Writing files

We’ve been able to do a lot of work with files that already exist, but what if we want to write our own files? We’re not going to type in a FASTA file, but we’ll see as we go through other tutorials, there are a lot of reasons we’ll want to write a file, or edit an existing file.

To add text to files, we’re going to use a text editor called Nano. We’re going to create a file to take notes about what we’ve been doing with the data files in ~/CF_Shell/untrimmed_fastq.

This is good practice when working in bioinformatics. We can create a file called README.txt that describes the data files in the directory or documents how the files in that directory were generated. As the name suggests, it’s a file that we or others should read to understand the information in that directory.

Let’s change our working directory to ~/CF_Shell/untrimmed_fastq using cd, then run nano to create a file called README.txt:

$ cd ~/CF_Shell/untrimmed_fastq
$ nano README.txt

You should see something like this:

nano201711.png

The text at the bottom of the screen shows the keyboard shortcuts for performing various tasks in nano. We will talk more about how to interpret this information soon.


Which Editor?

When we say, “nano is a text editor,” we really do mean “text”: nano can only work with plain character data, not tables, images, or any other human-friendly media. We use nano in examples because it is one of the least complex text editors. However, because of this trait, nano may not be powerful enough or flexible enough for the work you need to do after this workshop. On Unix systems (such as Linux and Mac OS X), many programmers use Emacs or Vim (both of which require more time to learn), or a graphical editor such as Gedit. On Windows, you may wish to use Notepad++. Windows also has a built-in editor called notepad that can be run from the command line in the same way as nano for the purposes of this lesson.

No matter what editor you use, you will need to know the default location where it searches for files and where files are saved. If you start an editor from the shell, it will (probably) use your current working directory as its default location. If you use your computer’s start menu, the editor may want to save files in your desktop or documents directory instead. You can change this by navigating to another directory the first time you “Save As…”


Let’s type in a few lines of text. Describe what the files in this directory are or what you’ve been doing with them. Once we’re happy with our text, we can press Ctrl-O (press the Ctrl or Control key and, while holding it down, press the O key) to write our data to disk. You’ll be asked what file we want to save this to: press Return to accept the suggested default of README.txt.

Once our file is saved, we can use Ctrl-X to quit the nano editor and return to the shell.


Control, Ctrl, or ^ Key

The Control key is also called the “Ctrl” key. There are various ways in which using the Control key may be described. For example, you may see an instruction to press the Ctrl key and, while holding it down, press the X key, described as any of:

  • Control-X
  • Control+X
  • Ctrl-X
  • Ctrl+X
  • ^X
  • C-x

In nano, along the bottom of the screen you’ll see ^G Get Help ^O WriteOut. This means that you can use Ctrl-G to get help and Ctrl-O to save your file.


Now you’ve written a file. You can take a look at it with less or cat, or open it up again and edit it with nano.



Challenge - Editing with nano

Open README.txt and add the date to the top of the file and save the file.

Solution - Editing with nano

Use nano README.txt to open the file. Add today’s date and then use Ctrl-X followed by y and Enter to save.



Writing scripts

A really powerful thing that we are now prepared for is writing scripts. Scripts let you save commands to run them, and also lets you put multiple commands together in an organized block. Though writing scripts may require an additional time investment initially, this can save you time as you run them repeatedly. Scripts can also address the challenge of reproducibility: if you need to repeat an analysis, you retain a record of your command history within the script.

One thing we will commonly want to do with sequencing results is pull out bad reads and write them to a file to see if we can figure out what’s going on with them. We’re going to look for reads with long sequences of N’s like we did before, but now we’re going to write a script, so we can run it each time we get new sequences, rather than type the code in by hand each time.

We’re going to create a new file to put this command in. We’ll call it bad-reads-script.sh. The sh isn’t required, but using that extension tells us that it’s a shell script.

