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Introduction to the Shell
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2014-07-30

Learning objectives

  • Navigate around the Unix file system
  • Explore the content of files
  • Learn how to manipulate files

Starting with the shell

Now that we are connected to the cloud, we have file directories available to us to explore. Let's learn a few commands by investigating the folders in the dc_sample_data directory:

$ cd dc_sample_data

cd stands for 'change directory'

Let's see what is inside the folder. Type:

$ ls

You will see:

sra_metadata  untrimmed_fastq

ls stands for 'list' and it lists the contents of a directory.

There are two items listed. What are they? We can use a command line "modifier" with ls to get more information; this modifier is called an argument (more below).

$ ls -F
sra_metadata/  untrimmed_fastq/

Anything with a "/" after it is a directory. Things with a "*" after them are programs. If there are no decorations after the name, it's a file.

You can also use the command ls -l to see whether items in a directory are files or directories.

$ ls -l
drwxr-x--- 2 dcuser dcuser 4096 Jul 30 11:37 sra_metadata
drwxr-xr-x 2 dcuser dcuser 4096 Jul 30 11:38 untrimmed_fastq

ls -l gives a lot more information too.

Let's go into the untrimmed_fastq directory and see what is in there.

$ cd untrimmed_fastq

$ ls -F
SRR097977.fastq  SRR098026.fastq

There are two items in this directory with no trailing slashes, so they are files.

Arguments

Most commands take additional arguments that control their exact behavior. For example, -F and -l are arguments to ls. The ls command, like many commands, takes a lot of arguments. Another useful one is '-a', which shows everything, including hidden files.

How do we know what arguments are available for particular commands? Most commonly used shell commands have a manual. You can access the manual using the man command. Try entering:

$ man ls

This will open the manual page for ls. Use the space key to go forward and b to go backwards. When you are done reading, just hit q to quit.

Commands that are run from the shell can get extremely complicated. To see an example, open up the manual page for the find command. No one can possibly learn all of these arguments, of course. So you will probably find yourself referring to the manual page frequently.

If the manual page within the terminal is hard to read and traverse, the manual exists online, use your web searching powers to get it! In addition to the arguments, you can also find good usage examples online; Google is your friend.

The Unix directory file structure (a.k.a. where am I?)

As you've already just seen, you can move around in different directories or folders at the command line. You are probably accustomed to navigating around the normal way using a GUI (GUI = Graphical User Interface, pronounced gooey), but you will find that it's not too difficult once you get the hang of it.

Moving around the file system

Let's practice moving around a bit. Previously, we moved to the untrimmed_fastq directory.

To get there, we first changed directories from the folder of our username (dcuser) to dc_sample_data then we changed directories to untrimmed_fastq

Let's draw out how that went.

Now let's draw some of the other files and folders we could have clicked on.

This is called a hierarchical file system structure, like an upside down tree with root (/) at the base that looks like this:

Unix

That root (/) is often also called the 'top' level.

When you are working at your computer or log in to a remote computer, you are on one of the branches of that tree, your home directory (/home/dcuser)

Now let's go do that same navigation at the command line.

Type:

$ cd

This puts you in your home directory. No matter where you are in the directory system, cd will always bring you back to your home directory.

Now using cd and ls, go in to the untrimmed_fastq directory and list its contents.

Let's also check to see where we are. Sometimes when we're wandering around in the file system, it's easy to lose track of where we are and get lost.

If you want to know what directory you're currently in, type:

$ pwd

This stands for 'print working directory'. The directory you're currently working in.

What if we want to move back up and out of the 'untrimmed_fastq' directory? Can we just type cd dc_sample_data? Try it and see what happens.

To go 'back up a level' we need to use ..

Type

$ cd ..

.. denotes parent directory, and you can use it anywhere in the system to go back to the parent directory.

Now do ls and pwd.


Exercise

Now we're going to try a hunt. Find a hidden directory in dc_sample_data and list its contents. What is the name of the text file in the hidden directory?

Hint: hidden files and folders in unix start with '.', for example .my_hidden_directory


Full vs. Relative Paths

The cd command takes an argument which is the directory name. Directories can be specified using either a relative path or a full path. As we know, the directories on the computer are arranged into a hierarchy. The full path tells you where a directory is in that hierarchy.

Navigate to the home directory (cd). Now, enter the pwd command and you should see:

/home/dcuser

which is the full path for your home directory. This tells you that you are in a directory called dcuser, which sits inside a directory called home which sits inside the very top directory in the hierarchy. The very top of the hierarchy is a directory called / which is usually referred to as the root directory. So, to summarize: dcuser is a directory in home which is a directory in /.

Now enter the following command:

$ cd /home/dcuser/dc_sample_data/.hidden

This jumps to .hidden. Now go back to the home directory (cd).

Now type the following:

$ cd dc_sample_data/.hidden

This command had the same effect as the previous command - taking us to the hidden directory. But instead of specifying the full path (/home/dcuser/dc_sample_data/.hidden), we specified a relative path. In other words, we specified the path relative to our current directory.

A full path always starts with a /, a relative path does not.

