_indels.paf')
 
 const exists = (p: string) => fs.existsSync(p)
 
-describe('create-pif', () => {
+describe('make-pif', () => {
   const fn = path.basename(simplePaf, '.paf') + '.pif.gz'
   setup
-    .command(['create-pif', simplePaf, '--out', fn])
+    .command(['make-pif', simplePaf, '--out', fn])
     .it('processes volvox paf', () => {
       expect(exists(fn)).toBeTruthy()
       expect(gunzipSync(fs.readFileSync(fn)).toString()).toMatchSnapshot()
     })
+  setup.command(['make-pif', simplePaf, '--out', fn, '--csi']).it('csi', () => {
+    expect(exists(fn)).toBeTruthy()
+    expect(exists(fn + '.csi')).toBeTruthy()
+  })
 })
diff --git a/...ts/jbrowse-cli/src/commands/create-pif.ts → ...ucts/jbrowse-cli/src/commands/make-pif.ts b/...ts/jbrowse-cli/src/commands/create-pif.ts → ...ucts/jbrowse-cli/src/commands/make-pif.ts
@@ -49,7 +49,7 @@ export function swapIndelCigar(cigar: string) {
 
 export async function createPIF(
   filename: string | undefined,
-  stream: { write: any },
+  stream: { write: (arg: string) => void },
 ) {
   const rl1 = filename ? getReadline(filename) : getStdReadline()
   for await (const line of rl1) {
@@ -76,22 +76,22 @@ export async function createPIF(
   rl1.close()
 }
 
-export default class CreatePIF extends JBrowseCommand {
+export default class MakePIF extends JBrowseCommand {
   static description =
     'creates pairwise indexed PAF (PIF), with bgzip and tabix'
 
   static examples = [
-    '$ jbrowse create-pif input.paf # creates input.pif.gz in same directory',
+    '$ jbrowse pif input.paf # creates input.pif.gz in same directory',
     '',
-    '$ jbrowse create-pif input.paf --out output.pif.gz # specify output file, creates output.pif.gz.tbi also',
+    '$ jbrowse pif input.paf --out output.pif.gz # specify output file, creates output.pif.gz.tbi also',
   ]
 
   static flags = {
     out: Flags.string({
       description:
-        'Where to write the output file. If unspecified, will be ${file}.pif.gz',
+        'Where to write the output file. will write ${file}.pif.gz and ${file}.pif.gz.tbi',
     }),
-    csi: Flags.string({
+    csi: Flags.boolean({
       description: 'Create a CSI index for the PIF file instead of TBI',
     }),
     help: Flags.help({ char: 'h' }),
@@ -107,8 +107,7 @@ export default class CreatePIF extends JBrowseCommand {
     const {
       args: { file },
       flags: { out, csi },
-    } = await this.parse(CreatePIF)
-    console.error('wtf')
+    } = await this.parse(MakePIF)
 
     if (
       commandExistsSync('sh') &&
@@ -117,13 +116,14 @@ export default class CreatePIF extends JBrowseCommand {
       commandExistsSync('tabix') &&
       commandExistsSync('bgzip')
     ) {
-      console.error('wtf')
-      const fn = out || `${path.basename(file, '.paf')}.pif.gz`
+      const fn = out || `${path.basename(file || 'output', '.paf')}.pif.gz`
       const child = spawn(
         'sh',
         [
           '-c',
-          `sort -t"\`printf '\t'\`" -k1,1 -k3,3n | bgzip > ${fn}; tabix -s1 -b3 -e4 ${fn}`,
+          `sort -t"\`printf '\t'\`" -k1,1 -k3,3n | bgzip > ${fn}; tabix ${
+            csi ? '-C ' : ''
+          }-s1 -b3 -e4 ${fn}`,
         ],
         {
           env: { ...process.env, LC_ALL: 'C' },