eResearch - Working with Files and Directories

Owned by Roberto Barrero Gumiel
Oct 05, 2023
15 min read

Overview

Questions

  • 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.

Creating 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, using the 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 in our home folder, which we can check using:

pwd
/home/username/shell-lesson-data

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 mkdir thesis (which has no output):

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:

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

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:

The -R option to the ls command will list all nested subdirectories within a directory. Let’s use ls -FR to recursively list the new directory hierarchy we just created in the project directory:

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 gyre and see what directory (or directories!) are made when you check with ls -F.

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

Commands treat names starting with - as options.

  1. 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 ("").

Create 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, before we can use Nano, we need to activate it with the module command:

(Details of the module command is covered later)

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 or VScode. 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 will be asked to provide a name for the file that will contain our text. Press Return to accept the suggested default of draft.txt.

Once our file is saved, we can use Ctrl+X to quit the editor and return to the shell.

nano doesn’t leave any output on the screen after it exits, but ls now shows that we have created a file called draft.txt:

  1. The touch command generates a new file called my_file.txt in your current 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 0 bytes. 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 files and Directories

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

In our thesis directory we have a file draft.txt which isn’t a particularly informative name, so let’s change the file’s name using mv, which is short for ‘move’:

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:

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. By default, mv will not ask for confirmation before overwriting files. However, an additional option, mv -i (or mv --interactive), will cause mv to request such confirmation.

Note that mv also works on directories.

Let’s move quotes.txt into the current working directory. We use mv once again, but this time we’ll use just the name of a directory as the second argument to tell 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.

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:

Alternatively, we can confirm the file quotes.txt is no longer present in the thesis directory by explicitly trying to list it:

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:

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

Copying files and directories

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 with two paths as arguments — like most Unix commands, ls can be given multiple paths at once:

We can also copy a directory and all its contents by using the recursive option -r, e.g. to back up a directory:

We can check the result by listing the contents of both the thesis and thesis_backup directory:

It is important to include the -r flag. If you want to copy a directory and you omit this option you will see a message that the directory has been omitted because -r not specified.

  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.

We start in the /Users/jamie/data directory, and create a new folder called recombined. The second line moves (mv) the file proteins.dat to 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.

  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/recombined

  4. No, see explanation above. proteins-saved.dat is located at /Users/jamie

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’):

We can confirm the file has gone using ls:

The -i option 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 -i option, 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 rm thesis, we get an error message:

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:

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. Wildcards are special characters that can be used to represent unknown characters or sets of characters when navigating the Unix file system.

Using wildcards for accessing multiple files at once