Working With Files and Directories (aka Organization)


Teaching: 15 min
Exercises: 5 min
  • cp, mkdir, mv, nano, rm, and rmdir

  • 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.

Creating directories

We now know how to explore files and directories, but how do we create them in the first place?

We should still be in the shell-lesson-data/north-pacific-gyre directory on the Desktop, which we can check using:

$ pwd

If necessary, navigate there with a command like the following:

$ cd ~/Desktop/shell-lesson-data/north-pacific-gyre

Since we created some files, this directory is now a mixture of raw data, summary data, and scripts.

$ ls 
NENE01729A.txt		NENE01843B.txt		NENE02043A.txt
NENE01729B.txt		NENE01971Z.txt		NENE02043B.txt
NENE01736A.txt		NENE01978A.txt
NENE01751A.txt		NENE01978B.txt
NENE01751B.txt		NENE02040A.txt		lengths.txt
NENE01812A.txt		NENE02040B.txt		sorted-lengths.txt
NENE01843A.txt		NENE02040Z.txt

Create a directory

Let’s create a new directory called results using the command mkdir results (which has no output):

$ mkdir results

As you might guess from its name, mkdir means ‘make directory’. Since thesis is a relative path (i.e., does not have a leading slash, like /what/ever/thesis), the new directory is created in the current working directory:

$ ls -F
NENE01729A.txt		NENE01843B.txt		NENE02043A.txt
NENE01729B.txt		NENE01971Z.txt		NENE02043B.txt
NENE01736A.txt		NENE01978A.txt
NENE01751A.txt		NENE01978B.txt
NENE01751B.txt		NENE02040A.txt		lengths.txt
NENE01812A.txt		NENE02040B.txt		results/
NENE01843A.txt		NENE02040Z.txt		sorted-lengths.txt

Since we’ve just created the results directory, there’s nothing in it yet:

$ ls -F results

Note that mkdir is not limited to creating single directories one at a time. The -p option allows mkdir to create a directory with nested subdirectories in a single operation:

$ mkdir -p results/lengths/2022-07/

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 thesis directory 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.

  1. 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 - or _ instead (e.g. north-pacific-gyre/ rather than north pacific gyre/). To test this out, try typing mkdir north pacific gyreand see what directory (or directories!) are made when you check with ls -F.

  2. Don’t begin the name with - (dash).

    Commands treat names starting with - as options.

  3. Stick with letters, numbers, . (period or ‘full stop’), - (dash) and _ (underscore).

    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 ("").

Open a text file

Let’s change our working directory to thesis using cd, then run a text editor called Nano to create a file called draft.txt:

$ nano sorted-lengths.txt

Which Editor?

When we say, ‘nano is 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 notepad that can be run from the command line in the same way as nano for 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 sorted-lengths.txt).

screenshot of nano text editor in action

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:

  • Control-X
  • Control+X
  • Ctrl-X
  • Ctrl+X
  • ^X
  • C-x

In nano, along the bottom of the screen you’ll see ^G Get Help ^O WriteOut. This means that you can use Control-G to get help and Control-O to save your file.

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 mythesis or 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: .txt signals a plain text file, .pdf indicates a PDF document, .cfg is a configuration file full of parameters for some program or other, .png is 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.mp3 doesn’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

We can use the mv command to move files from the working directory to the results directory.

$ mv lengths.txt results
$ mv sorted-lengths.txt results

The first argument tells mv what we’re ‘moving’, while the second is where it’s to go. In this case, we’re moving thesis/draft.txt to thesis/quotes.txt, which has the same effect as renaming the file. Sure enough, ls shows us that thesis now contains one file called quotes.txt:

$ ls results
lengths.txt		sorted-lengths.txt

One must be careful when specifying the target file name, since mv will silently overwrite any existing file with the same name, which could lead to data loss. An additional option, mv -i (or mv --interactive), can be used to make mv ask you for confirmation before overwriting.

Note that mv also works on directories.

Copying files and directories

It is good practice to save a copy of your raw data. This ensures that data can be recovered if lost or modified.

The cp command works very much like mv, except it copies a file instead of moving it. We can check that it did the right thing using ls. Let’s make a directory called raw-data and copy all the NENE*txt files there.

$ mkdir raw-data
$ cp NENE*txt raw-data
$ ls raw-data
NENE01729A.txt	NENE01751B.txt	NENE01971Z.txt	NENE02040B.txt
NENE01729B.txt	NENE01812A.txt	NENE01978A.txt	NENE02040Z.txt
NENE01736A.txt	NENE01843A.txt	NENE01978B.txt	NENE02043A.txt
NENE01751A.txt	NENE01843B.txt	NENE02040A.txt	NENE02043B.txt

Renaming Files

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: 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 .


  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.

Removing files and directories

Returning to the shell-lesson-data/exercise-data/writing directory, 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 NENE02040Z.txt

We can confirm the file has gone using ls:

$ ls NENE02040Z.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.

If we try to remove the thesis directory using rm thesis, we get an error message:

$ rm results
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 recursive option -r, and it will do so without any confirmation prompts:

$ rm -r results

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 shell-lesson-data/exercise-data directory.

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

$ mkdir backup
$ cp creatures/minotaur.dat creatures/unicorn.dat backup/

In the example below, what does cp do 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), cp copies the files to the named directory.

If given three file names, cp throws 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 shell-lesson-data/exercise-data/proteins directory: *.pdb matches ethane.pdb, propane.pdb, and every file that ends with ‘.pdb’. On the other hand, p*.pdb only matches pentane.pdb and 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 ?ethane.pdb would match methane.pdb whereas *ethane.pdb matches both ethane.pdb, and methane.pdb.

Wildcards can be used in combination with each other e.g. ???ane.pdb matches three characters followed by ane.pdb, giving 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 *.pdf in the proteins directory (which contains only files with names ending with .pdb) results in an error message that there is no file called *.pdf. However, generally commands like wc and ls see 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 proteins directory, which ls command(s) will produce this output?

ethane.pdb methane.pdb

  1. ls *t*ane.pdb
  2. ls *t?ne.*
  3. ls *t??ne.pdb
  4. ls ethane.*


The solution is 3.

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 (?), then ne. followed by zero or more characters (*). This will give us octane.pdb and pentane.pdb but doesn’t match anything which ends in thane.pdb.

3. fixes the problems of option 2 by matching two characters (??) between t and ne. This is the solution.

4. only shows files starting with ethane..

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/

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 data folder that in turn contains folders named raw and processed that contain data files. The goal is to copy the folder structure of the 2016-05-18 folder into a folder called 2016-05-20 so that your final directory structure looks like this:

└── 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 mkdir won’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 -p option, followed by a path of one or more directories, will cause mkdir to 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.

Key Points

  • 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 *.txt matches all files ending in .txt.

  • ? matches any single character in a filename, so ?.txt matches a.txt but not any.txt.

  • Use of the Control key may be described in many ways, including Ctrl-X, Control-X, and ^X.

  • 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.