Working With Files and Directories

Overview

Teaching: 15 min
Exercises: 5 min

Questions

• 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 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?

Step one: see where we are and what we already have

Let’s go back to our data-shell directory on the Desktop and use ls -F to see what it contains:

$ pwd

/home/lortizur/data-shell

$ ls -F

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

Create a directory

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., does not have a leading slash, like /what/ever/thesis), the new directory is created in the current working directory:

$ ls -F

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

Good names for files and directories

Complicated names of files and directories can make your life painful when working on the command line. But extremely short and cryptic filenames will make your life painful when you return after days (weeks, months…) and try to remember what you were doing. Here we provide a few useful tips for the names of your files.

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/).

   You may encounter files with spaces in their names if they have been uploaded from a laptop. To reference such files from the command line, enclose the entire name in quotes ("" or '').

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 ("").

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

$ ls -F thesis

Creating A File

$ touch my_file.txt

1. What did the touch command do?
2. Use ls -l to inspect the files. How large is my_file.txt?

Solution

1. The touch command generates a new file called my_file.txt in your current directory.

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. touching an existing file does not change it, but will update the date/time of its last edit to the current date/time.

Moving files and directories

Returning to the data-shell directory,

cd ~/data-shell/

Let’s create a file called draft.txt in our thesis directory using a text editor:

$ vi thesis/draft.txt

Let’s type a few lines. First, type the i character (this stands for insert)

It's not "publish or perish" any more, it's "share and thrive"

To save the file using this editor, use the esc key and then type ZZ

In our thesis directory we now have a file draft.txt that contains a quote. This is not 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 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.

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.

$ 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 Files to a new folder

After running the following commands, Jamie realizes that she put the files sucrose.dat and maltose.dat into the wrong folder. The files should have been placed in the raw folder.

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

Fill in the blanks to move these files to the raw/ folder (i.e. the one she forgot to put them in)

$ mv sucrose.dat maltose.dat ____/____

Solution

$ mv sucrose.dat maltose.dat ../raw

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/Linux 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

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

$ cp -r thesis thesis_backup

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

$ ls thesis thesis_backup

thesis:
quotations.txt

thesis_backup:
quotations.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 .

Solution

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.

Moving and Copying

What is the output of the closing ls command in the sequence shown below?

$ pwd

/home/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

Solution

We start in the /home/jamie/data directory, and create a new folder called recombine. The second line moves (mv) the file proteins.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 /home/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 /home/jamie/data) is the recombine folder.

1. No, see explanation above. proteins-saved.dat is located at /home/jamie
2. Yes
3. No, see explanation above. proteins.dat is located at /home/jamie/data/recombine
4. No, see explanation above. proteins-saved.dat is located at /home/jamie

Removing files and directories

Returning to the data-shell directory, let’s tidy up this directory by removing the quotes.txt file we created. The command we’ll use for this is rm (short for ‘remove’):

$ rm quotes.txt

We can confirm the file has gone using ls:

$ ls quotes.txt

ls: cannot access 'quotes.txt': No such file or directory

Deleting Is Forever

Shells don’t have a trash bin that we can recover deleted files from (though most graphical interfaces to Unix do - but interestingly, the one on HOPPER does not. But if you try to delete a file in HOPPER’s GUI, it will ask you if you are sure). 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 reuse the file’s disk space right away.

Using rm Safely

What happens when we execute rm -i thesis_backup/quotations.txt? Why would we want this protection when using rm?

Solution

$ rm: remove regular file 'thesis_backup/quotations.txt'? y

The -i option will prompt before (every) removal (use Y to confirm deletion or N to keep the file). The 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. Some systems have the -i option enabled by default. HOPPER accessed via a ssh terminal does not!

If we try to remove the 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.

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 thesis

Given that there is no way to retrieve files deleted using the shell, rm -r should be used with extreme caution (you might consider adding the interactive option rm -r -i).

If a directory is empty, rmdir (the complement of mkdir) will also remove it.

Operations with multiple files and directories

Oftent 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 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 such as the one below, because it is expecting a directory name as the last argument.

cp: target ‘morse.txt’ is not a directory

Using wildcards for accessing multiple files at once

Wildcards

* is a wildcard, which matches zero or more characters. Let’s consider the data-shell/molecules 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 molecules 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.

There are many other, fancier wildcards as well. For example:

[0-9] will match only numbers

[a-Z] will match any letters of either case. Unix/Linux alphabetizes as aAbBcCdD..zZ, so the mixed cases a and Z are necessary to include all the letters in the range.

[[:lower:]] will match only lower-case letters

[[:upper:]] will match only upper case letters

List filenames matching a pattern

When run in the molecules 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.*

Solution

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

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 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

Solution

mv *.dat analyzed

Jamie needs to move her files fructose.dat and sucrose.dat to the analyzed directory. The shell will expand *.dat to match all .dat files in the current directory. The mv command then moves the list of .dat files to the ‘analyzed’ directory.

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-data folder into a folder called 2016-05-20 so that your final directory structure looks like this:

2016-05-20/
└── 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 2016-05-20
$ cd 2016-05-20
$ mkdir data
$ mkdir raw processed

Solution

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 mkdir won’t create a subdirectory of a non-existant directory: the intermediate level folders must be created first.

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 notated 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. REALLY!

• 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.