Working with Files and Directories
Overview
Teaching: 30 min
Exercises: 15 minQuestions
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 wild cards (
*
) 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, lets
start working with our sequencing files. We did a sequencing experiment and
have two results files, which are stored in our untrimmed_fastq
directory.
Wild cards
Navigate to your untrimmed_fastq
directory.
$ cd ~/dc_sample_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:
$ ls *.fastq
SRR097977.fastq SRR098026.fastq
The *
character is a wildcard character which stands for “everything”.
Thus, *.fastq
matches every file that ends with .fastq
.
This command:
$ ls *977.fastq
SRR097977.fastq
lists only the file that ends with 977.fastq
.
We can use the command echo
to see how the wildcard character is intepreted by the
shell.
$ echo *.fastq
SRR097977.fastq SRR098026.fastq
The *
is expanded to include any file that ends with .fastq
.
This command:
$ ls /usr/bin/*.sh
/usr/bin/amuFormat.sh /usr/bin/gettext.sh /usr/bin/gvmap.sh
Lists every file in /usr/bin
that ends in the characters .sh
.
Home vs. Root
The
/
character is another navigational shortcut and refers to your root directory. The root directory is the highest level directory in your file system and contains files that are important for your computer to perform its daily work, but which you usually won’t have to interact with directly. In our case, the root directory is two levels above our home directory, socd
orcd ~
will take you to/home/dcuser
andcd /
will take you to/
, which is equivalent to~/../../
. Try not to worry if this is confusing, it will all become clearer with practice.
Exercise
Do each of the following tasks from your current directory using a single
ls
command for each.
- List all of the files in
/usr/bin
that start with the letter ‘c’.- List all of the files in
/usr/bin
that contain the letter ‘a’.- 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. Trying searching the internet for information about Unix wildcards to find what you need to solve the bonus problem.
Solution
ls /usr/bin/c*
ls /usr/bin/*a*
ls /usr/bin/*o
Bonus:ls /usr/bin/*[ac]*
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:
$ history
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:
$ !260
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.
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:
$ cat SRR098026.fastq
This will print out all of the contents of the SRR098026.fastq
to the screen.
Exercise
- Print out the contents of the
~/dc_sample_data/untrimmed_fastq/SRR097977.fastq
file. What is the last line of the file?- From your home directory, and without changing directories, use one short command to print the contents of all of the files in the
~/dc_sample_data/untrimmed_fastq
directory.Solution
- The last line of the file is
TC:CCC::CCCCCCCC<8?6A:C28C<608'&&&,'$
.cat ~/dc_sample_data/untrimmed_fastq/*
cat
is a terrific program, but when the file is really big, it can
be annoying to use. The program, less
, is useful for this
case. less
opens the file as read only, and lets you navigate through it. The navigation commands
are identical to the man
program.
Enter the following command:
$ less SRR097977.fastq
Some navigation commands in less
key | action |
---|---|
Space | to go forward |
b | to go backward |
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. Use the
“/” key to begin a search. Enter the word you would like
to search for and press enter
. The screen will jump to the next location where
that word is found.
Shortcut: If you hit “/” then “enter”, less
will repeat
the previous search. less
searches from the current location and
works its way forward. Note, if you are at the end of the file and search
for the sequence “CAA”, less
will not find it. You either need to go to the
beginning of the file (by typing g
) and search again using /
or you
can use ?
to search backwards in the same way you used /
previously.
For instance, let’s search forward for the sequence TTTTT
in our file.
You can see that we go right to that sequence, what it looks like,
and where it is in the file. If you continue to type /
and hit return, you will move
forward to the next instance of this sequence motif. If you instead type ?
and hit
return, you will search backwards and move up the file to previous examples of this motif.
Exercise
What are the next three nucleotides (characters) after the first instance of the sequence quoted above?
Solution
CAC
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 let you look at
the beginning and end of a file, respectively.
$ head SRR098026.fastq
@SRR098026.1 HWUSI-EAS1599_1:2:1:0:968 length=35
NNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNN
+SRR098026.1 HWUSI-EAS1599_1:2:1:0:968 length=35
!!!!!!!!!!!!!!!!#!!!!!!!!!!!!!!!!!!
@SRR098026.2 HWUSI-EAS1599_1:2:1:0:312 length=35
NNNNNNNNNNNNNNNNANNNNNNNNNNNNNNNNNN
+SRR098026.2 HWUSI-EAS1599_1:2:1:0:312 length=35
!!!!!!!!!!!!!!!!#!!!!!!!!!!!!!!!!!!
@SRR098026.3 HWUSI-EAS1599_1:2:1:0:570 length=35
NNNNNNNNNNNNNNNNANNNNNNNNNNNNNNNNNN
$ tail SRR098026.fastq
+SRR098026.247 HWUSI-EAS1599_1:2:1:2:1311 length=35
#!##!#################!!!!!!!######
@SRR098026.248 HWUSI-EAS1599_1:2:1:2:118 length=35
GNTGNGGTCATCATACGCGCCCNNNNNNNGGCATG
+SRR098026.248 HWUSI-EAS1599_1:2:1:2:118 length=35
B!;?!A=5922:##########!!!!!!!######
@SRR098026.249 HWUSI-EAS1599_1:2:1:2:1057 length=35
CNCTNTATGCGTACGGCAGTGANNNNNNNGGAGAT
+SRR098026.249 HWUSI-EAS1599_1:2:1:2:1057 length=35
A!@B!BBB@ABAB#########!!!!!!!######
The -n
option to either of these commands can be used to print the
first or last n
lines of a file.
