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‎.gitignore‎

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node_modules
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.DS_Store
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coverage
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tmp

‎.travis.yml‎

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language: node_js
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node_js:
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- "0.10"
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after_script:
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- npm run coveralls

‎LICENSE‎

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The MIT License (MIT)
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Copyright (c) 2014 Bruno Vieira <mail@bmpvieira.com>
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in
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all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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THE SOFTWARE.

‎README.md‎

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<p align="center">
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<a href="http://bionode.io">
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<img height="200" width="200" title="bionode" alt="bionode logo" src="https://rawgithub.com/bionode/bionode/master/docs/bionode-logo.min.svg"/>
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</a>
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<br/>
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<a href="http://bionode.io/">bionode.io</a>
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</p>
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# bionode-sra [![NPM version][npm-image]][npm-url] [![Build Status][travis-image]][travis-url] [![Coveralls Status][coveralls-image]][coveralls-url] [![Dependency Status](https://david-dm.org/bionode/bionode.png?theme=shields.io)](//david-dm.org/bionode/bionode)
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> A Node.js wrapper for SRA Toolkit.
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Install
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-------
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Install bionode-sra with [npm](//npmjs.org):
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```sh
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$ npm install bionode-sra
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```
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To use it as a command line tool, you can install it globally by adding ```-g``` .
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Usage
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-----
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If you're using bionode-sra with Node.js, you can require the module:
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```js
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var sra = require('bionode-sra')
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var fastqDump = sra('fastq-dump')
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fastqDump('SRR1509835.sra')
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```
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Please read the [documentation](http://rawgit.com/bionode/bionode-sra/master/docs/bionode-sra.html) for the methods exposed by bionode.
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### Command line examples
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```sh
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$ bionode-sra fastq-dump SRR1509835.sra
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$ bionode-sra fastq-dump SRR1509835.sra fastqOutputDirectory
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```
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Contributing
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------------
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To contribute, clone this repo locally and commit your code on a separate branch.
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Please write unit tests for your code, and check that everything works by running the following before opening a pull-request:
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```sh
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$ npm test
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```
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Please also check for code coverage:
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```sh
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$ npm run coverage
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```
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To rebuild the documentation using the comments in the code:
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```sh
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$ npm run build-docs
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```
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Check the [issues](http://github.com/bionode/bionode-sra/issues) for ways to contribute.
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Contacts
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--------
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Bruno Vieira <[mail@bmpvieira.com](mailto:mail@bmpvieira.com)> [@bmpvieira](//twitter.com/bmpvieira)
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Yannick Wurm ([yannick.poulet.org](http://yannick.poulet.org)) [@yannick__](//twitter.com/yannick__)
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License
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-------
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bionode-sra is licensed under the [MIT](https://raw.github.com/bionode/bionode/master/LICENSE) license.
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Check [ChooseALicense.com](http://choosealicense.com/licenses/mit) for details.
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[npm-url]: //npmjs.org/package/bionode-sra
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[npm-image]: https://badge.fury.io/js/bionode-sra.png
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[travis-url]: //travis-ci.org/bionode/bionode-sra
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[travis-image]: https://travis-ci.org/bionode/bionode-sra.png?branch=master
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[coveralls-url]: //coveralls.io/r/bionode/bionode-sra
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[coveralls-image]: https://coveralls.io/repos/bionode/bionode-sra/badge.png
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[depstat-url]: //david-dm.org/bionode/bionode-sra
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[depstat-image]: https://david-dm.org/bionode/bionode-sra.png
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[![Bitdeli Badge](https://d2weczhvl823v0.cloudfront.net/bionode/bionode-sra/trend.png)](https://bitdeli.com/free "Bitdeli Badge")

‎cli.js‎

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#!/usr/bin/env node
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var JSONStream = require('JSONStream')
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var sra = require('./')
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var args = process.argv.slice(2)
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var command = args[0]
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var srcFile = args[1]
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var destDir = args[2]
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var sraStream = sra(command)
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sraStream([srcFile, destDir]).pipe(JSONStream.stringify(false)).pipe(process.stdout)

