Navigating Files and Directories

Questions:

How can I move around on my computer?
How can I see what files and directories I have?
How can I specify the location of a file or directory on my computer?
Objectives:
Learn the basic shell commands for files and directories
Understand absolute paths vs. relative paths.
Demonstrate the use of tab completion, and explain its advantages.

Nelle learned about “home” first

Nelle has taken a workshop that taught her the basics of setting up her computer using the BASH shell. She learned that the part of the operating system responsible for managing files and directories is called the file system which organizes our data into files (which hold information), and directories (also called “folders” which hold files or other directories).

Several commands are frequently used to create, inspect, rename, and delete files and directories. To understand what Nelle is doing (and why) as she is setting up for her first analyses, we’ll need to use our BASH shell on our computers.

After opening our terminal window, let’s find out “where we are” in the file system by running a command pwd (which stands for “print working directory”). Directories are like places - at any time while we are using the shell we are in exactly one place, called our current working directory. Commands mostly read and write files in the current working directory, so knowing where you are in the file system before running a command is important. pwd shows you where you are:

$ pwd
/Users/nelle

Here, the computer’s response is /Users/nelle. This important directory is not only our current working directory, it is Nelle’s home directory.

So let’s go over that again… We can be at any place in the file structure, and pwd will tell us where we are, i.e. the current working directory. BUT there is only ONE home directory per user.

Home Directory Variations

Computers always give you a home directory. We have to understand and accept that different operating systems have different places for the scientists’ home directory. For Windows the home directory is on hard drive “C” and the output of pwd is usually:
$ pwd
/c/Users/<username>
On a Mac it would be:
$ pwd
/Users/<username>
NOTE that whenever you see this format: "<username>", it is referring to ANY username and substitutes for yours or mine. For any commands using this format, you would type in your username rather than the actual letters: “". Mine would be `/c/Users/hoyt`, but on a Mac mine would be `/Users/hoyt` and on a Linux/Unix system it would be: `/home/hoyt`.

A typical MacOS or Windows 10 file structure will look like the image below, and Windows in particular uses the hard drive C: as the “root” directory (more on that later), but our setup instructions should start you in your home directory (e.g. Users/<username>), with at least a Desktop directory inside Users/<username>/. There might be lots of files or directories in your Desktop directory, but we’ll only use the data-shell directory for this lesson. The differences may be confusing but
the GitBash window will show you similar outputs once we start our lesson about moving through files and directories.

The General File Structure

One more reminder: In future examples, we’ve used an Apple Macintosh output as the default - if you are on a Linux or Windows computer, the output may differ slightly, but should be generally similar.

To understand what a “home directory” is, let’s have a look at how the file system as a whole is organized. For the sake of this example, we’ll be illustrating the filesystem on our scientist Nelle’s MacOS computer. After this lesson, you will have learned commands to explore your own filesystem, which will be constructed in a similar way.

On Nelle’s computer, the filesystem looks like this:

The File System

At the top is the root directory that holds everything else. We refer to it using a slash character, /, and this is the leading slash in /Users/nelle.

Inside the root directory are several other directories like:

bin (which is where some built-in programs are stored),
data (for miscellaneous data files),
Users (where users’ personal home directories are located),
tmp (for temporary files that don’t need to be stored long-term),
and more.

We know that our current working directory /Users/nelle is located inside /Users because /Users is the first part of its name. Similarly, we know that /Users is stored inside the root directory / because its name begins with /.

Slashes

Notice that there are two meanings for the / character. When it appears at the front of a file or directory name, it refers to the root directory. When it appears inside or between directory or file names, it’s just a separator.

Inside (or “below”) the /Users directory, we find one directory for each user with an account on Nelle’s computer. We know Nelle has an account with the directory nelle, and also her colleagues imhotep and larry have accounts.

Home Directories

The user imhotep’s files are stored in /Users/imhotep, user larry’s in /Users/larry, and Nelle’s in /Users/nelle. Nelle is the current user logged in to the computer in our examples, and this is why we get /Users/nelle as our home directory.

