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  • 这是可能的,因为fastq-dump具有选项( -N和-X )来查询fastq-dump文件的特定范围,此工具的工作方式是将工作划分为请求的线程数,并行运行多个fastq-dump并连接结果返回一起,就好像您刚刚执行了普通的fastq-dump...
  • fastq-dump error

    2020-12-26 12:42:52
    2019-12-10T19:33:16 fastq-dump.2.8.2 err: item not found while constructing within virtual database module - the path 'SRR8232120' cannot be opened as database or table <p>What is the problem...
  • fastq-dump转换SRA文件到fastq文件很慢,并行版本成为趋势;无论怎么换,先要打好基础,使用并行版本的前提是要保证NCBI的fastq-dump可以在服务器上正常运行。首先安装Sratoolkit的最新版(v.2.9.2):mkdir -p/path-...

    fastq-dump转换SRA文件到fastq文件很慢,并行版本成为趋势;

    无论怎么换,先要打好基础,使用并行版本的前提是要保证NCBI的fastq-dump可以在服务器上正常运行。

    首先安装Sratoolkit的最新版(v.2.9.2):mkdir -p /path-to-Sratoolkit/ && cd /path-to-Sratoolkit/

    wget  https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.9.2/sratoolkit.2.9.2-ubuntu64.tar.gz && \

    tar zxfv sratoolkit.2.9.2-ubuntu64.tar.gz&& \

    mv sratoolkit.2.9.2-ubuntu64/* . && \ rm -rf sratoolkit.2.9.2-ubuntu64.tar.gz sratoolkit.2.9.2-ubuntu64

    下载pfastq-dump:git clone https://github.com/inutano/pfastq-dump && \

    cd pfastq-dump && \

    chmod a+x bin/pfastq-dump && \

    ln -s bin/pfastq-dump  /path-to-Sratoolkit/bin

    把安装的路径加入到账号下的$PATH中:echo 'PATH=/home/luna/Desktop/Software/Sratoolkit/bin:$PATH' >> ~/.bashrc && \

    cp ~/.bashrc ~/.bash_profile && \

    source ~/.bashrc ~/.bash_profile

    使用pfastq_dump,因为pfastq_dump是基于fastq_dump写的一个bash程序,所以参数是相同的:对于单端数据转换,转换后文件是fq.gz:

    for id in *sra;    do pfastq-dump --threads 10 ./$id --gzip;    done

    对于双端数据转换,转换后文件是fq.gz:

    for id in *sra;        do pfastq-dump  --threads 8 ./$id --split-3 --gzip;    done

    直接用sra号下载并解压fastq文件,但是推荐下载好文件再使用fastq_dump转换,且文件后缀是.sra(请注意):单端数据:

    for id in SRR799545  SRR799544;    do pfastq-dump --threads 10 -s $id --gzip;    done

    双端数据:

    for id in SRR799545  SRR799544;    do pfastq-dump --threads 10 -s $id --split-3 --gzip;    done

    经过测试,其实也不是那么的快啊!!很揪心!

    展开全文
  • <p>The .sra file is local in my computer, fastq-dump is also local, so why is it trying to connect to NCBI server? and why is the connection failing?</p><p>该提问来源于开源项目:ncbi/sra-tools...
  • sra是NCBI 推出的存储高通量数据的格式,下载后我们需要把sra 转成fastq,然后进行生信...选择适合自己的下载版本,下载后解压(解压命令:tar zxvf *.tar.gz)即可使用,转换软件(fastq-dump)位于bin文件夹下 ..

    sra是NCBI 推出的存储高通量数据的格式,下载后我们需要把sra 转成fastq,然后进行生信分析。下面分别讲一下下载和使用:

    下载

    下载地址:http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software&m=software&s=software
    选择适合自己的下载版本,下载后解压(解压命令:tar zxvf *.tar.gz)即可使用,转换软件(fastq-dump)位于bin文件夹下

