3. Working with Files and Directories¶
Lesson 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
historycommand to view and repeat recently used commands.
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?
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:
We are interested in looking at the FASTQ files in this directory. We can list all files with the .fastq extension using the command:
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 every file in /usr/bin that ends with the characters 11
/usr/bin/cpp-11 /usr/bin/gcc-ar-11 /usr/bin/gcov-11 /usr/bin/lto-dump-11 /usr/bin/x86_64-linux-gnu-gcc-11 /usr/bin/x86_64-linux-gnu-gcc-ranlib-11 /usr/bin/x86_64-linux-gnu-gcov-tool-11
/usr/bin/g++-11 /usr/bin/gcc-nm-11 /usr/bin/gcov-dump-11 /usr/bin/x86_64-linux-gnu-cpp-11 /usr/bin/x86_64-linux-gnu-gcc-ar-11 /usr/bin/x86_64-linux-gnu-gcov-11 /usr/bin/x86_64-linux-gnu-lto-dump-11
/usr/bin/gcc-11 /usr/bin/gcc-ranlib-11 /usr/bin/gcov-tool-11 /usr/bin/x86_64-linux-gnu-g++-11 /usr/bin/x86_64-linux-gnu-gcc-nm-11 /usr/bin/x86_64-linux-gnu-gcov-dump-11
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:
- List all of the files in
/usr/binthat start with the letter 'c'. - List all of the files in
/usr/binthat contain the letter 'a'. - List all of the files in
/usr/binthat 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
ls /usr/bin/c*ls /usr/bin/*a*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.
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.
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
clearcommand will clear your screen.
to see a numbered list of recent commands. You can reuse one of these commands directly by referring to the number of that command.
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
- Print out the contents of the
~/shell_data/untrimmed_fastq/SRR097977.fastqfile. 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
~/shell_data/untrimmed_fastqdirectory.
Solution
- The last line of the file is
C:CCC::CCCCCCCC<8?6A:C28C<608'&&&,'$. cat ~/shell_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.
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. Scroll up a couple lines on your terminal to verify
you are at the beginning of the file. 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.
code
@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
+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.
Details on the FASTQ format¶
Although it looks complicated (and it is), it's easy to understand the fastq format with a little decoding. Some rules about the format include...
| Line | Description |
|---|---|
| 1 | Always begins with '@' and then information about the read |
| 2 | The actual DNA sequence |
| 3 | Always begins with a '+' and sometimes the same info in line 1 |
| 4 | Has a string of characters which represent the quality scores; must have same number of characters as line 2 |
We can view the first complete read in one of the files in our dataset by using head to look at
the first four lines.
code
All but one of the nucleotides in this read are unknown (N). This is a pretty bad read!
Line 4 shows the quality for each nucleotide in the read. We'll cover the Fastq format more in depth tomorrow in when we look at assessing read quality in the DNA variant calling workshop.
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 ~/shell_data/untrimmed_fastq directory and enter:
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:
Moving / Renaming¶
We can now move our backup file to this directory. We can move files around using the command mv:
The mv command is also how you rename files. Let's rename this file to make it clear that this is a backup:
File Permissions¶
We've now made a backup copy of our file, but just because we have two copies, it 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:
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.
code
Removing¶
To prove to ourselves that you no longer have the ability to modify this file, try deleting it with the rm command:
You'll be asked if you want to override your file permissions:
You should enter n for no. 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 command 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.
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 ~/shell_data/untrimmed_fastq/ directory, do the following:
- Make sure that you have deleted your backup directory and all files it contains.
- Create a backup of each of your FASTQ files using
cp. (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 wildcard.) - 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 backupcp SRR098026.fastq SRR098026-backup.fastqandcp SRR097977.fastq SRR097977-backup.fastqmkdir backupandmv *-backup.fastq backupchmod -w backup/*-backup.fastq
It's always a good idea to check your work withls -l backup. You should see something like:
keypoints
- You can view file contents using
less,cat,headortail. - The commands
cp,mv, andmkdirare useful for manipulating existing files and creating new directories. - You can view file permissions using
ls -land change permissions usingchmod. - The
historycommand and the up arrow on your keyboard can be used to repeat recently used commands.