$ nano bad-reads-script.sh

Bad reads have a lot of N’s, so we’re going to look for NNNNNNNNNN with grep. We want the whole FASTQ record, so we’re also going to get the one line above the sequence and the two lines below. We also want to look in all the files that end with .fastq, so we’re going to use the * wildcard.

grep -B1 -A2 -h NNNNNNNNNN *.fastq | grep -v '^--' > scripted_bad_reads.txt


Custom grep control

We introduced the -v option in the previous episode, now we are using -h to “Suppress the prefixing of file names on output” according to the documentation shown by man grep.


Type your grep command into the file and save it as before. Be careful that you did not add the $ at the beginning of the line.

Now comes the neat part. We can run this script. Type:

$ bash bad-reads-script.sh

It will look like nothing happened, but now if you look at scripted_bad_reads.txt, you can see that there are now reads in the file.

Next we’ll edit the script to tell us when it’s done.

Let’s open bad-reads-script.sh and add the line echo "Script finished!" after the grep command and save the file.

nano bad-reads-script.sh

Then we’ll run the updated script

$ bash bad-reads-script.sh
Script finished!



Making the script into an executable program

We had to type bash because we needed to tell the computer to use the bash program to operate on our bad-reads-script.sh file. As another option, we can turn this script into its own executable program. To do this, we just need to change the file permissions, and make the script file executable. We talked about permissions in an earlier episode.

First, let’s look at the current permissions.

$ ls -l bad-reads-script.sh
-rw-rw-r-- 1 <username> <username> 0 Oct 25 21:46 bad-reads-script.sh

We see that it says -rw-r--r--. This shows that the file can be read by any user and written to by the file owner (you). We want to change these permissions so that the file can be executed as a program. We use the command chmod like we did earlier when we removed write permissions. Here we are adding (+) executable permissions (+x).

$ chmod +x bad-reads-script.sh

Now let’s look at the permissions again.

$ ls -l bad-reads-script.sh
-rwxrwxr-x 1 <username> <username> 0 Oct 25 21:46 bad-reads-script.sh

Now we see that it says -rwxr-xr-x. The x’s that are there now tell us we can run it as a program. So, let’s try it! We’ll need to put ./ at the beginning so the computer knows to look here in this directory for the program.

$ ./bad-reads-script.sh

The script should run the same way as before, but now we’ve created our very own computer program!



Moving and Downloading Data

So far, we’ve worked with data that is pre-loaded on the instance in the cloud. You can imagine, however, that some analyses may begin with moving data onto the instance. Below we’ll show you some commands to download data onto your instance, or to move data between your computer and the cloud.


Getting data from the cloud

There are two programs that will download data from a remote server to your local (or remote) machine: wget and curl. They were designed to do slightly different tasks by default, so you’ll need to give the programs somewhat different options to get the same behaviour, but they are mostly interchangeable.

  • wget is short for “world wide web get”, and it’s basic function is to download web pages or data at a web address.

  • cURL is a pun, it is supposed to be read as “see URL”, so its basic function is to display webpages or data at a web address.

Which one you need to use mostly depends on your operating system, as many computers will only have one or the other installed by default.

Let’s say you want to download some data from Ensembl. We’re going to download a very small tab-delimited file that just tells us what data is available on the Ensembl bacteria server. Before we can start our download, we need to know whether we’re using curl or wget.

To see which program you have, type:

$ which curl
$ which wget

which is a BASH program that looks through everything you have installed, and tells you what folder it is installed to. If it can’t find the program you asked for, it returns nothing, i.e. gives you no results.

On Mac OSX, you’ll likely get the following output:

$ which curl
/usr/bin/curl
$ which wget
$

This output means that you have curl installed, but not wget.

