bionode-fasta - npm Package Compare versions

Comparing version 0.5.5 to 0.5.6

cli.js

 #!/usr/bin/env node
 var fs = require('fs')
-var path = require('path')
 var minimist = require('minimist')
@@ -16,3 +15,3 @@ var fasta = require('./')
 if (argv.help) {
-  return console.log(
+  console.log(
     'Usage: bionode-fasta <options> <fasta file [required]> <output file>\n\n' +
@@ -36,6 +35,6 @@ 'You can also use fasta files compressed with gzip\n' +
 
-process.stdin.setEncoding('utf8');
+process.stdin.setEncoding('utf8')
 
 if (!process.stdin.isTTY) {
-  process.stdin.on('data', function(data) {
+  process.stdin.on('data', function (data) {
     if (data.trim() === '') { return }
@@ -42,0 +41,0 @@ parser.write(data)

index.js

@@ -1,1 +0,1 @@
-module.exports = require('./lib/bionode-fasta')
+module.exports = require('./lib/bionode-fasta')

lib/bionode-fasta.js

@@ -81,3 +81,3 @@ // # bionode-fasta
 
-module.exports.obj = function(arg1, arg2, arg3) {
+module.exports.obj = function (arg1, arg2, arg3) {
   var params = paramsParser(arg1, arg2, arg3)
@@ -89,13 +89,12 @@ params.options.objectMode = true
 
-module.exports.write = function() {
+module.exports.write = function () {
   var stream = through.obj(transform)
   return pumpify.obj(split(), stream)
 
-  function transform(obj, enc, next) {
+  function transform (obj, enc, next) {
     try {
       obj = JSON.parse(obj)
-      var fastaString = '>'+obj.id+'\n' + obj.seq.match(/.{1,80}/g).join('\n')+'\n'
+      var fastaString = '>' + obj.id + '\n' + obj.seq.match(/.{1,80}/g).join('\n') + '\n'
       this.push(fastaString)
-    }
-    catch(e) {}
+    } catch (e) {}
     next()
@@ -105,12 +104,9 @@ }
 
-function fasta(arg1, arg2, arg3) {
-  var self = this
+function fasta (arg1, arg2, arg3) {
   var params = paramsParser(arg1, arg2, arg3)
 
-  var jsparse
   var contentParser
   if (params.options.objectMode) {
     contentParser = pumpify.obj(fastaParser(), jsParse())
-  }
-  else {
+  } else {
     contentParser = fastaParser()
@@ -120,5 +116,5 @@ }
   var filesParser = through.obj(transform)
-  function transform(obj, enc, next){
+  function transform (obj, enc, next) {
     var self = this
-    var unzip = 'gz' === obj.split('.').pop() ? zlib.Gunzip() : through()
+    var unzip = obj.split('.').pop() === 'gz' ? zlib.Gunzip() : through()
     var includepath = params.options.includePath ? includePath(obj) : through()
@@ -128,6 +124,5 @@
     if (params.options.objectMode) {
-      jsparse =  jsParse()
+      jsparse = jsParse()
       pumpit = pumpify.obj
-    }
-    else {
+    } else {
       jsparse = through()
@@ -146,5 +141,5 @@ pumpit = pumpify
     pipeline
-    .on('error', function(error) { self.emit('error', error) })
-    .on('data', function(data) { self.push(data) })
-    .on('end', function() { self.push(null) })
+    .on('error', function (error) { self.emit('error', error) })
+    .on('data', function (data) { self.push(data) })
+    .on('end', function () { self.push(null) })
 
@@ -154,7 +149,7 @@ next()
 
-  stream = params.filename || params.options.filenameMode ? filesParser : contentParser
+  var stream = params.filename || params.options.filenameMode ? filesParser : contentParser
   if (params.filename) { stream.write(params.filename) }
   if (params.callback) {
     stream.on('error', params.callback)
-    stream.pipe(concat(function(data) { params.callback(null, data) }))
+    stream.pipe(concat(function (data) { params.callback(null, data) }))
   }
@@ -165,10 +160,9 @@
 
-
-function includePath(path) {
+function includePath (path) {
   var stream = through(transform)
   return stream
-  function transform(buf, enc, next) {
-    var openEnd = buf.slice(0, buf.length-2)
-    var pathBuf = new Buffer(',"path":"' + path + '"}\n')
-    var totalLen = buf.length-2 + pathBuf.length
+  function transform (buf, enc, next) {
+    var openEnd = buf.slice(0, buf.length - 2)
+    var pathBuf = Buffer.from(',"path":"' + path + '"}\n')
+    var totalLen = buf.length - 2 + pathBuf.length
     var newBuf = Buffer.concat([openEnd, pathBuf], totalLen)
@@ -180,8 +174,7 @@ this.push(newBuf)
 