    使用

    #single-end 单端测序

    .../bin/fastq-dump  SRR12816529.sra                 # 结果生成SRR12816529.fastq

    .../bin/fastq-dump  --gzip  SRR12816529.sra      # 结果生成SRR12816529.fastq.gz

    #pair-end  双端测序

    .../bin/fastq-dump  --split-files  SRR12816529.sra                #  结果生成   SRR12816529_1.fastq,SRR12816529_2.fastq

    .../bin/fastq-dump  --split-files  --gzip  SRR12816529.sra     #  结果生成   SRR12816529_1.fastq.gz,SRR12816529_2.fastq.gz

    展开全文
  • 之前写过一篇文章Fastq-dump: 一个神奇的软件, 详细介绍了fastq-dump的用法。 虽然fastq-dump参数很多,而且一直被吐槽参数说明写的太差,但是如果真的要用起来其实也就是一行代码 fastq-dump --gzip --split-3 --...

    之前写过一篇文章Fastq-dump: 一个神奇的软件, 详细介绍了fastq-dump的用法。
    虽然fastq-dump参数很多,而且一直被吐槽参数说明写的太差,但是如果真的要用起来其实也就是一行代码

    fastq-dump --gzip --split-3 --defline-qual '+' --defline-seq '@$ac-$si/$ri' SRRXXXXX| SRRXXXX.sra
    # 加上--gzip后需要时间进行文件压缩
    

    当然除了参数问题,还有一个让人诟病的地方就是他只能单个线程,所以速度特别的慢。尽管相对于下游分析要分析好几天而言,这点时间还能能等的。但是能快一点总是好的,所以在2018年的6月份,sra-tools更新了一个新的sra解压工具,fasterq-dump, a faster fastq-dump,它能利用临时文件和多线程加速从SRA文件提取FASTQ。

    fasterq-dump的用法和fastq-dump一样,如下所示

    fasterq-dump --split-3 SRR5318040.sra 
    

    此外还有建立了GitHub Wiki提供使用教程,参见https://github.com/ncbi/sra-tools/wiki/HowTo:-fasterq-dump

    重点参数是-e|threads, 用于选择使用多少线程进行运行,默认是6个线程。 同时考虑到有些人容易着急,还提供了-p选项用于显示当前进度。

    我用一个9G大小的SRA文件,分别以fastq-dumpfasterq-dump进行了测试。

    time fastq-dump --split-3 -O test SRR5318040.sra
    # 558.76s user 41.36s system 101% cpu 9:51.82 total
    time fasterq-dump --split-3 SRR5318040.sra -e 20 -o SRR5318040
    # 582.70s user 121.06s system 1130% cpu 1:02.25 total
    

    从用户模式(user mode)来看, 两者的总CPU使用时间都差不多是560秒,从内核模式来看(Kernel Mode)来看,fasterq-dump花了更多时间在调用底层硬件上,例如分配内存地址。fastq-dump基本上稳定在一个线程,而fasterq-dump尽管指定了20个线程,但平均只用了11.5个线程吧。

    对于我们而言,我们只要看最后的total部分,也就是实际花了多少时间。fastq-dump花了快10分钟,而fasterq-dump只需要1分钟,快了9倍多。

    最后还有一点不足之处:输出的fastq的ID目前暂时没有选项可以调整,需要自己写个脚本解决。

    img_5bd8249a58f3fa7fd04726b1787af2ae.png
    ID
    展开全文
  • fastq-dump 联网 IECSE速成课程:Swift开发 (IECSE Crash Course: Development with Swift) This article is going to be the fifth article of the series IECSE Crash Course: Development with Swift. Through ...

    fastq-dump 联网

    IECSE速成课程:Swift开发 (IECSE Crash Course: Development with Swift)

    This article is going to be the fifth article of the series IECSE Crash Course: Development with Swift. Through the course of 10 articles, we are going to make a small app which will display a set of users that we will fetch from the net. While making the app, we will cover some of the most important topics that every iOS developer must know.

    本文将成为IECSE速成课程系列:使用Swift开发的第五篇文章。 在完成10篇文章的过程中,我们将制作一个小型应用程序,该程序将显示一组将从网上获取的用户。 制作应用程序时,我们将介绍每个iOS开发人员必须知道的一些最重要的主题。

    In the last tutorial, we saw how to make structures for the data that we are going to receive from the API and we have this structure ready in our project. If you haven’t been following the whole course, I suggest you go through the code here and clone it.