A relative path is like getting directions from someone on the street. They tell you to "go right at the Stop sign, and then turn left on Main Street". That works great if you're standing there together, but not so well if you're trying to tell someone how to get there from another country. A full path is like GPS coordinates. It tells you exactly where something is no matter where you are right now.

You can usually use either a full path or a relative path depending on what is most convenient. If we are in the home directory, it is more convenient to just enter the relative path since it involves less typing.

Over time, it will become easier for you to keep a mental note of the structure of the directories that you are using and how to quickly navigate amongst them.

Examining the contents of other directories

By default, the ls commands lists the contents of the working directory (i.e. the directory you are in). You can always find the directory you are in using the pwd command. However, you can also give ls the names of other directories to view.

Navigate to the home directory if you are not already there.

Type:

$ cd

Then enter the command:

$ ls dc_sample_data

This will list the contents of the dc_sample_data directory without you having to navigate there.

The cd command works in a similar way. Try entering:

$ cd

$ cd dc_sample_data/untrimmed_fastq

$ pwd

You will jump directly to untrimmed_fastq without having to step through the intermediate directory.


Exercise

List the 'SRR097977.fastq' file from your home directory without changing directories


Saving time with shortcuts

There are several shortcuts which you should know about, but today we are going to talk about only a few. As you continue to work with the shell and on the terminal a lot more, you will come across and hopefully adapt many other shortcuts.

Dealing with the home directory is very common. So, in the shell the tilde character, "~", is a shortcut for your home directory. Navigate to the dc_sample_data/sra_metadata/ directory:

$ cd

$ cd dc_sample_data/sra_metadata/

Then enter the command:

$ ls ~

This prints the contents of your home directory, without you having to type the full path.

Another shortcut is the "..", which we encountered earlier:

$ ls ..

The shortcut .. always refers to the directory above your current directory. So, it prints the contents of the /home/dcuser/dc_sample_data. You can chain these together, so:

$ ls ../../

prints the contents of /home/dcuser which is your home directory.

Finally, the special directory . always refers to your current directory.

$ ls .

So, ls, ls ., and ls ././././. all do the same thing, they print the contents of the current directory. This may seem like a useless shortcut right now, but it is needed to specify a destination, e.g. cp ../data/counts.txt . or mv ~/james-scripts/parse-fasta.sh ..

To summarize, while you are in your home directory, the commands ls ~, ls ~/., and ls /home/dcuser all do exactly the same thing. These shortcuts are not necessary, but they are really convenient!

Tab Completion

Tab completion is an important shortcut to know; it improves efficiency navigating the file system and helps avoid typos.

To practice with tab completion, let's first navigate to your home directory.

$ cd

Typing out directory names can waste a lot of time. When you start typing out the name of a directory, then hit the tab key, the shell will try to fill in the rest of the directory name. For example, type cd to get back to your home directy, then enter:

$ cd dc_<tab>

The shell will fill in the rest of the directory name for dc_sample_data. Now go to dc_sample_data/untrimmed_fastq

$ cd un<tab>
$ ls SR<tab><tab>

When you hit the first tab, nothing happens. The reason is that there are multiple directories in the home directory which start with SR. Thus, the shell does not know which one to fill in. When you hit tab again, the shell will list the possible choices.

Wild cards

Navigate to the ~/dc_sample_data/untrimmed_fastq directory. This directory contains FASTQ files from our RNA-Seq experiment.

The * character is a shortcut for "everything". Thus, if you enter ls *, you will see all of the contents of a given directory. Now try this command:

$ ls *fastq

This lists every file that ends with a fastq. This command:

$ ls SRR*

lists every file in that starts with the characters SRR.

$ ls *977.fastq

Lists only the file that ends with '977.fastq'

So how does this actually work? Well...when the shell (bash) sees a word that contains the * character, it automatically looks for filenames that match the given pattern.

We can use the command 'echo' to see wilcards are they are intepreted by the shell.

$ echo *.fastq
SRR097977.fastq SRR098026.fastq

The '*' is expanded to include any file that ends with '.fastq'


Exercise

  1. Change directories to your home directory, and list the contents of dc_sample_data/sra_metadata/ without changing directories again.

  2. List the contents of the /bin directory. Do you see anything familiar in there? How can you tell these are programs rather than plain files?

  3. Do each of the following using a single ls command without navigating to a different directory.

    1. List all of the files in /bin that start with the letter 'c
    2. List all of the files in /bin that contain the letter 'a'
    3. List all of the files in /bin that end with the letter 'o'

    BONUS: List all of the files in '/bin' that contain the letter 'a' or 'c'


Command History

You can easily access previous commands. Hit the up arrow. Hit it again. You can step backwards through your command history. The down arrow takes your forwards in the command history.

^-C will cancel the command you are writing, and give you a fresh prompt.

^-R will do a reverse-search through your command history. This is very useful.

You can also review your recent commands with the history command. Just enter:

$ history

to see a numbered list of recent commands, including this just issued history command. You can reuse one of these commands directly by referring to the number of that command.

If your history looked like this:

259  ls *
260  ls /usr/bin/*.sh
261  ls *R1*fastq

then you could repeat command #260 by simply entering:

$ !260

(that's an exclamation mark). You will be glad you learned this when you try to re-run very complicated commands.


