Working With Files and Directories

Overview

Teaching: 15 min
Exercises: 0 min

Questions

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

• How can I edit files?

Objectives

Renaming Files

Suppose that you created a .txt file in your current directory to contain a list of the statistical tests you will need to do to analyze your data, and named it: statstics.txt

After creating and saving this file you realize you misspelled the filename! You want to correct the mistake, which of the following commands could you use to do so?

1. cp statstics.txt statistics.txt
2. mv statstics.txt statistics.txt
3. mv statstics.txt .
4. cp statstics.txt .

Solution

1. No. While this would create a file with the correct name, the incorrectly named file still exists in the directory and would need to be deleted.
2. Yes, this would work to rename the file.
3. No, the period(.) indicates where to move the file, but does not provide a new file name; identical file names cannot be created.
4. No, the period(.) indicates where to copy the file, but does not provide a new file name; identical file names cannot be created.

Moving and Copying

What is the output of the closing ls command in the sequence shown below?

$ pwd

/Users/jamie/data

$ ls

proteins.dat

$ mkdir recombine
$ mv proteins.dat recombine
$ cp recombine/proteins.dat ../proteins-saved.dat
$ ls

1. proteins-saved.dat recombine
2. recombine
3. proteins.dat recombine
4. proteins-saved.dat

Solution

We start in the /Users/jamie/data directory, and create a new folder called recombine. The second line moves (mv) the file proteins.dat to the new folder (recombine). The third line makes a copy of the file we just moved. The tricky part here is where the file was copied to. Recall that .. means “go up a level”, so the copied file is now in /Users/jamie. Notice that .. is interpreted with respect to the current working directory, not with respect to the location of the file being copied. So, the only thing that will show using ls (in /Users/jamie/data) is the recombine folder.

1. No, see explanation above. proteins-saved.dat is located at /Users/jamie
2. Yes
3. No, see explanation above. proteins.dat is located at /Users/jamie/data/recombine
4. No, see explanation above. proteins-saved.dat is located at /Users/jamie

Organizing Directories and Files

Jamie is working on a project and she sees that her files aren’t very well organized:

$ ls -F

analyzed/  fructose.dat    raw/   sucrose.dat

The fructose.dat and sucrose.dat files contain output from her data analysis. What command(s) covered in this lesson does she need to run so that the commands below will produce the output shown?

$ ls -F

analyzed/   raw/

$ ls analyzed

fructose.dat    sucrose.dat

Solution

mv *.dat analyzed

Jamie needs to move her files fructose.dat and sucrose.dat to the analyzed directory. The shell will expand *.dat to match all .dat files in the current directory. The mv command then moves the list of .dat files to the “analyzed” directory.

Copy with Multiple Filenames

For this exercise, you can test the commands in the data-shell/data directory.

In the example below, what does cp do when given several filenames and a directory name?

$ mkdir backup
$ cp amino-acids.txt animals.txt backup/

In the example below, what does cp do when given three or more file names?

$ ls -F

amino-acids.txt  animals.txt  backup/  elements/  morse.txt  pdb/  planets.txt  salmon.txt  sunspot.txt

$ cp amino-acids.txt animals.txt morse.txt

Solution

If given more than one file name followed by a directory name (i.e. the destination directory must be the last argument), cp copies the files to the named directory.

If given three file names, cp throws an error because it is expecting a directory name as the last argument.

cp: target ‘morse.txt’ is not a directory

Listing Recursively and By Time

The command ls -R lists the contents of directories recursively, i.e., lists their sub-directories, sub-sub-directories, and so on in alphabetical order at each level. The command ls -t lists things by time of last change, with most recently changed files or directories first. In what order does ls -R -t display things?

Solution

The command ls -R -t displays the directories recursively in chronological order at each level, and the files in each directory are displayed chronologically.

Creating Files a Different Way

We have seen how to create text files using the nano editor. Now, try the following command in your home directory:

$ cd                  # go to your home directory
$ touch my_file.txt

1. What did the touch command do? When you look at your home directory using the GUI file explorer, does the file show up?

2. Use ls -l to inspect the files. How large is my_file.txt?

3. When might you want to create a file this way?

Solution

1. The touch command generates a new file called ‘my_file.txt’ in your home directory. If you are in your home directory, you can observe this newly generated file by typing ‘ls’ at the command line prompt. ‘my_file.txt’ can also be viewed in your GUI file explorer.

2. When you inspect the file with ‘ls -l’, note that the size of ‘my_file.txt’ is 0kb. In other words, it contains no data. If you open ‘my_file.txt’ using your text editor it is blank.

3. Some programs do not generate output files themselves, but instead require that empty files have already been generated. When the program is run, it searches for an existing file to populate with its output. The touch command allows you to efficiently generate a blank text file to be used by such programs.

Moving to the Current Folder

After running the following commands, Jamie realizes that she put the files sucrose.dat and maltose.dat into the wrong folder:

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

Fill in the blanks to move these files to the current folder (i.e., the one she is currently in):

$ mv ___/sucrose.dat  ___/maltose.dat ___

Solution

$ mv ../analyzed/sucrose.dat ../analyzed/maltose.dat .

Recall that .. refers to the parent directory (i.e. one above the current directory) and that . refers to the current directory.

Using rm Safely

What happens when we type rm -i thesis/quotations.txt? Why would we want this protection when using rm?

Solution

$ rm: remove regular file 'thesis/quotations.txt'?

The -i option will prompt before every removal. The Unix shell doesn’t have a trash bin, so all the files removed will disappear forever. By using the -i flag, we have the chance to check that we are deleting only the files that we want to remove.

Copy a folder structure sans files

You’re starting a new experiment, and would like to duplicate the file structure from your previous experiment without the data files so you can add new data.

Assume that the file structure is in a folder called ‘2016-05-18-data’, which contains folders named ‘raw’ and ‘processed’ that contain data files. The goal is to copy the file structure of the 2016-05-18-data folder into a folder called 2016-05-20-data and remove the data files from the directory you just created.

Which of the following set of commands would achieve this objective? What would the other commands do?

$ cp -r 2016-05-18-data/ 2016-05-20-data/
$ rm 2016-05-20-data/raw/*
$ rm 2016-05-20-data/processed/*

$ rm 2016-05-20-data/raw/*
$ rm 2016-05-20-data/processed/*
$ cp -r 2016-05-18-data/ 2016-5-20-data/

$ cp -r 2016-05-18-data/ 2016-05-20-data/
$ rm -r -i 2016-05-20-data/

Solution

The first set of commands achieves this objective. First we have a recursive copy of a data folder. Then two rm commands which remove all files in the specified directories. The shell expands the ‘*’ wild card to match all files and subdirectories.

The second set of commands have the wrong order: attempting to delete files which haven’t yet been copied, followed by the recursive copy command which would copy them.

The third set of commands would achieve the objective, but in a time-consuming way: the first command copies the directory recursively, but the second command deletes interactively, prompting for confirmation for each file and directory.

Key Points