Working With Files and Directories
OverviewTeaching: 30 min
Exercises: 20 minQuestions
How can I create, copy, and delete files and directories?
How can I edit files?Objectives
Create a directory hierarchy that matches a given diagram.
Create files in that hierarchy using an editor or by copying and renaming existing files.
Delete, copy and move specified files and/or directories.
We now know how to explore files and directories, but how do we create them in the first place?
In this episode we will learn about creating and moving files and directories,
exercise-data/writing directory as an example.
Step one: see where we are and what we already have
We should still be in the
shell-lesson-data directory on the Desktop,
which we can check using:
Next we’ll move to the
exercise-data/writing directory and see what it contains:
$ cd exercise-data/writing/
$ ls -F
Create a directory
Let’s create a new directory called
thesis using the command
(which has no output):
$ mkdir thesis
As you might guess from its name,
mkdir means ‘make directory’.
thesis is a relative path
(i.e., does not have a leading slash, like
the new directory is created in the current working directory:
$ ls -F
haiku.txt LittleWomen.txt thesis/
Since we’ve just created the
thesis directory, there’s nothing in it yet:
$ ls -F thesis
mkdir is not limited to creating single directories one at a time.
-p option allows
mkdir to create a directory with nested subdirectories
in a single operation:
$ mkdir -p ../project/data ../project/results
-R option to the
ls command will list all nested subdirectories within a directory.
ls -FR to recursively list the new directory hierarchy we just created in the
$ ls -FR ../project
../project/: data/ results/ ../project/data: ../project/results:
Two ways of doing the same thing
Using the shell to create a directory is no different than using a file explorer. If you open the current directory using your operating system’s graphical file explorer, the
thesisdirectory will appear there too. While the shell and the file explorer are two different ways of interacting with the files, the files and directories themselves are the same.
Good names for files and directories
Complicated names of files and directories can make your life painful when working on the command line. Here we provide a few useful tips for the names of your files and directories.
Don’t use spaces.
Spaces can make a name more meaningful, but since spaces are used to separate arguments on the command line it is better to avoid them in names of files and directories. You can use
north pacific gyre/). To test this out, try typing
mkdir north pacific gyreand see what directory (or directories!) are made when you check with
Don’t begin the name with
Commands treat names starting with
Stick with letters, numbers,
.(period or ‘full stop’),
Many other characters have special meanings on the command line. We will learn about some of these during this lesson. There are special characters that can cause your command to not work as expected and can even result in data loss.
If you need to refer to names of files or directories that have spaces or other special characters, you should surround the name in quotes (
Create a text file
Let’s change our working directory to
then run a text editor called Nano to create a file called
$ cd thesis $ nano draft.txt
When we say, ‘
nanois a text editor’ we really do mean ‘text’: it can only work with plain character data, not tables, images, or any other human-friendly media. We use it in examples because it is one of the least complex text editors. However, because of this trait, it may not be powerful enough or flexible enough for the work you need to do after this workshop. On Unix systems (such as Linux and macOS), many programmers use Emacs or Vim (both of which require more time to learn), or a graphical editor such as Gedit. On Windows, you may wish to use Notepad++. Windows also has a built-in editor called
notepadthat can be run from the command line in the same way as
nanofor the purposes of this lesson.
No matter what editor you use, you will need to know where it searches for and saves files. If you start it from the shell, it will (probably) use your current working directory as its default location. If you use your computer’s start menu, it may want to save files in your desktop or documents directory instead. You can change this by navigating to another directory the first time you ‘Save As…’
Let’s type in a few lines of text.
Once we’re happy with our text, we can press Ctrl+O
(press the Ctrl or Control key and, while
holding it down, press the O key) to write our data to disk
(we’ll be asked what file we want to save this to:
press Return to accept the suggested default of
Once our file is saved, we can use Ctrl+X to quit the editor and return to the shell.
Control, Ctrl, or ^ Key
The Control key is also called the ‘Ctrl’ key. There are various ways in which using the Control key may be described. For example, you may see an instruction to press the Control key and, while holding it down, press the X key, described as any of:
In nano, along the bottom of the screen you’ll see
^G Get Help ^O WriteOut. This means that you can use
Control-Gto get help and
Control-Oto save your file.
nano doesn’t leave any output on the screen after it exits,
ls now shows that we have created a file called
Creating Files a Different Way
We have seen how to create text files using the
nanoeditor. Now, try the following command:
$ touch my_file.txt
What did the
touchcommand do? When you look at your current directory using the GUI file explorer, does the file show up?
ls -lto inspect the files. How large is
When might you want to create a file this way?
touchcommand generates a new file called
my_file.txtin your current directory. You can observe this newly generated file by typing
lsat the command line prompt.
my_file.txtcan also be viewed in your GUI file explorer.