Once you know whether you have curl or wget, use one of the following commands to download the file:

$ cd
$ wget ftp://ftp.ensemblgenomes.org/pub/release-37/bacteria/species_EnsemblBacteria.txt

or

$ cd
$ curl -O ftp://ftp.ensemblgenomes.org/pub/release-37/bacteria/species_EnsemblBacteria.txt

Since we wanted to download the file rather than just view it, we used wget without any modifiers. With curl however, we had to use the -O flag, which simultaneously tells curl to download the page instead of showing it to us and specifies that it should save the file using the same name it had on the server: species_EnsemblBacteria.txt

It’s important to note that both curl and wget download to the computer that the command line belongs to. So, if you are logged into AWS on the command line and execute the curl command above in the AWS terminal, the file will be downloaded to your AWS machine, not your local one.


Moving files between your laptop and your instance

What if you need to grab some information from the remote instance? Or what if the data you need is on your local computer, but you need to get it into the cloud? There are also several ways to do this, but it’s always easier to start the transfer locally. This means if you’re typing into a terminal, the terminal should not be logged into your instance, it should be showing your local computer. If you’re using a transfer program, it needs to be installed on your local machine, not your instance.



Transferring Data Between your Local Machine and the Cloud

These directions are platform specific, so please follow the instructions for your system:

Please select the platform you wish to use for the exercises:


Using scp to Move Data to/from your Virtual Machine

scp stands for ‘secure copy protocol’, and is a widely used UNIX tool for moving files between computers. The simplest way to use scp is to run it in your local terminal, and use it to copy a single file:

scp <file I want to move> <where I want to move it>

Note that you are always running scp locally, but that doesn’t mean that you can only move files from your local computer. In order to move a file from your local computer to an AWS instance, the command would look like this:

$ scp <local file> <AWS instance>

To move a file from the AWS instance to your local computer, you re-order the to and from fields:

$ scp <AWS instance> <local file>


Downloading Data from your Virtual Machine with scp

Let’s download a text file from our remote machine. You should have a file that contains bad reads called ~/CF_Shell/untrimmed_fastq/scripted_bad_reads.txt.

Download the bad scripted_bad_reads.txt to your local Downloads directory using the following command (make sure to use your username in place of <username> in the command):

$ scp <username>@bfx-workshop01.med.umich.edu:/home/workshop/<username>/CF_Shell/untrimmed_fastq/scripted_bad_reads.txt ~/Downloads

Uploading Data to your Virtual Machine with scp

The process to upload is very similar. You’ll once again use the scp command, but just switch the order of arguments to upload a file (e.g. local_file.txt) to your remote home directory:

$  scp local_file.txt <username>@bfx-workshop01.med.umich.edu:/home/workshop/<username>/



Using scp to Move Data to/from your Virtual Machine

If you’re using a Windows PC, you should likewise be able to use the scp program. It is installed on Windows 10 by default, though you may have to enable it.

  1. Open the windows PowerShell; go to your start menu/search enter the term ‘cmd’; Select the ‘Command Prompt’ application and it will start the shell (the shell prompt should say the local location e.g. C:-pc-username>).
  2. Change to the Downloads directory:
C:\User\your-pc-username> cd Downloads
  1. Now let’s transfer the scripted_bad_reads.txt file from our AWS instance to our personal computer. You will need to provide login credentials in order to perform the transfer.

Download the text file to your current working directory (represented by a .) using the following command (make sure you substitute <username> for your actual username).

C:\User\your-pc-username\Downloads> scp <username>@:/home/workshop/<username>/CF_Shell/untrimmed_fastq/scripted_bad_reads.txt .


Uploading Data to your Virtual Machine with scp

  1. Follow the instructions in the above section to open the powershell and change to the Downloads folder (steps 1-2)
  2. Locate a file on your computer that you wish to upload (be sure you know the path). Then upload it to your remote machine. You will need to provide login credentials in order to perform the transfer.
C:\User\your-pc-username\Downloads> scp local_file.txt <username>@bfx-workshop01.med.umich.edu:/home/workshop/<username>/

Remember that in both instances, the command is run from your local machine, we’ve just flipped the order of the to and from parts of the command.