Writing Scripts and Working with Data

Overview

Teaching: 20 min
Exercises: 20 min

Questions

• How can we automate a commonly used set of commands?

Objectives

• Use the nano text editor to modify text files.

• Write a basic shell script.

• Use the bash command to execute a shell script.

• Use chmod to make a script an executable program.

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 ~/shell_data/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 ~/shell_data/untrimmed_fastq using cd, then run nano to create a file called README.txt:

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

You should see something like this:

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”: it can only work with plain character data, not tables, images, or any other human-friendly media. We use it in examples because it is one of the least complex text editors. However, because of this trait, it 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 where it searches for and saves files. If you start it from the shell, it will (probably) use your current working directory as its default location. If you use your computer’s start menu, it 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 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.

Exercise

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

Solution

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 about the command line is that you can write scripts. Scripts let you save commands to run them and also lets you put multiple commands together. 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.

Exercise

We want the script to tell us when it’s done.

1. Open bad-reads-script.sh and add the line echo "Script finished!" after the grep command and save the file.
2. Run the updated script.

Solution

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

File Permissions

We made a backup copy of our files in a previous episode, but then removed the folder and the backup fastq file in order to practise removing files. We would like to make sure we can’t accidentally mess up or remove these backup file, so we’re going to change the permissions on the files so that we’re only allowed to read (i.e. view) them, not write to them (i.e. make new changes).

We need to remake the backup folder we made earlier, make sure you are in the untrimmed_fastq folder:

$pwd

Check you are in the untrimmed_fastq folder if not move to that directory with the following:

$ cd ~/shell_data/untrimmed_fastq/

Then remake the backup folder and make a backup copy of the fastq

mkdir backup
cp SRR098026.fastq backup/SRR098026-backup.fastq
cp SRR097977.fastq backup/SRR097977-backup.fastq
cd backup

View the current permissions on a file using the -l (long) flag for the ls command:

$ ls -l

-rw-r--r-- 1 csuser csuser 47552 Oct 27 15:17 SRR097977-backup.fastq
-rw-r--r-- 1 csuser csuser 43332 Oct 27 15:17 SRR098026-backup.fastq

The first part of the output for the -l flag gives you information about the file’s current permissions. There are ten slots in the permissions list. The first character in this list is related to file type, not permissions, so we’ll ignore it for now. The next three characters relate to the permissions that the file owner has, the next three relate to the permissions for group members, and the final three characters specify what other users outside of your group can do with the file. We’re going to concentrate on the three positions that deal with your permissions (as the file owner).

Here the three positions that relate to the file owner are rw-. The r means that you have permission to read the file, the w indicates that you have permission to write to (i.e. make changes to) the file, and the third position is a -, indicating that you don’t have permission to carry out the ability encoded by that space (this is the space where x or executable ability is stored, we’ll talk more about this in a later lesson).

Our goal for now is to change permissions on one of our files so that you no longer have w or write permissions. We can do this using the chmod (change mode) command and subtracting (-) the write permission -w.

$ chmod -w SRR098026-backup.fastq
$ ls -l

-rw-r--r-- 1 csuser csuser 47552 Nov  9 17:34 SRR097977-backup.fastq
-r--r--r-- 1 csuser csuser 43332 Nov  9 17:16 SRR098026-backup.fastq

Exercise

Now repeat what we just did for your other backup file.

Solution

$ chmod -w SRR097977-backup.fastq
$ ls -l

-r--r--r-- 1 csuser csuser 47552 Nov  9 17:34 SRR097977-backup.fastq
-r--r--r-- 1 csuser csuser 43332 Nov  9 17:16 SRR098026-backup.fastq

Making the script into a program

We had to type bash because we needed to tell the computer what program to use to run this script. Instead, we can turn this script into its own program. We need to tell it that it’s a program by making it executable. We can do this by changing the file permissions. We are going to use the bad-read-scripts.sh file we generated earlier in the episode.

First, let’s move back to our ~/shell_data/untrimmed_fastq working directory using cd and look at the current permissions for bad-read-scripts.sh .

$ cd ../
$ ls -l bad-reads-script.sh

-rw-rw-r-- 1  csuser 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 csuser csuser 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!

You will learn more about writing scripts in a later lesson.

Moving and Downloading Data

So far, we’ve worked with data that is pre-loaded on the instance in the cloud. Usually, however, most analyses 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 most 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.

Another possibility is that you will get an output which says no wget in... followed by a list of file paths where wget was not found. Either way, it should be obvious which of the two you have installed.

If you run these commands in the Cloud-SPAN AMI you will find that both are installed so you can use either.

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 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

Using scp for file transfer

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:

If you are using a Windows machine, you should be able to use scp as long as you have Git Bash/Git for Windows installed. Just make sure you run the commands below in a Git Bash terminal and not the built-in Windows terminal.

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

Note that you always run 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 it back to your local computer, you re-order the to and from fields:

$ scp <AWS instance> <local file>

To keep your instance secure, you also need a way to tell it that you are authorised to have access. You do this using the login key file you downloaded on the first day of the course. It will have the name login-key-instanceNN.pem, where NN is replaced by your instance’s unique number.

You tell the instance to look for your login key using the flag -i.

What is your AWS instance called?

The address you should use for your AWS instance has two main parts: your login credentials and your file path.

• the first part has the format csuser@instanceNN-gc.cloud-span.aws.york.ac.uk where NN is replaced by your instance’s unique number.
• the second part is the file path where you want to send/download your file, for example /home/csuser/.
• the two parts are separated by a colon with no spaces.

Uploading Data to your Virtual Machine with scp

Open a new terminal/GitBash window and use the scp command to upload a file (e.g. local_file.txt) to the csuser home directory (make sure you substitute instanceNN with your instance’s number):

$  scp -i login-key-instanceNN.pem test.txt csuser@instanceNN-gc.cloud-span.aws.york.ac.uk:/home/csuser/

If you were using instance01 and copying the file test.txt the command would look like this. Note this presumes that the file test.txt and the login key file are in the directory you are currently in. You also need to use scp in a window that is not logged onto the instance:

$  scp -i login-key-instance01.pem test.txt csuser@instance01-gc.cloud-span.aws.york.ac.uk:/home/csuser/

Tip: you should be running this command while in the same folder as the file you want to send (local_file.txt). If you aren’t, then you need to specify the path in your command. The same goes for your login key 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 ~/shell_data/scripted_bad_reads.txt.

Download the bad reads file in ~/shell_data/scripted_bad_reads.txt to your home ~/Downloads directory using the following command (make sure you substitute instanceNN with your instance’s number):

$ scp -i login-key-instanceNN.pem test.txt csuser@instanceNN-gc.cloud-span.aws.york.ac.uk:/home/csuser/shell_data/untrimmed_fastq/scripted_bad_reads.txt ~/Downloads

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.

Key Points

• Scripts are a collection of commands executed together.

• Transferring information to and from virtual and local computers.