Typically, when you open a new command prompt you will be in your home directory to start.

The `ls` command

Now let’s learn a command to see the contents of our own filesystem. We can see what’s in our home directory by running ls which stands for “listing”:

$ ls
Applications Documents    Library      Music        Public
Desktop      Downloads    Movies       Pictures

(Again, your results may be slightly different depending on your operating system and how your filesystem is customized.)

ls prints the names of the files and directories in the current directory. We can make its output more comprehensible by using the flag -F (also known as a switch or an option), which tells ls to add a trailing / indicating that the items are directories rathre than files. Any item name with a / at the end is a directory. Depending on your settings, the ls command might also use colors to indicate whether each entry is a file or directory.

$ ls -F
Applications/ Documents/    Library/      Music/        Public/
Desktop/      Downloads/    Movies/       Pictures/

In our example (typically a Mac output), we can see our home directory contains mostly other directories (also commonly called: sub-directories). If you see any names in your output that don’t have trailing slashes, those must be files.

Getting help

ls has lots of other flags. There are two common ways to find out how to use a command and what flags it accepts:

We can pass a --help flag to the command, such as:
```
 $ ls --help
```
We can read its manual with man, such as:
```
 $ man ls 
```

Depending on your operating system you might find that only one of these works (On Macs, usually man, but on Windows, usually --help). The outputs however are very similar.

The `--help` flag

Many bash commands, and programs that people have written that can be run from within bash, support a --help flag to display more information on how to use the command or program.

$ ls --help

Usage: ls [OPTION]... [FILE]...
List information about the FILEs (the current directory by default).
Sort entries alphabetically if none of -cftuvSUX nor --sort is specified.