-
-function jsParse() {
+function jsParse () {
   var stream = through.obj(transform, flush)
   return stream
-  function transform(obj, enc, next) {
-    if (typeof obj === 'Buffer') { obj = obj.toString() }
+  function transform (obj, enc, next) {
+    if (Buffer.isBuffer(obj)) { obj = obj.toString() }
     JSON.parse(obj)
@@ -191,6 +184,6 @@ this.push(JSON.parse(obj))
   }
-  function flush() { this.push(null) }
+  function flush () { this.push(null) }
 }
 
-function paramsParser(arg1, arg2, arg3) {
+function paramsParser (arg1, arg2, arg3) {
   var params = {}
@@ -205,4 +198,3 @@ if (typeof arg1 === 'object') {
     }
-  }
-  else if (typeof arg1 === 'string') {
+  } else if (typeof arg1 === 'string') {
     params.options = {}
@@ -213,4 +205,3 @@ params.filename = arg1
     }
-  }
-  else {
+  } else {
     params.options = {}
@@ -217,0 +208,0 @@ }

package.json

 {
   "name": "bionode-fasta",
   "description": "Streamable FASTA parser",
-  "version": "0.5.5",
+  "version": "0.5.6",
   "homepage": "http://bionode.io",
@@ -16,23 +16,24 @@ "repository": {
   "dependencies": {
-    "concat-stream": "~1.4.6",
+    "concat-stream": "~1.6.0",
     "fasta-parser": "0.1.0",
-    "minimist": "~1.1.0",
-    "pumpify": "~1.3.0",
-    "split2": "^2.0.1",
-    "through2": "~0.6.0"
+    "minimist": "~1.2.0",
+    "pumpify": "~1.3.5",
+    "split2": "^2.1.1",
+    "through2": "~2.0.3"
   },
   "devDependencies": {
-    "async": "~0.9.0",
-    "beefy": "^2.1.0",
+    "async": "~2.3.0",
+    "beefy": "^2.1.8",
     "browserify": "git+https://github.com/bmpvieira/node-browserify#3.46.1/http-browserify-1.6.0-pull-53-61-62",
     "browserify-fs": "~1.0.0",
-    "contributor": "~0.1.22",
-    "coveralls": "~2.11.1",
-    "docco": "~0.6.3",
-    "istanbul": "~0.3.0",
-    "request": "~2.40.0",
-    "tap-spec": "~0.2.0",
-    "tape": "~2.14.0",
+    "contributor": "~0.1.25",
+    "coveralls": "~2.13.0",
+    "docco": "~0.7.0",
+    "istanbul": "~0.4.5",
+    "request": "~2.81.0",
+    "standard": "^10.0.2",
+    "tap-spec": "~4.1.1",
+    "tape": "~4.6.3",
     "testling": "^1.7.1",
-    "uglify-js": "~2.4.15"
+    "uglify-js": "~2.8.22"
   },
@@ -58,3 +59,3 @@ "keywords": [
   "scripts": {
-    "test": "node test/bionode-fasta.js | tap-spec",
+    "test": "standard && node test/bionode-fasta.js | tap-spec",
     "test-browser": "browserify test/bionode-fasta.js | testling -x 'open -a \"Google Chrome\"' | tap-spec",
@@ -61,0 +62,0 @@ "coverage": "istanbul cover test/bionode-fasta.js --report lcovonly -- | tap-spec && rm -rf ./coverage",

test/bionode-fasta.js

@@ -7,7 +7,3 @@ var fs = require('fs')
 var data = require('./data')
-var zlib = require('zlib')
-var through = require('through2')
-var buffer = require('buffer')
 
-
 // Node.js fs is implemented in the browser by browserify-fs using leveldb.
@@ -20,7 +16,7 @@ // So we need to fetch the file and save it locally (server) or in leveldb (client) with fs.
 