When you inspect the file with
ls -l, note that the size of
my_file.txtis 0 bytes. In other words, it contains no data. If you open
my_file.txtusing your text editor it is blank.
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.
To avoid confusion later on, we suggest removing the file you’ve just created before proceding with the rest of the episode, otherwise future outputs may vary from those given in the lesson. To do this, use the following command:
$ rm my_file.txt
What’s In A Name?
You may have noticed that all of Nelle’s files are named ‘something dot something’, and in this part of the lesson, we always used the extension
.txt. This is just a convention: we can call a file
mythesisor almost anything else we want. However, most people use two-part names most of the time to help them (and their programs) tell different kinds of files apart. The second part of such a name is called the filename extension and indicates what type of data the file holds:
.txtsignals a plain text file,
.cfgis a configuration file full of parameters for some program or other,
.pngis a PNG image, and so on.
This is just a convention, albeit an important one. Files contain bytes: it’s up to us and our programs to interpret those bytes according to the rules for plain text files, PDF documents, configuration files, images, and so on.
Naming a PNG image of a whale as
whale.mp3doesn’t somehow magically turn it into a recording of whale song, though it might cause the operating system to try to open it with a music player when someone double-clicks it.
Moving files and directories
Returning to the
$ cd ~/Desktop/shell-lesson-data/exercise-data/writing
thesis directory we have a file
which isn’t a particularly informative name,
so let’s change the file’s name using
which is short for ‘move’:
$ mv thesis/draft.txt thesis/quotes.txt
The first argument tells
mv what we’re ‘moving’,
while the second is where it’s to go.
In this case,
which has the same effect as renaming the file.
ls shows us that
thesis now contains one file called
$ ls thesis
One must be careful when specifying the target file name, since
silently overwrite any existing file with the same name, which could
lead to data loss. An additional option,
mv -i (or
can be used to make
mv ask you for confirmation before overwriting.
mv also works on directories.
quotes.txt into the current working directory.
mv once again,
but this time we’ll use just the name of a directory as the second argument
mv that we want to keep the filename
but put the file somewhere new.
(This is why the command is called ‘move’.)
In this case,
the directory name we use is the special directory name
. that we mentioned earlier.
$ mv thesis/quotes.txt .
The effect is to move the file from the directory it was in to the current working directory.
ls now shows us that
thesis is empty:
$ ls thesis
Alternatively, we can confirm the file
quotes.txt is no longer present in the
by explicitly trying to list it:
$ ls thesis/quotes.txt
ls: cannot access 'thesis/quotes.txt': No such file or directory
ls with a filename or directory as an argument only lists the requested file or directory.
If the file given as the argument doesn’t exist, the shell returns an error as we saw above.
We can use this to see that
quotes.txt is now present in our current directory:
$ ls quotes.txt
Moving Files to a new folder
After running the following commands, Jamie realizes that she put the files
maltose.datinto the wrong folder. The files should have been placed in the
$ ls -F analyzed/ raw/ $ ls -F analyzed fructose.dat glucose.dat maltose.dat sucrose.dat $ cd analyzed
Fill in the blanks to move these files to the
raw/folder (i.e. the one she forgot to put them in)
$ mv sucrose.dat maltose.dat ____/____
$ mv sucrose.dat maltose.dat ../raw
..refers to the parent directory (i.e. one above the current directory) and that
.refers to the current directory.
Copying files and directories
cp command works very much like
except it copies a file instead of moving it.
We can check that it did the right thing using
with two paths as arguments — like most Unix commands,
ls can be given multiple paths at once:
$ cp quotes.txt thesis/quotations.txt $ ls quotes.txt thesis/quotations.txt
We can also copy a directory and all its contents by using the
e.g. to back up a directory:
$ cp -r thesis thesis_backup
We can check the result by listing the contents of both the
$ ls thesis thesis_backup
thesis: quotations.txt thesis_backup: quotations.txt
Suppose that you created a plain-text 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:
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?
cp statstics.txt statistics.txt
mv statstics.txt statistics.txt
mv statstics.txt .
cp statstics.txt .
- 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.
- Yes, this would work to rename the file.
- No, the period(.) indicates where to move the file, but does not provide a new file name; identical file names cannot be created.
- 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
lscommand in the sequence shown below?
$ mkdir recombined $ mv proteins.dat recombined/ $ cp recombined/proteins.dat ../proteins-saved.dat $ ls
We start in the
/Users/jamie/datadirectory, and create a new folder called
recombined. The second line moves (
mv) the file
proteins.datto the new folder (
recombined). 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 recombined folder.
- No, see explanation above.
proteins-saved.datis located at
- No, see explanation above.
proteins.datis located at
- No, see explanation above.
proteins-saved.datis located at
Removing files and directories
Returning to the
let’s tidy up this directory by removing the
quotes.txt file we created.