    在上教程中,我们了解了如何为将要从API接收的数据建立结构,并且在项目中已准备好该结构。 如果您还没有完成整个课程,那么建议您在此处遍历代码并进行克隆。

    Image for post
    Struct User
    结构用户

    We’ve made this structure according to what “https://jsonplaceholder.typicode.com/users" sends to us. Now we are going to try and get the User data from here and display it on our app.

    我们已经根据“ https://jsonplaceholder.typicode.com/users ”发送给我们的内容建立了这种结构。现在,我们将尝试从此处获取User数据并将其显示在我们的应用程序中。

    Image for post
    The json object we receive from our API
    我们从API收到的json对象

    联网和REST API (Networking and REST APIs)

    Whatever data we see in the apps we use comes from the internet. This is where networking and APIs come in. This exchange of data between the device and a server is called networking. REST is basically a type of architecture that allows us to create services and applications that can be used by any device or client that understands HTTP. For example in our case, we will make a get request on https://jsonplaceholder.typicode.com/users and this will return to us the data in the form of a JSON Object. Knowing this much is enough for us right now but if you want to understand the REST APIs a little better, give this a read.

    无论我们在使用的应用程序中看到什么数据,都来自互联网。 这就是网络和API进入的地方。设备和服务器之间的数据交换称为网络。 REST基本上是一种体系结构,它使我们能够创建可被理解HTTP的任何设备或客户端使用的服务和应用程序。 例如,在我们的例子中,我们将在https://jsonplaceholder.typicode.com/users上发出一个get请求,这将以JSON Object的形式返回给我们数据。 多了解这对我们来说是足够的,但现在,如果你想了解REST API的好一点,给这个一读。

    URLSession (URLSession)

    Since iOS 7, the default way of making an HTTP Networking Request is by using a class URLSession. The URLSession class is actually part of a group of classes that work together to make and respond to HTTP requests.

    从iOS 7开始,发出HTTP网络请求的默认方法是使用URLSession类。 URLSession类实际上是一组类的一部分,这些类一起工作以发出并响应HTTP请求。

    URLSession includes a number of core classes. This is how the environment works:

    URLSession包含许多核心类。 环境是这样工作的:

    1. You use URLSession to create a session. You can think of a session as an open tab or window in your web browser, which groups together many HTTP requests over subsequent website visits.

      您使用URLSession创建会话。 您可以将会话视为Web浏览器中的打开选项卡或窗口,该会话将随后的网站访问中的许多HTTP请求分组在一起。
    2. The URLSession is used to create URLSessionTask instances, which can fetch and return data to your app, and download and upload files to webservices.

      URLSession用于创建URLSessionTask实例,该实例可以获取数据并将其返回到您的应用程序,以及将文件下载和上传到Web服务。

    3. You configure a session with a URLSessionConfiguration object. This configuration manages caching, cookies, connectivity and credentials.

      您可以使用URLSessionConfiguration对象配置会话。 此配置管理缓存,cookie,连接性和凭据。

    4. To make a request, you create a data task, of class URLSessionDataTask, and you provide it with a URL, and a completion handler. This is a closure that’s executed when the request’s response is returned to your app. (We’ll talk about closures in a while)

      要发出请求,请创建类URLSessionDataTask的数据任务,并为其提供URL和完成处理程序。 这是当请求的响应返回到您的应用程序时执行的闭包。 (我们将在一段时间内讨论闭包)

    5. When the completion handler is executed, you can inspect the returned data and take appropriate action, such as loading the data into the TableView, like we will be doing in a while.

      执行完成处理程序后,您可以检查返回的数据并采取适当的操作,例如将数据加载到TableView中,就像我们将在一段时间内做的那样。

    We can think of URLSession as a factory that produces certain URLSessionTask and each task is responsible for a networking request.