Exercise

  1. Find the line number in your history for the last exercise (listing files in /bin) and reissue that command.

Examining Files

We now know how to move around the file system and look at the contents of directories, but how do we look at the contents of files?

The easiest way (but really not the ideal way in most situations) to examine a file is to just print out all of the contents using the command cat. Enter the following command:

$ cd ~/dc_sample_data/sra_metadata
$ cat SraRunTable.txt 

This prints out the all the contents of the the SraRunTable.txt to the screen.

cat stands for concatenate; it has many uses and printing the contents of a files onto the terminal is one of them.

What does this file contain?

cat is a terrific command, but when the file is really big, it should be avoided; less, is preferred for files larger than a few bytes. Let's take a look at the fastq files in ~/dc_sample_data/untrimmed_fastq. These files are quite large, so we probably do not want to use the cat command to look at them. Instead, we can use the less command.

Move to the untrimmed_fastq directory and enter the following command:

$ cd ~/dc_sample_data/untrimmed_fastq/
$ less SRR098026.fastq

less opens the file, and lets you navigate through it. The commands are identical to the man program.

Some commands in less

key action
"space" to go forward
"b" to go backwarsd
"g" to go to the beginning
"G" to go to the end
"q" to quit

less also gives you a way of searching through files. Just hit the "/" key to begin a search. Enter the name of the word you would like to search for and hit enter. It will jump to the next location where that word is found. If you hit "/" then "enter", less will just repeat the previous search. less searches from the current location and works its way forward. If you are at the end of the file and search the word, less will not find it. You need to go to the beginning of the file and search.

For instance, let's search for the sequence GTTGATC in our file. You can see that we go right to that sequence and can see what it looks like.

Remember, the man program actually uses less internally and therefore uses the same commands, so you can search documentation using "/" as well!

There's another way that we can look at files, and in this case, just look at part of them. This can be particularly useful if we just want to see the beginning or end of the file, or see how it's formatted.

The commands are head and tail and they just let you look at the beginning and end of a file respectively.

$ head SRR098026.fastq

$ tail SRR098026.fastq

The -n option to either of these commands can be used to print the first or last n lines of a file. To print the first line of the file use:

$ head -n 1 SRR098026.fastq

Creating, moving, copying, and removing

Now we can move around in the file structure, look at files, and search files. But what if we want to do normal things like copy files or move them around or get rid of them.

Our raw data in this case is fastq files. We don't want to change the original files, so let's make a copy to work with.

Lets copy the file using the cp command. The copy command requires 2 things, the name of the file to copy, and the location to copy it to. Navigate to the untrimmed_fastq directory and enter:

$ cp SRR098026.fastq SRR098026-copy.fastq

$ ls -F
SRR097977.fastq  SRR098026-copy.fastq  SRR098026.fastq 

Now SRR098026-copy.fastq has been created as a copy of SRR098026.fastq

Let's make a backup directory where we can put this file.

The mkdir command is used to make a directory. Just enter mkdir followed by a space, then the directory name.

$ mkdir backup

We can now move our backed up file in to this directory. We can move files around using the command mv. Enter this command:

$ mv *-copy.fastq backup

$ ls -al backup
total 52
drwxrwxr-x 2 dcuser dcuser  4096 Jul 30 15:31 .
drwxr-xr-x 3 dcuser dcuser  4096 Jul 30 15:31 ..
-rw-r--r-- 1 dcuser dcuser 43421 Jul 30 15:28 SRR098026-copy.fastq

The mv command is also how you rename files. Since this file is so important, let's rename it:

$ cd backup

$ mv SRR098026-copy.fastq SRR098026-copy.fastq_DO_NOT_TOUCH!

$ ls 
SRR098026-copy.fastq_DO_NOT_TOUCH!

Finally, we decided this was silly and want to start over.

$ rm SRR098026-copy.fastq_DO_NOT_TOUCH!

The rm file permanently removes the file. Be careful with this command. The shell doesn't just nicely put the files in the Trash, they're really gone!

Same with moving and renaming files. It will not ask you if you are sure that you want to "replace existing file".


Exercise

  1. Change directories to the untrimmed_fastq folder and create a backup directory called new_backup
  2. Copy both fastq files files there with 1 command

By default, rm, will NOT delete directories. You can tell rm to delete a directory using the -r option. Let's delete our backup and new_backup directories we just made. Enter the following command:

$ rm -r backup
$ rm -r new_backup

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. Obviously, we're not going to type in a FASTA file, but you'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 write in files, we're going to use the program nano. We're going to create a file within your home direcory with the name 'awesome.sh'.

$ cd
$ nano awesome.sh

Now you have something that looks like

nano1.png

Type in your command, so it looks like

nano2.png

Now we want to save the file and exit. At the bottom of nano, you see the "^X Exit". That means that we use Ctrl-X to exit. Type Ctrl-X. It will ask if you want to save it. Type y for yes. Then it asks if you want that file name. Hit 'Enter'.

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.

We're going to come back and use this file in just a bit.