Mandatory arguments to long options are mandatory for short options too.
  -a, --all                  do not ignore entries starting with .
  -A, --almost-all           do not list implied . and ..
      --author               with -l, print the author of each file
  -b, --escape               print C-style escapes for nongraphic characters
      --block-size=SIZE      scale sizes by SIZE before printing them; e.g.,
                               '--block-size=M' prints sizes in units of
                               1,048,576 bytes; see SIZE format below
  -B, --ignore-backups       do not list implied entries ending with ~
  -c                         with -lt: sort by, and show, ctime (time of last
                               modification of file status information);
                               with -l: show ctime and sort by name;
                               otherwise: sort by ctime, newest first
  -C                         list entries by columns
      --color[=WHEN]         colorize the output; WHEN can be 'always' (default
                               if omitted), 'auto', or 'never'; more info below
  -d, --directory            list directories themselves, not their contents
  -D, --dired                generate output designed for Emacs' dired mode
  -f                         do not sort, enable -aU, disable -ls --color
  -F, --classify             append indicator (one of */=>@|) to entries
      --file-type            likewise, except do not append '*'
      --format=WORD          across -x, commas -m, horizontal -x, long -l,
                               single-column -1, verbose -l, vertical -C
      --full-time            like -l --time-style=full-iso
  -g                         like -l, but do not list owner
      --group-directories-first
                             group directories before files;
                               can be augmented with a --sort option, but any
                               use of --sort=none (-U) disables grouping
  -G, --no-group             in a long listing, don't print group names
  -h, --human-readable       with -l and/or -s, print human readable sizes
                               (e.g., 1K 234M 2G)
      --si                   likewise, but use powers of 1000 not 1024
  -H, --dereference-command-line
                             follow symbolic links listed on the command line
      --dereference-command-line-symlink-to-dir
                             follow each command line symbolic link
                               that points to a directory
      --hide=PATTERN         do not list implied entries matching shell PATTERN
                               (overridden by -a or -A)
      --indicator-style=WORD  append indicator with style WORD to entry names:
                               none (default), slash (-p),
                               file-type (--file-type), classify (-F)
  -i, --inode                print the index number of each file
  -I, --ignore=PATTERN       do not list implied entries matching shell PATTERN
  -k, --kibibytes            default to 1024-byte blocks for disk usage
  -l                         use a long listing format
  -L, --dereference          when showing file information for a symbolic
                               link, show information for the file the link
                               references rather than for the link itself
  -m                         fill width with a comma separated list of entries
  -n, --numeric-uid-gid      like -l, but list numeric user and group IDs
  -N, --literal              print raw entry names (don't treat e.g. control
                               characters specially)
  -o                         like -l, but do not list group information
  -p, --indicator-style=slash
                             append / indicator to directories
  -q, --hide-control-chars   print ? instead of nongraphic characters
      --show-control-chars   show nongraphic characters as-is (the default,
                               unless program is 'ls' and output is a terminal)
  -Q, --quote-name           enclose entry names in double quotes
      --quoting-style=WORD   use quoting style WORD for entry names:
                               literal, locale, shell, shell-always,
                               shell-escape, shell-escape-always, c, escape
  -r, --reverse              reverse order while sorting
  -R, --recursive            list subdirectories recursively
  -s, --size                 print the allocated size of each file, in blocks
  -S                         sort by file size, largest first
      --sort=WORD            sort by WORD instead of name: none (-U), size (-S),
                               time (-t), version (-v), extension (-X)
      --time=WORD            with -l, show time as WORD instead of default
                               modification time: atime or access or use (-u);
                               ctime or status (-c); also use specified time
                               as sort key if --sort=time (newest first)
      --time-style=STYLE     with -l, show times using style STYLE:
                               full-iso, long-iso, iso, locale, or +FORMAT;
                               FORMAT is interpreted like in 'date'; if FORMAT
                               is FORMAT1<newline>FORMAT2, then FORMAT1 applies
                               to non-recent files and FORMAT2 to recent files;
                               if STYLE is prefixed with 'posix-', STYLE
                               takes effect only outside the POSIX locale
  -t                         sort by modification time, newest first
  -T, --tabsize=COLS         assume tab stops at each COLS instead of 8
  -u                         with -lt: sort by, and show, access time;
                               with -l: show access time and sort by name;
                               otherwise: sort by access time, newest first
  -U                         do not sort; list entries in directory order
  -v                         natural sort of (version) numbers within text
  -w, --width=COLS           set output width to COLS.  0 means no limit
  -x                         list entries by lines instead of by columns
  -X                         sort alphabetically by entry extension
  -Z, --context              print any security context of each file
  -1                         list one file per line.  Avoid '\n' with -q or -b
      --help     display this help and exit
      --version  output version information and exit

The SIZE argument is an integer and optional unit (example: 10K is 10*1024).
Units are K,M,G,T,P,E,Z,Y (powers of 1024) or KB,MB,... (powers of 1000).

Using color to distinguish file types is disabled both by default and
with --color=never.  With --color=auto, ls emits color codes only when
standard output is connected to a terminal.  The LS_COLORS environment
variable can change the settings.  Use the dircolors command to set it.

Exit status:
 0  if OK,
 1  if minor problems (e.g., cannot access subdirectory),
 2  if serious trouble (e.g., cannot access command-line argument).

GNU coreutils online help: <http://www.gnu.org/software/coreutils/>
Full documentation at: <http://www.gnu.org/software/coreutils/ls>
or available locally via: info '(coreutils) ls invocation'

That’s a lot of help! We can’t go through all this today, just remember you should always know that --help is there for you.

And when things go wrong there are also error messages that can be helpful:

The `man` command

The other way to learn about ls is to type:

$ man ls

This doesn’t work on Windows machines, but on Macs and Linux machines, this will turn your terminal into a page with a description of the ls command and its options and, if you’re lucky, some examples of how to use it.

To navigate through the man pages, you may use ↑ and ↓ to move line-by-line, or try B and Spacebar to skip up and down by a full page. To search for a character or word in the man pages, use / followed by the character or word you are searching for. Sometimes a search will result in multiple hits. If so, you can move between hits using N (for moving forward) and Shift+N (for moving backward).

To quit the man pages, press Q.