The Unix command we’ll use for this is
rm (short for ‘remove’):
$ rm quotes.txt
We can confirm the file has gone using
$ ls quotes.txt
ls: cannot access 'quotes.txt': No such file or directory
Deleting Is Forever
The Unix shell doesn’t have a trash bin that we can recover deleted files from (though most graphical interfaces to Unix do). Instead, when we delete files, they are unlinked from the file system so that their storage space on disk can be recycled. Tools for finding and recovering deleted files do exist, but there’s no guarantee they’ll work in any particular situation, since the computer may recycle the file’s disk space right away.
What happens when we execute
rm -i thesis_backup/quotations.txt? Why would we want this protection when using
rm: remove regular file 'thesis_backup/quotations.txt'? y
-ioption will prompt before (every) removal (use Y to confirm deletion or N to keep the file). The Unix shell doesn’t have a trash bin, so all the files removed will disappear forever. By using the
-ioption, we have the chance to check that we are deleting only the files that we want to remove.
If we try to remove the
thesis directory using
we get an error message:
$ rm thesis
rm: cannot remove `thesis': Is a directory
This happens because
rm by default only works on files, not directories.
rm can remove a directory and all its contents if we use the
-r, and it will do so without any confirmation prompts:
$ rm -r thesis
Given that there is no way to retrieve files deleted using the shell,
rm -r should be used with great caution
(you might consider adding the interactive option
rm -r -i).
Operations with multiple files and directories
Oftentimes one needs to copy or move several files at once. This can be done by providing a list of individual filenames, or specifying a naming pattern using wildcards.
Copy with Multiple Filenames
For this exercise, you can test the commands in the
In the example below, what does
cpdo when given several filenames and a directory name?
$ mkdir backup $ cp creatures/minotaur.dat creatures/unicorn.dat backup/
In the example below, what does
cpdo when given three or more file names?
$ cd creatures $ ls -F
basilisk.dat minotaur.dat unicorn.dat
$ cp minotaur.dat unicorn.dat basilisk.dat
If given more than one file name followed by a directory name (i.e. the destination directory must be the last argument),
cpcopies the files to the named directory.
If given three file names,
cpthrows an error such as the one below, because it is expecting a directory name as the last argument.
cp: target 'basilisk.dat' is not a directory
Using wildcards for accessing multiple files at once
*is a wildcard, which matches zero or more characters. Let’s consider the
propane.pdb, and every file that ends with ‘.pdb’. On the other hand,
propane.pdb, because the ‘p’ at the front only matches filenames that begin with the letter ‘p’.
?is also a wildcard, but it matches exactly one character. So
Wildcards can be used in combination with each other e.g.
???ane.pdbmatches three characters followed by
cubane.pdb ethane.pdb octane.pdb.
When the shell sees a wildcard, it expands the wildcard to create a list of matching filenames before running the command that was asked for. As an exception, if a wildcard expression does not match any file, Bash will pass the expression as an argument to the command as it is. For example, typing
ls *.pdfin the
proteinsdirectory (which contains only files with names ending with
.pdb) results in an error message that there is no file called
lssee the lists of file names matching these expressions, but not the wildcards themselves. It is the shell, not the other programs, that deals with expanding wildcards.
List filenames matching a pattern
When run in the
lscommand(s) will produce this output?
The solution is
1.shows all files whose names contain zero or more characters (
*) followed by the letter
t, then zero or more characters (
*) followed by
ane.pdb. This gives
ethane.pdb methane.pdb octane.pdb pentane.pdb.
2.shows all files whose names start with zero or more characters (
*) followed by the letter
t, then a single character (
ne.followed by zero or more characters (
*). This will give us
pentane.pdbbut doesn’t match anything which ends in
3.fixes the problems of option 2 by matching two characters (
ne. This is the solution.
4.only shows files starting with
More on Wildcards
Sam has a directory containing calibration data, datasets, and descriptions of the datasets:
. ├── 2015-10-23-calibration.txt ├── 2015-10-23-dataset1.txt ├── 2015-10-23-dataset2.txt ├── 2015-10-23-dataset_overview.txt ├── 2015-10-26-calibration.txt ├── 2015-10-26-dataset1.txt ├── 2015-10-26-dataset2.txt ├── 2015-10-26-dataset_overview.txt ├── 2015-11-23-calibration.txt ├── 2015-11-23-dataset1.txt ├── 2015-11-23-dataset2.txt ├── 2015-11-23-dataset_overview.txt ├── backup │ ├── calibration │ └── datasets └── send_to_bob ├── all_datasets_created_on_a_23rd └── all_november_files
Before heading off to another field trip, she wants to back up her data and send some datasets to her colleague Bob. Sam uses the following commands to get the job done:
$ cp *dataset* backup/datasets $ cp ____calibration____ backup/calibration $ cp 2015-____-____ send_to_bob/all_november_files/ $ cp ____ send_to_bob/all_datasets_created_on_a_23rd/
Help Sam by filling in the blanks.
