# Working With Files and Directories

## Overview

Teaching: 15 min
Exercises: 0 min
Questions
• How can I create, copy, and delete files and directories?

• How can I edit files?

Objectives
• Create files in that hierarchy using an editor or by copying and renaming existing files.

• Display the contents of a directory using the command line.

• Delete specified files and/or directories.

Directories are created with the mkdir (“make directory”) command. Let’s create a new directory called thesis in our home directory, using the command mkdir thesis (which has no output):

$cd$ mkdir thesis


Since thesis is a relative path (i.e., doesn’t have a leading slash), the new directory is created in the current working directory. If you type ls, you should see it listed.

## Good Names for Files and Directories

Complicated names of files and directories can make your life very painful when working on the command line. Here we provide a few useful tips for the names of your files from now on.

1. Don’t use whitespaces.

White spaces can make a name more meaningful but since whitespace is used to break arguments on the command line is better to avoid them on name of files and directories. You can use - or _ instead of whitespace.

Commands treat names starting with - as options.

2. Stay with letters, numbers, ., - and _.

3. Don’t begin the name with -.

If you need to refer to names of files or directories that have whitespace or another non-alphanumeric character you should put quotes around the name.

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  ## 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 almost anyone can drive it anywhere without training, but please use something more powerful for real work. On Unix systems (such as Linux and Mac OS X), many programmers use Emacs or Vim (both of which are completely unintuitive, even by Unix standards), 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 draft.txt). 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 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. 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


## Deleting Is Forever

The Linux shell doesn’t have a trash bin that we can recover deleted files from (though most graphical interfaces to Linux 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 to your home directory using cd ..:

$pwd  /home/<your Palmetto username>/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


## With Great Power Comes Great Responsibility

Removing the files in a directory recursively can be very dangerous operation. If we’re concerned about what we might be deleting we can add the “interactive” flag -i to rm 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 nano with the path thesis/draft.txt, rather than going into the thesis directory and running nano on draft.txt there.) $ pwd

/home/<your Palmetto username>

$mkdir thesis$ nano thesis/draft.txt
$ls thesis  draft.txt  To rename the file, we can use the mv command, which stands for “move”. The same command is used to move a file from one folder to another. Let’s rename draft.txt to quotes.txt: $ 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 Linux 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.

## 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?

1. cp statstics.txt statistics.txt
2. mv statstics.txt statistics.txt
3. mv statstics.txt .
4. cp statstics.txt .

## 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

1. proteins-saved.dat recombine
2. recombine
3. proteins.dat recombine
4. proteins-saved.dat

## 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 and sucrose.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  ## Listing Recursively and By Time The command ls -R lists the contents of directories recursively, i.e., lists their sub-directories, sub-sub-directories, and so on in alphabetical order at each level. The command ls -t lists things by time of last change, with most recently changed files or directories first. In what order does ls -R -t display things? ## Moving to the Current Folder After running the following commands, Jamie realizes that she put the files sucrose.dat and maltose.dat into the wrong folder: $ ls -F
raw/ analyzed/
$ls -F analyzed fructose.dat glucose.dat maltose.dat sucrose.dat$ 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 ___


## 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.

• rmdir path` removes (deletes) an empty directory.

• The shell does not have a trash bin: once something is deleted, it’s really gone.