Manual pages on the web

Of course there is a third way to access help for commands: searching the internet via your web browser. When using an internet search, including the phrase unix man page in your search query will help to find relevant results (e.g. unix man page ls). Many manual pages will take you to the GNU/Linux operating system pages, because GNU is a Unix-like operating system that produced much of the original code used in the shell. GNU provides links to its manuals including the core GNU utilities, which covers many commands introduced within this lesson.

Unsupported command-line options

If you try to use an option (flag) that is not supported, ls and other commands will usually print an error message similar to:

$ ls -j
ls: invalid option -- 'j'
Try 'ls --help' for more information.

Looking at our project directories

We can also use ls to see the contents of a different directory. Let’s take a look at our Desktop directory by running ls -F Desktop. This means we want to run the command ls, with the -F flag, using the argument Desktop. Using the argument Desktop tells ls that we want a listing of something other than our current working directory:

$ ls -F Desktop
data-shell/
(NOTE: all other files and directories will be listed)

Your output should be a list of all the files and sub-directories on your Desktop, including the data-shell directory you downloaded at the setup for this lesson. You should look at your Desktop in your operating system’s graphical user interface (the GUI) to confirm that your output is accurate.

It’s important to recognize that when using a bash shell the organization of the files in a file system is critical. This hierarchical organizing helps us keep track of our work. Rather than putting hundreds of files in our home directory (which would be like piling hundreds of printed papers on our desk) we should use informative names for the directories or files, and place our directories in a meaningful hierarchy.

Now that we know the data-shell directory is located on our Desktop, we can do two things.

First, we can look at its contents, using the ls command just as before.

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

(Note that the data-shell directory has both directories and ordinary files.)

Second, we can actually change our location to a different directory, so we are no longer located in our home directory. The command to change locations is cd followed by a directory name.

Although cd stands for “change directory”, it’s misleading because the command doesn’t change the directory, it changes which directory we are “in” (changes the working directory) based on the shell’s hierarchical directory structure.

Let’s say we want to move to the data directory we saw above. We can use the following series of commands to get there:

$ cd Desktop
$ cd data-shell
$ cd data

Type these commands to move us from our home directory, onto our Desktop, then into the data-shell directory, then into the data directory.

You might notice that after typing each command, nothing is printed to the terminal. This is normal. Many shell commands will not output anything to the screen when successfully executed.

If we run pwd (“print working directory”) we can see where we are;

$ pwd
/Users/nelle/Desktop/data-shell/data

If we run ls -F now, it lists only the contents of the working directory: data,
because… that’s where we are!

$ ls -F
amino-acids.txt   elements/     pdb/	        salmon.txt
animals.txt       morse.txt     planets.txt     sunspot.txt

We now know how to go down the directory tree, but how do we go up? We might try the following:

$ cd data-shell
-bash: cd: data-shell: No such file or directory

But we get an error! Why is this?

Because cd can only see sub-directories inside (or “below”) your current working directory. There are different ways to see directories above your current location and we’ll start with the simplest.

There is a shortcut in the shell to move up one directory level that looks like this:

$ cd ..

The .. is a special directory indicator meaning: “the directory containing this one”, or more commonly, the parent of the current directory. After running the cd .. command, we can run pwd, and we’re in /Users/nelle/Desktop/data-shell.

$ pwd
/Users/nelle/Desktop/data-shell

We haven’t seen the special directory indicator .. before because it doesn’t show up when we run ls. But if we want to display it, we can give ls the -a flag:

$ ls -F -a
./   .bash_profile  data/      north-pacific-gyre/  pizza.cfg  thesis/
../  creatures/     molecules/ notes.txt            solar.pdf  writing/

Let’s go through this output carefully. The flag -a stands for “show all”. It forces ls to show us all files and directories, including the parent directory’s .. special indicator. Notice the flag -a makes ls display another special directory indicator that’s a single “dot” or: ., which is a shortcut for “the current working directory”. For example, and to be clear, if we’re in the /Users/nelle directory, the .. refers to the /Users directory, and a . by itself means the “current working directory” or in this example:
/Users/nelle

About Hidden Files

Finally, the bash shell will “hide” any file or directory from the ls command if their name begins with “.” This is completely different than the . special directory indicator!

