The Unix Shell

Working With Files and Directories

We now know how to explore files and directories, but how do we create them in the first place? Let’s go back to our data-shell directory on the Desktop and use ls -F to see what it contains:

$ pwd

/Users/nelle/Desktop/data-shell

$ ls -F

creatures/  molecules/           pizza.cfg
data/       north-pacific-gyre/  solar.pdf
Desktop/    notes.txt            writing/

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

$ mkdir thesis

As you might guess from its name, mkdir means “make directory”. Since thesis is a relative path (i.e., doesn’t have a leading slash), the new directory is created in the current working directory:

$ ls -F

creatures/  north-pacific-gyre/  thesis/
data/       notes.txt            writing/
Desktop/    pizza.cfg
molecules/  solar.pdf

However, there’s nothing in it yet:

$ ls -F thesis

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

$ cd thesis
$ nano draft.txt

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 draft.txt).

Nano in action

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:

$ ls

draft.txt

Let’s tidy up by running rm draft.txt:

$ rm draft.txt

This command removes files (rm is short for “remove”). If we run ls again, its output is empty once more, which tells us that our file is gone:

$ ls

Let’s re-create that file and then move up one directory to /Users/nelle using cd ..:

$ pwd

/Users/nelle/thesis

$ nano draft.txt
$ ls

draft.txt

$ cd ..

If we try to remove the entire thesis directory using rm thesis, 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.

To really get rid of thesis we must also delete the file draft.txt. We can do this with the recursive option for rm:

$ rm -r thesis

Let’s create that directory and file one more time. (Note that this time we’re running nano with the path thesis/draft.txt, rather than going into the thesis directory and running nano on draft.txt there.)

$ pwd

/Users/nelle

$ mkdir thesis

$ nano thesis/draft.txt
$ ls thesis

draft.txt

draft.txt isn’t a particularly informative name, so let’s change the file’s name using mv, which is short for “move”:

$ mv thesis/draft.txt thesis/quotes.txt

The first parameter 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 thesis

quotes.txt

One has to 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 flag, mv -i (or mv --interactive), can be used to make mv ask you for confirmation before overwriting.

Just for the sake of inconsistency, mv also works on directories — there is no separate mvdir command.

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

$ 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

Further, ls with a filename or directory name as a parameter only lists that file or directory. We can use this to see that quotes.txt is still in our current directory:

$ ls quotes.txt

quotes.txt

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 parameters — like most Unix commands, ls can be given thousands of paths at once:

$ cp quotes.txt thesis/quotations.txt
$ ls quotes.txt thesis/quotations.txt

quotes.txt   thesis/quotations.txt

To prove that we made a copy, let’s delete the quotes.txt file in the current directory and then run that same ls again.

$ rm quotes.txt
$ ls quotes.txt thesis/quotations.txt

ls: cannot access quotes.txt: No such file or directory
thesis/quotations.txt

This time it tells us that it can’t find quotes.txt in the current directory, but it does find the copy in thesis that we didn’t delete.

$ pwd
/Users/jamie/data
$ ls
proteins.dat
$ mkdir recombine
$ mv proteins.dat recombine
$ cp recombine/proteins.dat ../proteins-saved.dat
$ ls

$ ls -F
analyzed/  fructose.dat    raw/   sucrose.dat

$ ls -F
analyzed/   raw/
$ ls analyzed
fructose.dat    sucrose.dat

$ mkdir backup
$ cp thesis/citations.txt thesis/quotations.txt backup

$ ls -F
intro.txt    methods.txt    survey.txt
$ cp intro.txt methods.txt survey.txt

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

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