$ head -n 1 SRR098026.fastq
@SRR098026.1 HWUSI-EAS1599_1:2:1:0:968 length=35
$ tail -n 1 SRR098026.fastq
A!@B!BBB@ABAB#########!!!!!!!######
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 copy files or move them around or get rid of them? Most of the time, you can do these sorts of file manipulations without the command line, but there will be some cases (like when you’re working with a remote computer like we are for this lesson) where it will be impossible. You’ll also find that you may be working with hundreds of files and want to do similar manipulations to all of those files. In cases like this, it’s much faster to do these operations at the command line.
Copying Files
When working with computational data, it’s important to keep a safe copy of that data that can’t be accidentally overwritten or deleted. For this lesson, our raw data is our FASTQ files. We don’t want to accidentally change the original files, so we’ll make a copy of them and change the file permissions so that we can read from, but not write to, the files.
First, let’s make a copy of one of our FASTQ files using the cp
command.
Navigate to the dc_sample_data/untrimmed_fastq
directory and enter:
$ cp SRR098026.fastq SRR098026-copy.fastq
$ ls -F
SRR097977.fastq SRR098026-copy.fastq SRR098026.fastq
We now have two copies of the SRR098026.fastq
file, one of them named SRR098026-copy.fastq
. We’ll move this file to a new directory
called backup
where we’ll store our backup data files.
Creating Directories
The mkdir
command is used to make a directory. Enter mkdir
followed by a space, then the directory name you want to create.
$ mkdir backup
Moving / Renaming
We can now move our backup file to this directory. We can
move files around using the command mv
.
$ mv SRR098026-copy.fastq backup
$ ls backup
SRR098026-copy.fastq
The mv
command is also how you rename files. Let’s rename this file to make it clear that this is a backup.
$ cd backup
$ mv SRR098026-copy.fastq SRR098026-backup.fastq
$ ls
SRR098026-backup.fastq
File Permissions
We’ve now made a backup copy of our file, but just because we have two copies doesn’t make us safe. We can still accidentally delete or overwrite both copies. To make sure we can’t accidentally mess up this backup file, we’re going to change the permissions on the file so that we’re only allowed to read (i.e. view) the file, not write to it (i.e. make new changes).
View the current permissions on a file using the -l
(long) flag for the ls
command.
$ ls -l
-rw-r--r-- 1 dcuser dcuser 43332 Nov 15 23:02 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 this file 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
-r--r--r-- 1 dcuser dcuser 43332 Nov 15 23:02 SRR098026-backup.fastq
Removing
To prove to ourselves that you no longer have the ability to modify this file, try deleting it with the rm
command.
$ rm SRR098026-backup.fastq
You’ll be asked if you want to override your file permissions.
rm: remove write-protected regular file ‘SRR098026-backup.fastq’?
If you enter n
(for no), the file will not be deleted. If you enter y
, you will delete the file. This gives us an extra
measure of security, as there is one more step between us and deleting our data files.
Important: The rm
file permanently removes the file. Be careful with this command. It doesn’t
just nicely put the files in the Trash. They’re really gone.
By default, rm
will not delete directories. You can tell rm
to
delete a directory using the -r
(recursive) option. Let’s delete the backup directory
we just made.
Enter the following command:
$ cd ..
$ rm -r backup
This will delete not only the directory, but all files within the directory. If you have write-protected files in the directory, you will be asked whether you want to override your permission settings.
Exercise
Starting in the
dc_sample_data/untrimmed_fastq/
directory, do the following:
- Make sure that you have deleted your backup directory and all files it contains.
- Create a copy of each of your FASTQ files. (Note: You’ll need to do this individually for each of the two FASTQ files. We haven’t learned yet how to do this with a wild-card.)
- Use a wildcard to move all of your backup files to a new backup directory.
- Change the permissions on all of your backup files to be write-protected.
Solution
rm -r backup
cp SRR098026.fastq SRR098026-backup.fastq
andcp SRR097977.fastq SRR097977-backup.fastq
mkdir backup
andmv *-backup.fastq backup
chmod -w backup/*-backup.fastq
It’s always a good idea to check your work withls -l backup
. You should see something like:-r--r--r-- 1 dcuser dcuser 47552 Nov 15 23:06 SRR097977-backup.fastq -r--r--r-- 1 dcuser dcuser 43332 Nov 15 23:06 SRR098026-backup.fastq
Key Points
You can view file contents using
less
,cat
,head
ortail
.The commands
cp
,mv
, andmkdir
are useful for manipulating existing files and creating new directories.You can view file permissions using
ls -l
and change permissions usingchmod
.The
history
command and the up arrow on your keyboard can be used to repeat recently used commands.