Working With Files and Directories
Overview
Teaching: 30 min
Exercises: 20 minQuestions
How can I create, copy, and delete files and directories?
Objectives
Create a directory hierarchy that matches a given diagram.
Create files in that hierarchy 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?
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
data/ fig_11_10.csv humphrey_keeble_1976.pdf
fig_11_01.csv finches_01.jpg lab_notes/
fig_11_02.csv finches_02.jpg lab_notes.zip
fig_11_03.csv finches_03.jpg loewenberg_1965.pdf
fig_11_04.csv finches_04.jpg oldroyd_1984.pdf
fig_11_05.csv greenleaf_et_al_1998.pdf olsen_2017.pdf
fig_11_07.csv habitat_01.jpg readme for fig files.txt
fig_11_08.csv habitat_02.jpg van_leeuwen_2002.pdf
fig_11_09.csv habitat_03.jpg
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
data/ fig_11_10.csv humphrey_keeble_1976.pdf
fig_11_01.csv finches_01.jpg lab_notes/
fig_11_02.csv finches_02.jpg lab_notes.zip
fig_11_03.csv finches_03.jpg loewenberg_1965.pdf
fig_11_04.csv finches_04.jpg oldroyd_1984.pdf
fig_11_05.csv greenleaf_et_al_1998.pdf olsen_2017.pdf
fig_11_07.csv habitat_01.jpg readme for fig files.txt
fig_11_08.csv habitat_02.jpg thesis/
fig_11_09.csv habitat_03.jpg van_leeuwen_2002.pdf
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 they 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.
Don’t use whitespaces.
Whitespaces can make a name more meaningful but since whitespace is used to break arguments on the command line it is better to avoid them in names of files and directories. You can use
-
or_
instead of whitespace.Don’t begin the name with
-
(dash).Commands treat names starting with
-
as options.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 whitespace or another non-alphanumeric character, you should surround the name in quotes (
""
).
Since we’ve just created the thesis
directory, there’s nothing in it yet:
$ ls -F thesis
Let’s change our working directory to thesis
using cd
,
then use the touch
command to create a file called draft.txt
:
$ cd thesis
$ touch draft.txt
Returning to the data-shell
directory,
let’s tidy up the thesis
directory by removing the draft we created:
$ cd thesis
$ 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
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 unhooked 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.
Let’s re-create that file
and then move up one directory to /Users/nelle/Desktop/data-shell
using cd ..
:
$ pwd
/Users/nelle/Desktop/data-shell/thesis
$ touch 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
Using
rm
SafelyWhat happens when we type
rm -i thesis/quotations.txt
? Why would we want this protection when usingrm
?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.
With Great Power Comes Great Responsibility
Removing the files in a directory recursively can be a very dangerous operation. If we’re concerned about what we might be deleting we can add the “interactive” flag
-i
torm
which will ask us for confirmation before each step$ rm -r -i thesis rm: descend into directory ‘thesis’? y rm: remove regular file ‘thesis/draft.txt’? y rm: remove directory ‘thesis’? y
This removes everything in the directory, then the directory itself, asking at each step for you to confirm the deletion.
Let’s create that directory and file one more time.
(Note that this time we’re running touch
with the path thesis/draft.txt
,
rather than going into the thesis
directory and running touch
on draft.txt
there.)
$ pwd
/Users/nelle/Desktop/data-shell
$ mkdir thesis
$ touch 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 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 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 consistency,
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 just use 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.
$ 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 an argument 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
Moving to the Current Folder
After running the following commands, Jamie realizes that she put the files
sucrose.dat
andmaltose.dat
into the wrong folder:$ ls -F analyzed/ raw/ $ 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.
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:
$ 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.
What’s In A Name?
You may have noticed that all of Nelle’s files’ names are “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 filemythesis
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,.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 whalesong, though it might cause the operating system to try to open it with a music player when someone double-clicks it.
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?
cp statstics.txt statistics.txt
mv statstics.txt statistics.txt
mv statstics.txt .
cp statstics.txt .
Solution
- 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
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
proteins-saved.dat recombine
recombine
proteins.dat recombine
proteins-saved.dat
Solution
We start in the
/Users/jamie/data
directory, and create a new folder calledrecombine
. The second line moves (mv
) the fileproteins.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.
- No, see explanation above.
proteins-saved.dat
is located at/Users/jamie
- Yes
- No, see explanation above.
proteins.dat
is located at/Users/jamie/data/recombine
- No, see explanation above.
proteins-saved.dat
is located at/Users/jamie
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
Wildcards
*
is a wildcard. It matches zero or more characters, so*.pdb
matchesethane.pdb
,propane.pdb
, and every file that ends with ‘.pdb’. On the other hand,p*.pdb
only matchespentane.pdb
andpropane.pdb
, because the ‘p’ at the front only matches filenames that begin with the letter ‘p’.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 themolecules
directory (which contains only files with names ending with.pdb
) results in an error message that there is no file calledwc
andls
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, and this is another example of orthogonal design.
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
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.
Solution
$ 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
The
fructose.dat
andsucrose.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
andsucrose.dat
to theanalyzed
directory. The shell will expand *.dat to match all .dat files in the current directory. Themv
command then moves the list of .dat files to the “analyzed” 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.The shell does not have a trash bin: once something is deleted, it’s really gone.