    我们可以将URLSession视为产生某些URLSessionTask的工厂,并且每个任务都负责网络请求。

    We can make 3 kinds of requests with URLSession:

    我们可以使用URLSession发出3种请求:

    • Data tasks: send and receive data with URLSessionDataTask, by using NSData objects. They’re the most common for webservice requests, for example when working with JSON.

      数据任务:通过使用NSData对象,使用URLSessionDataTask发送和接收数据。 它们是最常见的Web服务请求,例如在处理JSON时。

    • Upload tasks: send files to a webserver with URLSessionUploadTask. They’re similar to data tasks, but URLSessionUploadTask instances can also upload data in the background (or when an app is suspended).

      上载任务:使用URLSessionUploadTask将文件发送到Web服务器。 它们类似于数据任务,但是URLSessionUploadTask实例也可以在后台(或应用暂停时)上载数据。

    • Download tasks: download files from a webserver with URLSessionDownloadTask by directly writing to a temporary file. You can track the progress of file downloads, and pause and resume them.

      下载任务:通过直接写入临时文件,使用URLSessionDownloadTask从Web服务器下载文件。 您可以跟踪文件下载的进度,并暂停和继续它们。

    We’ll look at the rest of the theory as and when we need it. So, let’s get back to building our app!

    在需要时,我们将研究该理论的其余部分。 因此,让我们回到构建我们的应用程序!

    First, we make a new file “Networking.swift”. This file will be a networking layer i.e. this is the file where we will make all the networking calls for out app.

    首先,我们创建一个新文件“ Networking.swift ”。 该文件将是一个网络层,即我们将在其中进行应用程序的所有网络调用的文件。

    Let’s set up a few things in this file, before we make our GET request.

    在发出GET请求之前,让我们在此文件中设置一些内容。

    Image for post

    When you look at this code the first time, it seems broken. One might wonder how can we make sharedInstance an object of structure Networking , when it itself is inside the struct Networking. And you are not wrong to be thinking that. But what we have written here, is called a Singleton. A singleton is an object that should only be created once and then be shared everywhere it has to be used. So, the struct Networking creates an instance of itself as a static variable, which means the only instance of the Networking struct is the one it created: Networking.sharedInstance. This is the only instance of Networking that will be used throughout our app to make networking calls.

    第一次查看此代码时,它似乎坏了。 有人可能想知道sharedInstance本身位于结构Networking内部时,如何使它sharedInstance结构Networking的对象。 想到这一点,您没有错。 但是我们在这里写的被称为Singleton 。 单例是仅应创建一次然后在必须使用的任何地方共享的对象。 因此,结构Networking将自身创建为静态变量的实例,这意味着Networking结构的唯一实例是它创建的实例: Networking.sharedInstance 。 这是将在整个应用程序中用于进行网络呼叫的唯一网络实例。

    The next line, let session = URLSession.shared, with this we get a reference to URLSession by invoking shared of URLSession class. This returns a shared session object, which again is a singleton.

    下一行, let session = URLSession.shared ,通过调用URLSession类的shared,我们获得对URLSession的引用。 这将返回一个共享会话对象,该对象也是单例。

    In the last line the URL, we are going to make the get request. Before we make the final networking call, we are going to try and understand all the other basics that make understanding the network call very easy.

    在URL的最后一行,我们将发出get请求。 在进行最终的网络通话之前,我们将尝试了解所有其他使理解网络通话非常容易的基础知识。

    封闭和完成处理程序 (Closures And Completion Handlers)

    Closures are self-contained blocks of functionality that can be passed around and used in your code. What this means is that you can pass functions as an argument to other functions. The function that you pass may be used at some point of time by the function that it is passed to. These can also be considered as Nested Functions.

    闭包是独立的功能块,可以在代码中传递和使用。 这意味着您可以将函数作为参数传递给其他函数。 您传递的函数可能会在某些时候被传递给它的函数使用。 这些也可以视为嵌套函数

    Completion Handlers can be thought of as the closures that are executed once the function’s body is executed, i.e. Whenever a function with a completion handler finishes (the isFinished property of the function changes to true), the completion handler code is executed. It is very useful when dealing with functions which can take quite a bit of time, such as network calls.