-function download(file, callback) {
+function download (file, callback) {
   var proxy = 'http://cors.inb.io/'
   var rooturl = 'https://raw.githubusercontent.com/bionode/bionode-fasta/master/test/'
   fs.mkdir('test', gotDir)
-  function gotDir() {
+  function gotDir () {
     var get = request(proxy + rooturl + file, {encoding: null})
@@ -33,7 +29,6 @@ var write = fs.createWriteStream('test/' + file)
 
-function startTests() {
+function startTests () {
   test('Read a fasta file and pipe content to parser.', function (t) {
     t.plan(3)
     var msg
-    var pushFunc
 
@@ -49,4 +44,3 @@ msg = 'should return a Buffer for each sequence'
 
-
-    function testPipeParser(msg, parser, jsparse) {
+    function testPipeParser (msg, parser, jsparse) {
       var result = []
@@ -57,5 +51,5 @@
       .on('data', pushResult)
-      .on('end', function() { t.deepEqual(result, data.fasta, msg) })
+      .on('end', function () { t.deepEqual(result, data.fasta, msg) })
 
-      function pushResult(data) {
+      function pushResult (data) {
         if (jsparse) { data = JSON.parse(data.toString()) }
@@ -72,20 +66,20 @@ result.push(data)
 
-
-  function testFilename(file, includePath) {
+  function testFilename (file, includePath) {
     var solution = JSON.parse(JSON.stringify(data.fasta))
     var extramsg = ''
+
     if (includePath) {
       extramsg = ' (add path to results)'
       solution.forEach(addPath)
-      function addPath(obj, i) {
-        obj.path = file
-        solution[i] = obj
-      }
     }
 
-    if ('gz' === file.split('.').pop()) {
+    function addPath (obj, i) {
+      obj.path = file
+      solution[i] = obj
+    }
+
+    if (file.split('.').pop() === 'gz') {
       extramsg += ' (read gzipped file)'
     }
 
-
     test('Use parser to read file by passing filename' + extramsg, function (t) {
@@ -95,3 +89,2 @@ t.plan(3)
       var parser
-      var pushFunc
 
@@ -112,8 +105,8 @@ msg = 'should return a Buffer for each sequence'
 
-      function testFilenamePipe(msg, parser, jsparse) {
+      function testFilenamePipe (msg, parser, jsparse) {
         var result = []
         parser
         .on('data', pushResult)
-        .on('end', function() { t.deepEqual(result, solution, msg) })
-        function pushResult(data) {
+        .on('end', function () { t.deepEqual(result, solution, msg) })
+        function pushResult (data) {
           if (jsparse) { data = JSON.parse(data.toString()) }
@@ -125,3 +118,2 @@ result.push(data)
 
-
     test('Use parser to read file by passing filename and get results with callback' + extramsg, function (t) {
@@ -132,11 +124,10 @@ t.plan(6)
         fasta({ includePath: true }, file, callback1)
-      }
-      else {
+      } else {
         fasta(file, callback1)
       }
-      function callback1(err, result) {
+      function callback1 (err, result) {
         t.error(err, 'callback error should be null')
         var objects = []
         result.toString().split('\n').forEach(pushObject)
-        function pushObject(obj) {
+        function pushObject (obj) {
           if (obj !== '') {
@@ -150,6 +141,5 @@ objects.push(JSON.parse(obj))
 
-
       var options = { objectMode: true }
       if (includePath) { options.includePath = true }
-      fasta(options, file, function(err, result) {
+      fasta(options, file, function (err, result) {
         t.error(err, 'callback error should be null')
@@ -160,10 +150,8 @@ var msg = 'should return an array of Objects'
 
-
       if (includePath) {
         fasta.obj({ includePath: true }, file, callback2)
-      }
-      else {
+      } else {
         fasta.obj(file, callback2)
       }
-      function callback2(err, result) {
+      function callback2 (err, result) {
         t.error(err, 'callback error should be null')
@@ -176,9 +164,8 @@ var msg = 'should return an array of Objects'
 
-
-  test('Errors should be caught', function(t) {
+  test('Errors should be caught', function (t) {
     t.plan(1)
     var msg = 'should return a ENOENT error for non-existing path'
     fasta('./nosuchfile.fasta')
-    .on('error', function(error) { t.equal(error.code, 'ENOENT', msg) })
+    .on('error', function (error) { t.equal(error.code, 'ENOENT', msg) })
   })
 }

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Worsened metrics

Total package byte prevSize

614323

decreased by-0.03%

Dev dependency count

14

increased by7.69%

Lines of code

1842

decreased by-0.75%

Dependency changes

• + Addedbuffer-from@1.1.2(transitive)

• + Addedconcat-stream@1.6.2(transitive)

• + Addedminimist@1.2.8(transitive)

• + Addedtypedarray@0.0.6(transitive)

• - Removedconcat-stream@1.4.11(transitive)

• - Removedminimist@1.1.3(transitive)

• - Removedreadable-stream@1.1.14(transitive)

• - Removedtypedarray@0.0.7(transitive)

• Updatedconcat-stream@~1.6.0

• Updatedminimist@~1.2.0

• Updatedpumpify@~1.3.5

• Updatedsplit2@^2.1.1

• Updatedthrough2@~2.0.3