Writing Scripts and Working with Data
Last updated on 2024-06-21 | Edit this page
Overview
Questions
- How can we automate a commonly used set of commands?
Objectives
- Use the
nanotext editor to modify text files. - Write a basic shell script.
- Use the
bashcommand to execute a shell script. - Use
chmodto 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 ~/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 ~/untrimmed_fastq
using cd, then run nano to create a file
called 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.
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-XControl+XCtrl-XCtrl+X^XC-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.
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.
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.
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:
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.
- Open
bad-reads-script.shand add the lineecho "Script finished!"after thegrepcommand and save the file. - Run the updated script.
$ bash bad-reads-script.sh
Script finished!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 the computer that this
script is a program by making the script file executable. We can do this
by changing the file permissions. We talked about permissions in an earlier episode.
First, let’s look at the current permissions.
OUTPUT
-rw-rw-r-- 1 jlchang sequence 76 Jun 18 13:33 bad-reads-script.shWe 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) and
anyone in the sequence group. 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).
Now let’s look at the permissions again.
OUTPUT
-rwxrwxr-x 1 jlchang sequence 76 Jun 18 13:33 bad-reads-script.shNow we see that it says -rwxrwxr-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.
The script should run the same way as before, but now we’ve created our very own computer program!
You can learn more about writing scripts in this Data Carpentries lesson.
Moving and Downloading Data
Often, analyses begin with moving data onto the machine where you’ll be running the analysis. Below we’ll show you some options for downloading data onto a remote server, or to move data between your computer and the cloud.
Getting data from the cloud
There are two programs that will download data from the internet to
your local machine (or a remote server): 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.
wgetis short for “world wide web get”, and it’s basic function is to download web pages or data at a web address.cURLis 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 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 might see the following output:
OUTPUT
/usr/bin/curlOUTPUT
$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:
or
BASH
$ cd
$ curl -O ftp://ftp.ensemblgenomes.org/pub/release-37/bacteria/species_EnsemblBacteria.txtSince 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 a remote server on the command line and
execute the curl command above in the terminal for the
remote machine, the file will be downloaded to the remote 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 remote server (or a cloud server)? 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
If you’re using Linux, Mac OS, or Windows with Git Bash on your local
machine, you can use scp to upload data to 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:
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 remote
server, the command would look like this:
To move it back to your local computer, you re-order the
to and from fields:
Uploading Data to your Virtual Machine with scp
Open the terminal and use the scp command to upload a
file (e.g. local_file.txt) to the dcuser home directory:
At Broad, remote servers used for data transfer are xfer1.broadinstitute.org, xfer2.broadinstitute.org and xfer3.broadinstitute.org
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 ~/untrimmed_fastq/scripted_bad_reads.txt.
Tip: If you are looking for another (or any really) text file in your home directory to use instead, try:
Download the bad reads file in
~/untrimmed_fastq/scripted_bad_reads.txt to your home ~/Download
directory using the following command (make sure you substitute
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.
If you are using Windows without Git Bash on your local machine, you
can use pscp.exe to upload data to your virtual
machine.
If you’re using a Windows PC without Git Bash, one option is the PSCP program. This program is from a suite of tools that offers PuTTY, a freeware terminal program.
- If you haven’t done so, download PSCP from http://the.earth.li/~sgtatham/putty/latest/x86/pscp.exe
- Make sure the PSCP program is somewhere you know on your computer. In this case, your Downloads folder is appropriate.
- Open the windows PowerShell; go to your start menu/search enter the term ‘cmd’; you will be able to start the shell (the shell should start from C:\Users\your-pc-username>).
- Change to the Downloads directory:
- 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 know the name of the remote machine. At Broad, remote servers
used for data transfer are xfer1.broadinstitute.org,
xfer2.broadinstitute.org and xfer3.broadinstitute.org, and your login
credentials). You will be prompted to enter a password, and
then your upload will begin. (make sure you substitute
‘your-pc-username’ for your actual pc username and ‘
@remote.server.address’ with your username and a Broad data transfer server address)
BASH
C:\User\your-pc-username\Downloads> pscp.exe local_file.txt <username>@remote.server.address:~/Downloading Data from your Virtual Machine with PSCP
- Follow the instructions in the Upload section to download (if needed) and access the PSCP program (steps 1-3)
- Download the text file to your current working directory
(represented by a .) using the following command (make sure you
substitute ‘your-pc-username’ for your actual pc username and
‘
@remote.server.address’ with your username and a Broad data transfer server address)
Key Points
- Scripts are a collection of commands executed together.
- Transferring information to and from virtual and local computers.