    可以将完成处理程序视为执行完函数主体后执行的闭包,即,只要具有完成处理程序的函数完成(函数的isFinished属性更改为true),就会执行完成处理程序代码。 在处理可能要花费大量时间的功能(例如网络调用)时,此功能非常有用。

    @转义 (@escaping)

    When you define a closure as @escaping, you want the closure to be preserved into memory. As you want the closure to be executed once the function with the closure has been executed. Like here, we want the closure to be executed once we have received the JSON data from the API.

    当将闭包定义为@escaping时 ,您希望将闭包保存到内存中。 您希望在执行带有闭包的函数后立即执行闭包。 像这里一样,我们希望一旦从API接收到JSON数据后就执行闭包。

    For a better understanding of closures, visit here.

    为了更好地了解闭包,请访问此处

    We’ll understand this better once we look at the code. Let’s have a look at the syntax for making a networking call.

    查看代码后,我们将更好地理解这一点。 让我们看一下进行网络调用的语法。

    Image for post

    Now when we look at the function getUsers, we have defined an escaping closure in this code, ie this gets executed when the getUsers has been executed. The completion handler here returns us Result.

    现在,当我们查看函数getUsers时,我们在此代码中定义了一个转义的闭包,即,当执行getUsers时将执行该闭包。 这里的完成处理程序将结果返回给我们。

    Let’s take a second and understand what Result means over here. With Swift 5.1, Apple introduced Result type in its library, it was basically used to deal with ambiguity when we are waiting for the data to be received from an API. At this point we do not know whether data was received or if it is going to return an error, this is where Result comes in.

    让我们花点时间了解Result在这里的含义。 在Swift 5.1中,Apple在其库中引入了Result类型,当我们等待从API接收数据时,它基本上用于处理歧义。 在这一点上,我们不知道是否接收到数据或是否要返回错误,这就是Result出现的地方。

    Result type is implemented as enum, it has two cases,

    结果类型实现为enum ,它有两种情况,

    1. .success, this helps you in returning the data that was received.

      .success ,这有助于您返回接收到的数据。

    2. .failure, this helps you define and return proper errors.

      .failure ,这可以帮助您定义并返回正确的错误。

    Here, Result will return an array of Users if the function call was successful or a user defined error if there was a failure.

    在此,如果函数调用成功,则Result将返回一组用户;如果失败,则将返回用户定义的错误。

    Next, let’s try and understand what is happening inside the function.

    接下来,让我们尝试了解函数内部正在发生的事情。

    • guard let UserURL = URL(string: userURL) else { ..} , here the guard statement helps us deal with errors, i.e. if the string could not be converted to a URL, only then the else block is executed and this is where we throw an error.

      guard let UserURL = URL(string: userURL) else { ..} ,此处的guard语句可帮助我们处理错误,即,如果无法将字符串转换为URL,则仅执行else块,这就是我们在这里抛出一个错误。

    • When you use guard else statements, make sure that we return something or exit the scope. As execution cannot be continued if the condition associated with it is false or cannot be executed.

      当您使用guard else语句时,请确保我们返回了某些内容或退出了范围。 如果执行条件为假或无法执行,则无法继续执行。

    • In this, we are just converting our string to a URL. If the string is not converted we throw an error, however this will never happen for us as we know the string that we have defined will work fine.

      在此,我们只是将字符串转换为URL。 如果未转换字符串,则将引发错误,但是对于我们来说,这将永远不会发生,因为我们知道定义的字符串可以正常工作。
    • It is the next line where we use URLSession and create a dataTask with the URL, this is going to return data to us as JSON if it is successful, otherwise, it’ll give us an error. Hence, we try and unwrap this JSON data, and we call this jsonData, if this fails and there is no data to unwrap, we return the Result as “.failure” with the user defined error.

      这是我们使用URLSession并使用URL创建dataTask的下一行,如果成功,它将以JSON形式将数据返回给我们,否则将给我们带来错误。 因此,我们尝试解包此JSON数据,并将其称为jsonData,如果失败,并且没有要解包的数据,我们将返回Result为“ .failure ”,并带有用户定义的错误。

    • If the above line did not result in an error, this means that we now have the data that the API sent as JSON, now we need to parse it and return the array of type User as Result “.success”. We do this with the help of JSONDecoder.