The ls -F -a command shows the hidden directories .. and ., plus we also see the hidden file .bash_profile. This is a common file and usually contains shell configuration settings. If you see other hidden files and directories beginning with . they are probably special files and directories used to configure different programs on your computer. These aren’t changed very often. The prefix . is used to prevent these configuration files from being changed accidently, and to reduce clutter in the terminal when a standard ls command is used.

Orthogonality

To make memorizing commands and flags of the BASH shell easier, the special indicators . and .. don’t belong to just the command cd; they are interpreted the same way by every command program. For example, if we are in /Users/nelle, the command ls .. will give us a listing of /Users (without changing our current working directory). When meanings of flags are the same no matter which command uses them, programmers say they are orthogonal. Orthogonal systems are easier for people to learn because there are fewer parts to memorize. Also note that in most command line tools, multiple flags can be combined with no spaces between the flags and a single dash -. For example: ls -Fa is equivalent to ls -F -a.

Moving on!

These then, are the basic commands for navigating the filesystem on your computer: pwd, ls and cd. Let’s explore some variations on those commands.
First, type cd on its own, without specifying a directory.

$ cd

How can you check what happened? pwd gives us the answer!

$ pwd
/Users/nelle

It turns out that cd without any argument will return you to your home directory, which is great if you’ve gotten lost in your own filesystem.

Let’s try returning to the data directory. Last time we used three commands, but we can actually string together the directories to move to data in one step:

$ cd Desktop/data-shell/data

Check that we’ve moved to the right place by running pwd and ls -F

Relative vs. Absolute Paths

If we want to move up one level from the data directory, we could use the cd .. command. But there is another way to move to any directory, regardless of your current location.

So far, when specifying directory names, or even a directory path (as above), we have been using relative paths. When you use a relative path with a command like ls or cd, it tries to find that location from where we are, rather than from the root of the file system.

However, it is possible to specify the absolute path to a directory by including its entire path from the root directory, which is indicated by a leading slash. The leading / tells the computer to follow the path from the root of the file system, so it always refers to exactly one directory, no matter where we are when we run the command.

Probably the best example of an absolute path is when you use the pwd command. This always displays your location in the filesystem hierarchy starting at the root directory. From within data we can type pwd and it gives us the absolute path to data-shell. This absolute path lets us move to our data-shell directory from anywhere on the filesystem.

$ pwd
/Users/nelle/Desktop/data-shell/data

Now we know that we can get to our data-shell folder from anywhere in the filesystem by typing:

$ cd /Users/nelle/Desktop/data-shell

Try running the cd command without arguments to go to our home folder, then run the cd command above substituting your for "nelle". Afterwards run `pwd` and `ls -F` to ensure that we're in the directory we expect. (NOTE: This may not work exactly the same depending on your operating system)

Two More Shortcuts

The shell interprets the character ~ (tilde) at the start of a path to mean “the current user’s home directory”. For example, if Nelle’s home directory is /Users/nelle, then ~/data is equivalent to /Users/nelle/data. This only works when ~ is the first character in the path: here/there/~/elsewhere is not here/there/Users/nelle/elsewhere.

Another shortcut is the - (dash) character. cd will translate - into the previous directory I was in, which is faster than having to remember, then type, the full path. This is a very efficient way of moving back and forth between directories. The difference between cd .. and cd - is that the former brings you up, while the latter brings you back. You can think of it as the Previous Channel button on a TV remote.

Example Exercises

Relative Path Resolution

Using the filesystem diagram below, if pwd displays /Users/thing, what will ls -F ../backup display?

../backup: No such file or directory

2012-12-01 2013-01-08 2013-01-27

2012-12-01/ 2013-01-08/ 2013-01-27/

original/ pnas_final/ pnas_sub/

Solution

No: there is a directory backup in /Users.

No: this is the content of Users/thing/backup, but with .. we asked for one level further up.

No: see previous explanation.