The resulting directory structure should look like this
. ├── 2015-10-23-calibration.txt ├── 2015-10-23-dataset1.txt ├── 2015-10-23-dataset2.txt ├── 2015-10-23-dataset_overview.txt ├── 2015-10-26-calibration.txt ├── 2015-10-26-dataset1.txt ├── 2015-10-26-dataset2.txt ├── 2015-10-26-dataset_overview.txt ├── 2015-11-23-calibration.txt ├── 2015-11-23-dataset1.txt ├── 2015-11-23-dataset2.txt ├── 2015-11-23-dataset_overview.txt ├── backup │ ├── calibration │ │ ├── 2015-10-23-calibration.txt │ │ ├── 2015-10-26-calibration.txt │ │ └── 2015-11-23-calibration.txt │ └── datasets │ ├── 2015-10-23-dataset1.txt │ ├── 2015-10-23-dataset2.txt │ ├── 2015-10-23-dataset_overview.txt │ ├── 2015-10-26-dataset1.txt │ ├── 2015-10-26-dataset2.txt │ ├── 2015-10-26-dataset_overview.txt │ ├── 2015-11-23-dataset1.txt │ ├── 2015-11-23-dataset2.txt │ └── 2015-11-23-dataset_overview.txt └── send_to_bob ├── all_datasets_created_on_a_23rd │ ├── 2015-10-23-dataset1.txt │ ├── 2015-10-23-dataset2.txt │ ├── 2015-10-23-dataset_overview.txt │ ├── 2015-11-23-dataset1.txt │ ├── 2015-11-23-dataset2.txt │ └── 2015-11-23-dataset_overview.txt └── all_november_files ├── 2015-11-23-calibration.txt ├── 2015-11-23-dataset1.txt ├── 2015-11-23-dataset2.txt └── 2015-11-23-dataset_overview.txt
$ cp *calibration.txt backup/calibration $ cp 2015-11-* send_to_bob/all_november_files/ $ cp *-23-dataset* send_to_bob/all_datasets_created_on_a_23rd/
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
sucrose.datfiles 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
$ ls analyzed
mv *.dat analyzed
Jamie needs to move her files
analyzeddirectory. The shell will expand *.dat to match all .dat files in the current directory. The
mvcommand then moves the list of .dat files to the ‘analyzed’ directory.
Reproduce a folder structure
You’re starting a new experiment and would like to duplicate the directory structure from your previous experiment so you can add new data.
Assume that the previous experiment is in a folder called
2016-05-18, which contains a
datafolder that in turn contains folders named
processedthat contain data files. The goal is to copy the folder structure of the
2016-05-18folder into a folder called
2016-05-20so that your final directory structure looks like this:
2016-05-20/ └── data ├── processed └── raw
Which of the following set of commands would achieve this objective? What would the other commands do?
$ mkdir 2016-05-20 $ mkdir 2016-05-20/data $ mkdir 2016-05-20/data/processed $ mkdir 2016-05-20/data/raw
$ mkdir 2016-05-20 $ cd 2016-05-20 $ mkdir data $ cd data $ mkdir raw processed
$ mkdir 2016-05-20/data/raw $ mkdir 2016-05-20/data/processed
$ mkdir -p 2016-05-20/data/raw $ mkdir -p 2016-05-20/data/processed
$ mkdir 2016-05-20 $ cd 2016-05-20 $ mkdir data $ mkdir raw processed
The first two sets of commands achieve this objective. The first set uses relative paths to create the top-level directory before the subdirectories.
The third set of commands will give an error because the default behavior of
mkdirwon’t create a subdirectory of a non-existent directory: the intermediate level folders must be created first.
The fourth set of commands achieve this objective. Remember, the
-poption, followed by a path of one or more directories, will cause
mkdirto create any intermediate subdirectories as required.
The final set of commands generates the ‘raw’ and ‘processed’ directories at the same level as the ‘data’ directory.
cp [old] [new]copies a file.
mkdir [path]creates a new directory.
mv [old] [new]moves (renames) a file or directory.
rm [path]removes (deletes) a file.
*matches zero or more characters in a filename, so
*.txtmatches all files ending in
?matches any single character in a filename, so
Use of the Control key may be described in many ways, including
The shell does not have a trash bin: once something is deleted, it’s really gone.
Most files’ names are
something.extension. The extension isn’t required, and doesn’t guarantee anything, but is normally used to indicate the type of data in the file.
Depending on the type of work you do, you may need a more powerful text editor than Nano.