      如果上面的行没有导致错误,则意味着我们现在拥有API作为JSON发送的数据,现在我们需要对其进行解析,并将用户类型的数组作为结果“ .success ”返回。 我们借助JSONDecoder做到这一点。

    • If a failure occurs here, we return the error again.

      如果此处发生故障,我们将再次返回错误。
    • Last but not least, we schedule the data task by invoking resume() on the data task. This is often overlooked by developers that are new to URLSession, but your network call will not get executed if resume is not invoked.

      最后但并非最不重要的一点是,我们通过对数据任务调用resume()来调度数据任务。 刚接触URLSession的开发人员通常会忽略这一点,但是如果未调用resume,则不会执行网络调用

    With this, our Network call is done and when we call the function getUsers, we will either get the array of type User or the appropriate error.

    这样,我们的网络调用就完成了,当我们调用函数getUsers时,我们将获得User类型的数组或相应的错误。

    让我们看看结果 (Let’s see the results)

    Finally, we are going to make a few changes in TableViewController.

    最后,我们将在TableViewController中进行一些更改。

    Image for post

    Let's try break down and understand what's happening here.

    让我们尝试分解并了解这里发生的事情。

    1. Dispatch Queues basically are queues to which our apps submit tasks that have to be carried out. Here, where initially we were defining an empty array, now we pass a closure that checks if the array was set, in case it is then it asks the Main DispatchQueue to reload the tableView so that the newly fetched content can be displayed.

      调度队列基本上是我们的应用程序向其提交必须执行的任务的队列。 在这里,最初是在定义一个空数组的地方,现在我们通过一个闭包检查该数组是否已设置,以防万一它要求Main DispatchQueue重新加载tableView以便显示新获取的内容。

    2. func fetchData is the function where we make the network call and receive either the array of type User or the error.

      func fetchData是我们进行网络调用并接收User类型或错误类型的数组的函数。

    3. We make the function call as “Networking.sharedInstance.getUsers{..}, where we receive the result. The result will always have to be of type [weak self], as the closure we sent was @escaping, we check the type of result with switch case, if its success we set our array Users to the array that is returned by the network call.

      我们将函数调用为“ Networking.sharedInstance.getUsers {..} ,从中接收结果。 结果总是必须为[weak self]类型,因为我们发送的闭包是@escaping,我们用switch大小写检查结果的类型,如果成功,我们将数组Users设置为网络返回的数组呼叫。

    4. Here, we use weak self so that once the Network call is made, our app does not hold any references to Networking as we won’t be needing that class once the data has already been loaded. This basically takes care of memory leaks.

      在这里,我们使用弱自我,以便在进行网络调用后,我们的应用程序不会保存对网络的任何引用,因为一旦加载了数据,我们将不需要该类。 这基本上可以解决内存泄漏问题。

    5. We call the function fetchData() once the view is loaded in the window.

      视图加载到窗口后,我们将调用fetchData()函数

    Now, if you run the app, you should get the data that we have received.

    现在,如果您运行该应用程序,则应该获取我们收到的数据。

    Image for post

    结语 (Wrapping Up)

    In this article, we have learned to fetch data from an API, and display them in our apps. You can continue with the series in the next article where we play with tab bars and navigation controls.

    在本文中,我们学习了如何从API提取数据,并将其显示在我们的应用程序中。 您可以在下一篇文章中继续学习该系列,我们将在其中使用标签栏和导航控件。

    恭喜🎉! 您刚刚完成了第五个教程!! (Congratulations 🎉! You have just finished the fifth tutorial!!)

    All of the above-written code is available on Github. Watch this space for more interesting challenges, up next in this series!

    所有上面编写的代码都可以在Github上找到 观看此空间,了解更多有趣的挑战,本系列中的下一个!

    Confused about something? Let us know in the responses below. 😄

    对某事感到困惑? 在下面的回复中告诉我们。 😄

    翻译自: https://medium.com/iecse-hashtag/swift-part-5-networking-with-urlsession-6b56783f289a

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