Which of the following commands can be used to read the contents of a file in the form of list?

Overview

Teaching: 30 min
Exercises: 15 min

Questions

• How can I view and search file contents?

• How can I create, copy and delete files and directories?

• How can I control who has permission to modify a file?

• How can I repeat recently used commands?

Objectives

• View, search within, copy, move, and rename files. Create new directories.

• Use wildcards [*] to perform operations on multiple files.

• Make a file read only.

• Use the history command to view and repeat recently used commands.

Working with Files

Our data set: FASTQ files

Now that we know how to navigate around our directory structure, let’s start working with our sequencing files. We did a sequencing experiment and have two results files, which are stored in our untrimmed_fastq directory.

Wildcards

Navigate to your untrimmed_fastq directory:

$ cd ~/shell_data/untrimmed_fastq

We are interested in looking at the FASTQ files in this directory. We can list all files with the .fastq extension using the command:

SRR097977.fastq SRR098026.fastq

The * character is a special type of character called a wildcard, which can be used to represent any number of any type of character. Thus, *.fastq matches every file that ends with .fastq.

This command:

lists only the file that ends with 977.fastq.

This command:

/usr/bin/amuFormat.sh /usr/bin/gettext.sh /usr/bin/gvmap.sh

Lists every file in /usr/bin that ends in the characters .sh. Note that the output displays full paths to files, since each result starts with /.

Exercise

Do each of the following tasks from your current directory using a single ls command for each:

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

Bonus: List all of the files in /usr/bin that contain the letter ‘a’ or the letter ‘c’.

Hint: The bonus question requires a Unix wildcard that we haven’t talked about yet. Try searching the internet for information about Unix wildcards to find what you need to solve the bonus problem.

Solution

1. ls /usr/bin/c*
2. ls /usr/bin/*a*
3. ls /usr/bin/*o
   Bonus: ls /usr/bin/*[ac]*

Exercise

echo is a built-in shell command that writes its arguments, like a line of text to standard output. The echo command can also be used with pattern matching characters, such as wildcard characters. Here we will use the echo command to see how the wildcard character is interpreted by the shell.

SRR097977.fastq SRR098026.fastq

The * is expanded to include any file that ends with .fastq. We can see that the output of echo *.fastq is the same as that of ls *.fastq.

What would the output look like if the wildcard could not be matched? Compare the outputs of echo *.missing and ls *.missing.

Solution

ls: cannot access '*.missing': No such file or directory

Command History

If you want to repeat a command that you’ve run recently, you can access previous commands using the up arrow on your keyboard to go back to the most recent command. Likewise, the down arrow takes you forward in the command history.

A few more useful shortcuts:

• Ctrl+C will cancel the command you are writing, and give you a fresh prompt.
• Ctrl+R will do a reverse-search through your command history. This is very useful.
• Ctrl+L or the clear command will clear your screen.

You can also review your recent commands with the history command, by entering:

to see a numbered list of recent commands. You can reuse one of these commands directly by referring to the number of that command.

For example, if your history looked like this:

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

then you could repeat command #260 by entering:

Type ! [exclamation point] and then the number of the command from your history. You will be glad you learned this when you need to re-run very complicated commands. For more information on advanced usage of history, read section 9.3 of Bash manual.

Exercise

Find the line number in your history for the command that listed all the .sh files in /usr/bin. Rerun that command.

Solution

First type history. Then use ! followed by the line number to rerun that command.

Examining Files

We now know how to switch directories, run programs, and look at the contents of directories, but how do we look at the contents of files?

One way to examine a file is to print out all of the contents using the program cat.

Enter the following command from within the untrimmed_fastq directory:

This will print out all of the contents of the SRR098026.fastq to the screen.

Exercise

1. Print out the contents of the ~/shell_data/untrimmed_fastq/SRR097977.fastq file. What is the last line of the file?
2. From your home directory, and without changing directories, use one short command to print the contents of all of the files in the ~/shell_data/untrimmed_fastq directory.

Solution

1. The last line of the file is C:CCC::CCCCCCCC