Altering files and directories

Questions to think about:

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

• How can I edit files?

Creating Directories or Files

mkdir creates a new directory, followed by the name of the new directory.

Bash

$ mkdir new_dir
$ ls -F

Output

new_dir/

mkdir -p can be used to make subdirectories.

Bash

$ mkdir -p code/python/analysis
$ ls -RF # displays subdirectory structure

Output

code/

./code:
python/

./code/python:
analysis/

./code/python/analysis:

nano filename.txt runs a text editor called nano to create a new file by the name given. For example, nano thesis.txt creates a text file named thesis.txt in the working directory.

Bash

$ nano filename.txt

touch filename.txt creates an empty (0 byte) file by the new name given. Why bother? Some programs require empty files to populate with output.

Bash

$ touch filename2.txt
$ ls -F

Output

filename.txt
filename2.txt

Moving or renaming directories or files safely

mv filename.txt new_location command move has two arguments. The first tells mv what we’re moving, while the second is where it will go.

Bash

$ mv filename.txt new_dir
$ ls -F new_dir

Output

filename.txt

mv -i or mv -interactive must be used to make mv ask for confirmation before overwriting any existing file or directory with the same name as the second argument. (Otherwise, beware! It will silently overwrite.)

Copying directories and/or files

cp old new command copies a file (first argument) to a new location (second argument)

Bash

$ cp filename2.txt new_dir
$ ls -F

Output

filename2.txt
new_dir/

• cp -r adds the recursive option to copy a directory and all its contents to another directory (second argument). For example, we can make a backup with cp -r thesis thesis_backup.

• cp can be used on multiple filenames as long as a destination directory is the last argument. For example, cp a.txt b.txt c.txt backup/ will copy the three text files into the subdirectory backup/.

Removing files and directories safely: Deleting is forever

rm is used to remove items from a directory. Using it without any options, however, can be dangerous, as deleted items do not go to a trash or recycling bin.

• rm -i path command for remove with interactive option to ask for confirmation before deleting.

• rm -i -r path command with interactive option and recursive option will remove a directory and all its contents with confirmation prompts.

Bash

$ rm -i -r new_dir
$ ls

Output

filename2.txt

Tips for good names for files and directories

1. Don’t use spaces. Use - or _ or camelCase.

2. Don’t begin a name with a - (dash). It will look like a command option. Names should start with letters or numbers.

3. Avoid special characters. Some have special meanings.

Note

If you need to refer to names of files or directories that have spaces, put them in quotes (““).

What’s in a name?

A filename extension is the second part of the filename after the dot (.). They help us and programs tell different kinds of files apart. A few examples:

• .txt: plain text file

• .csv: comma separated value file

• .pdf: PDF document

• .cfg: configuration file of parameters for a program

• .png: an image file

The wildcard * matches zero or more characters. For example, to copy all text files in a directory, use cp *.txt DIR_NAME.

The wildcard ? matches exactly one character.

Which editor should I use?

nano is a built-in text editor that only works with plain character data (i.e. no tables, images, or other media). It is the least complex, but you may want to try more powerful editors.

For Unix Systems (Linux and macOS)

• Emacs

• Vim

• Gedit is a graphical editor

For Windows

• Notepad++

• notepad is built-in and can be run in the command line

Editor tips

If you start an editor from the shell, it will use your current working directory as its default location.

In editor commands, the Control key is also called Ctrl or ^.

Challenge Questions

(1) Moving files. We accidentally put the files sucrose.dat and maltose.dat into the wrong folder, analyzed/. Fill in the blanks to move these files into the raw/ folder.

Bash

$ ls -F
analyzed/  raw/
$ ls -F analyzed/
fructose.dat glucose.dat maltose.dat sucrose.dat
$ cd analyzed

My next line of code should be (fill in the blanks):

Bash

$ mv sucrose.dat matose.dat ___/___

Solution

Think about ../raw Recall that .. refers to the parent directory (i.e. one above the current directory).

(2) Renaming Files. We mispelled a filename! Which of the following commands will correct our mistake?

1. cp statstics.txt statistics.txt

2. mv statstics.txt statistics.txt

3. lmv statistics.txt .

4. cp statstics.txt .

Solution

1. Will copy the file, so we will end up with the mispelled and correct version.

2. Will move (i.e. rename) the incorrect file name to a correct filename.

3. Not a working command.

4. Will not work. Remember . is the current directory.

(3) Removal. What happens when we execute rm -i thesis/finaldraft.txt? Why would we want this protection when using rm?

Solution

The program will confirm that we want to delete the thesis final draft file. Remember, deletion is forever! There is no trash can or recycle bin.

(4) Removal. What is wrong with the command rm -i thesis?

Solution

The remove command will not act on a directory unless the recursive option -r is given.

(5) Removal. What is wrong with the command rm -r thesis?

Solution

This remove command will successfully delete the directory thesis and all its contents, but we forgot to check for confirmation with the interaction option (-i). Remember, deletion is permanent!

(6) Wildcards. Which of the following matches the file names ethane.dat and methane.dat?

1. ls ?ethane.dat

2. ls *ethane.dat

3. ls ???ane.dat

4. ls ethane.*

Hint

Remember the ? wildcard matches to exactly one character. The * wildcard can match to zero to many characters.

Solution

1. Matches methane.dat only (needs one character before ethane.dat).

2. Matches both, can have any number of characters (including zero) before ethane.dat.

3. Matches ethane.dat only (requires only 3 characters before ane.dat).

4. Matches ethane.dat only (requires no characters before ethane).

Challenge Project

Before heading on a trip, you want to back up your data and send some datasets to Ford. Fill in the following commands to get the job done. First, let’s set up a directory and files.

Bash

# Hashtag denotes a comment. The line will be skipped

# Change to your desktop
cd ~/Desktop

# Make a new folder for our fake data
mkdir fake_data
cd fake_data

# Create some empty files.
touch 2020-06-09-data.txt
touch 2020-06-09-calibration.txt

# Make sure the new files are created. Notice we can combine options)
ls -Fs

# Let's add some info to our file and confirm it with the editor (spoiler alert - redirects!)
echo Hello World > 2020-06-09-data.txt
nano 2020-06-09-data.txt

# Let's edit and add information to another.
nano 2020-06-09-calibration.txt

The next piece is provided in the shell script session2challenge.sh.

While in your fake_data directory, copy and paste the code from this file and run it.

Bash

# session2challenge.sh creates more fake data and callibration files

fmonth="2020-06"
echo $fmonth

# Loop through days to create data files and calibration files
for i in `seq -w 10 30`
do
   # Define the filename
   printf -v fname '%s-%02d-data.txt' "$fmonth" "$i"
   # Create an empty file
   touch "$fname"
   # Redirect in some data
   echo data $i > "$fname"

   printf -v fname '%s-%02d-calibration.txt' "$fmonth" "$i"
   touch "$fname"
   echo $i > "$fname"
done

Now, it’s your turn!

1. Create a backup directory with separate subdirectories for data and calibration files. Copy files to the appropriate locations.

2. Create a directory named send_to_ford and copy all the data from June 11th to it.

Hint

Create a backup directory with subdirectories for data and calibration files

• Hint: You will use mkdir

Bash

mkdir ___
mkdir ___/___
mkdir ___/___

Copy data files to backup/data. (Use a similiar approach for calibration files.)

• Hint: Use the copy command cp with wildcards

Bash

cp *-data.txt backup/___

Copy June 11th files to send_to_ford/.

• Hint: Use the copy command cp with wildcards!

Bash

cp *-11-*.txt send_to_ford/

Resources

This lesson is adapted from The Unix Shell on Software Carpentry.