‎docs/bionode-sra.html‎

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<!DOCTYPE html>
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<html>
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<head>
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<title>bionode-sra</title>
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<meta http-equiv="content-type" content="text/html; charset=UTF-8">
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<meta name="viewport" content="width=device-width, target-densitydpi=160dpi, initial-scale=1.0; maximum-scale=1.0; user-scalable=0;">
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<link rel="stylesheet" media="all" href="docco.css" />
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</head>
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<body>
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<div id="container">
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<div id="background"></div>
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<ul class="sections">
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<li id="section-1">
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<div class="annotation">
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<div class="pilwrap ">
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<a class="pilcrow" href="#section-1">&#182;</a>
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</div>
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<h1 id="bionode-sra">bionode-sra</h1>
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<blockquote>
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<p>A Node.js wrapper for SRA Toolkit.</p>
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<p>doi: <a href="?">?</a>
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author: <a href="http://bmpvieira.com">Bruno Vieira</a>
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email: <a href="&#109;&#x61;&#x69;&#108;&#x74;&#111;&#58;&#x6d;&#x61;&#x69;&#x6c;&#64;&#x62;&#109;&#112;&#x76;&#x69;&#x65;&#105;&#114;&#x61;&#46;&#x63;&#x6f;&#109;">&#x6d;&#x61;&#x69;&#x6c;&#64;&#x62;&#109;&#112;&#x76;&#x69;&#x65;&#105;&#114;&#x61;&#46;&#x63;&#x6f;&#109;</a>
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license: <a href="https://raw.githubusercontent.com/bionode/bionode-sra/master/LICENSE">MIT</a></p>
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</blockquote>
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<hr>
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</div>
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</li>
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<li id="section-2">
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<div class="annotation">
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<div class="pilwrap ">
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<a class="pilcrow" href="#section-2">&#182;</a>
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</div>
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<h2 id="usage">Usage</h2>
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<p>This module can be used in Node.js as described further below, or as a command line tool.
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Examples:</p>
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<pre><code>$ npm install -g bionode-sra
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# bionode-sra [command] [<span class="hljs-built_in">arguments</span>...]
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$ bionode-sra fastq-dump SRR1509835.sra
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$ bionode-sra fastq-dump SRR1509835.sra fastqOutputDirectory
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</code></pre>
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</div>
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<div class="content"><div class='highlight'><pre>
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<span class="hljs-keyword">var</span> path = <span class="hljs-built_in">require</span>(<span class="hljs-string">'path'</span>)
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<span class="hljs-keyword">var</span> spawn = <span class="hljs-built_in">require</span>(<span class="hljs-string">'child_process'</span>).spawn
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<span class="hljs-keyword">var</span> through = <span class="hljs-built_in">require</span>(<span class="hljs-string">'through2'</span>)
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<span class="hljs-built_in">module</span>.exports = exports = SRA</pre></div></div>
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</li>
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<li id="section-3">
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<div class="annotation">
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<div class="pilwrap ">
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<a class="pilcrow" href="#section-3">&#182;</a>
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</div>
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<h2 id="sra">SRA</h2>
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<p>Takes a SRA toolkit command and returns a Stream that accepts arguments for it.
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For example, for <code>fastq-dump</code>, arguments can be an array with <code>[srcSRA, destDir]</code>,
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a string like <code>&#39;srcSRA destDir&#39;</code>. If <code>destDir</code> is omitted, the current directory will be used.</p>
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<pre><code><span class="hljs-keyword">var</span> sra = <span class="hljs-built_in">require</span>(<span class="hljs-string">'bionode-sra'</span>)
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<span class="hljs-keyword">var</span> fastqDump = sra(<span class="hljs-string">'fastq-dump'</span>)()
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fastqDump.on(<span class="hljs-string">'data'</span>, <span class="hljs-built_in">console</span>.log)
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fastqDump.write([<span class="hljs-string">'SRR1509835.sra'</span>, <span class="hljs-string">'fastqOutDir'</span>])
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=&gt; { srcFile: <span class="hljs-string">'SRR1509835.sra'</span>,
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command: <span class="hljs-string">'fastq-dump'</span>,
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destDir: <span class="hljs-string">'fastqOutDir'</span> }
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</code></pre><p>A callback style can also be used:</p>
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<pre><code><span class="hljs-keyword">var</span> fastqDump = sra(<span class="hljs-string">'fastq-dump'</span>)
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fastqDump(<span class="hljs-string">'SRR1509835.sra fastqOutDir'</span>, <span class="hljs-function"><span class="hljs-keyword">function</span><span class="hljs-params">(err, data)</span> </span>{
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<span class="hljs-built_in">console</span>.log(data)
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})
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</code></pre><p>Or pipes, for example, from a file with just a list of SRA file names:</p>
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<pre><code><span class="hljs-keyword">var</span> split = <span class="hljs-built_in">require</span>(<span class="hljs-string">'split'</span>)
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<span class="hljs-keyword">var</span> fastqDump = sra(<span class="hljs-string">'fastq-dump'</span>)()
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fs.createReadStream(<span class="hljs-string">'sraFilesList.txt'</span>)
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.pipe(split())
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.pipe(fastqDump)
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</code></pre>
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</div>
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<div class="content"><div class='highlight'><pre>
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<span class="hljs-function"><span class="hljs-keyword">function</span> <span class="hljs-title">SRA</span><span class="hljs-params">(command)</span> </span>{
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<span class="hljs-keyword">var</span> command = command || <span class="hljs-string">'fastq-dump'</span>
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<span class="hljs-keyword">return</span> sraStream
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<span class="hljs-function"><span class="hljs-keyword">function</span> <span class="hljs-title">sraStream</span><span class="hljs-params">(srcFileDestDir, callback)</span> </span>{
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<span class="hljs-keyword">var</span> stream = through.obj(transform)
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<span class="hljs-keyword">if</span> (srcFileDestDir) { stream.write(srcFileDestDir); stream.end() }
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<span class="hljs-keyword">if</span> (callback) {
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stream.on(<span class="hljs-string">'data'</span>, <span class="hljs-function"><span class="hljs-keyword">function</span><span class="hljs-params">(data)</span> </span>{
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callback(<span class="hljs-literal">null</span>, data)
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})
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stream.on(<span class="hljs-string">'error'</span>, callback)
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}
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<span class="hljs-keyword">return</span> stream
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<span class="hljs-function"><span class="hljs-keyword">function</span> <span class="hljs-title">transform</span><span class="hljs-params">(obj, enc, next)</span> </span>{
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<span class="hljs-keyword">var</span> self = <span class="hljs-keyword">this</span>
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<span class="hljs-keyword">if</span> (<span class="hljs-keyword">typeof</span> obj === <span class="hljs-string">'string'</span>) { obj = obj.split(<span class="hljs-string">' '</span>) }
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<span class="hljs-keyword">if</span> (obj.length &gt; <span class="hljs-number">2</span>) { self.emit(<span class="hljs-string">'error'</span>, <span class="hljs-keyword">new</span> <span class="hljs-built_in">Error</span>(<span class="hljs-string">'Too many arguments for aspera'</span>)); next() }
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<span class="hljs-keyword">if</span> (obj.length === <span class="hljs-number">1</span>) { obj.push(<span class="hljs-string">'.'</span>) }
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<span class="hljs-keyword">var</span> sraPath = path.join(__dirname, <span class="hljs-string">'../sra/bin/'</span>+command)
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<span class="hljs-keyword">var</span> srcFile = obj[<span class="hljs-number">0</span>]
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<span class="hljs-keyword">var</span> destDir = obj[<span class="hljs-number">1</span>]
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<span class="hljs-keyword">var</span> options
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<span class="hljs-keyword">if</span> (destDir === <span class="hljs-string">'.'</span>) {
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options = [srcFile]
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}
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<span class="hljs-keyword">else</span> {
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<span class="hljs-keyword">var</span> options = [srcFile, <span class="hljs-string">'-O'</span>, destDir]
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}
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<span class="hljs-keyword">var</span> sra = spawn(sraPath, options)
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sra.stderr.on(<span class="hljs-string">'data'</span>, <span class="hljs-function"><span class="hljs-keyword">function</span><span class="hljs-params">(data)</span> </span>{
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self.emit(<span class="hljs-string">'error'</span>, <span class="hljs-keyword">new</span> <span class="hljs-built_in">Error</span>(data.toString()))
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next()
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})
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sra.on(<span class="hljs-string">'close'</span>, <span class="hljs-function"><span class="hljs-keyword">function</span><span class="hljs-params">(code)</span> </span>{
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<span class="hljs-keyword">if</span> (code) {
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self.emit(<span class="hljs-string">'error'</span>, <span class="hljs-keyword">new</span> <span class="hljs-built_in">Error</span>(<span class="hljs-string">'Unknown error, check that "'</span>+obj[<span class="hljs-number">0</span>]+<span class="hljs-string">'" exists'</span>))
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}
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<span class="hljs-keyword">else</span> {
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self.push({srcFile: obj[<span class="hljs-number">0</span>], command: command, destDir: obj[<span class="hljs-number">1</span>]})
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next()
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}
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})
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}
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}
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}</pre></div></div>
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</li>
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</ul>
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</div>
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</body>
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</html>

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