Yes: ../backup/ refers to /Users/backup/.

ls Reading Comprehension

Assuming a directory structure as in the above Figure (File System for Challenge Questions), if pwd displays /Users/backup, and the flag: -r tells ls to display things in reverse order, what command will result in the following output:
pnas_sub/ pnas_final/ original/
ls pwd

ls -r -F

ls -r -F /Users/backup

Either #2 or #3 above, but not #1.

Solution

No: pwd is not the name of a directory.

Yes: ls without directory argument lists files and directories in the current directory.

Yes: uses the absolute path explicitly.

Correct: see explanations above.

Nelle’s Pipeline: Organizing Files

Knowing just this much about files and directories, Nelle is ready to organize the files that the protein assay machine will create. First, she creates a directory called north-pacific-gyre (to remind herself where the data came from). Inside that, she creates a directory called 2012-07-03, which is the date she started processing the samples. She used to use names like conference-paper and revised-results, but she found them hard to understand after a couple of years. (The final straw was when she found herself creating a directory called revised-revised-results-3)

Using dates in filenames

Nelle names her directories beginning with “year-month-day”, including leading zeroes for months and days, (“yyyy-mm-dd”) because the shell displays file and directory names in alphabetical order. If she used month names, December would come before July; if she didn’t use leading zeroes, November (‘11’) would come before July (‘7’) (Do you know why this is true?). Similarly, putting the year first means that June 2012 will come before June 2013.

Each of her physical samples is labeled according to her lab’s convention with a unique ten-character ID, such as “NENE01729A”. This is what she used in her collection log to record the location, time, depth, and other characteristics of the sample, so she decides to use it as part of each data file’s name. Since the assay machine’s output will be plain text, she will call her files NENE01729A.txt, NENE01812A.txt, and so on. All 1520 files will go into the same directory.

TAB-completion

Now in her current directory data-shell, Nelle can see her files using the command:

$ ls north-pacific-gyre/2012-07-03/

This is a lot to type, but she can let the shell do most of the work using what is called tab completion. If she types:

$ ls nor

and then presses Tab (the tab key on her keyboard), the shell automatically completes the directory name for her:

$ ls north-pacific-gyre/

If she presses Tab again, Bash will add 2012-07-03/ to the command, since it’s the only possible completion. Pressing Tab again does nothing, since there are 19 possibilities; but pressing Tab one more time shows the list of all the files to help her choose. This tab completion is an extremely useful tool that you should practice and we will use it with many other tools as we go on.

Lesson Keypoints:

Information is stored in files, which are stored in directories (folders).
Directories can also store other directories, which forms a hierarchical directory tree.
cd <path> changes the current working directory.
ls <path> prints a listing of a specific file or directory; ls on its own lists the current working directory.
pwd prints the user’s current working directory.
/ on its own is the root directory of the whole file system.
A relative path specifies a location starting from the current working directory.
An absolute path specifies a location from the root of the file system.
.. means ‘the directory above the current one’; . by itself means ‘the current directory’.

Data Science in Omics Introduction

Notes

Questions:

Objectives:

Nelle learned about “home” first

Home Directory Variations

Slashes

The `ls` command

Getting help

The `--help` flag

The `man` command

Manual pages on the web

Unsupported command-line options

Looking at our project directories

About Hidden Files

Orthogonality

Moving on!

Relative vs. Absolute Paths

Two More Shortcuts

Example Exercises

Relative Path Resolution

Solution

`ls` Reading Comprehension

Solution

Nelle’s Pipeline: Organizing Files

Using dates in filenames

TAB-completion

Lesson Keypoints:

Data Science in Omics Introduction

Navigating Files and Directories

Notes

Questions:

Objectives:

Nelle learned about “home” first

Home Directory Variations

Slashes

The ls command

Getting help

The --help flag

The man command

Manual pages on the web

Unsupported command-line options

Looking at our project directories

About Hidden Files

Orthogonality

Moving on!

Relative vs. Absolute Paths

Two More Shortcuts

Example Exercises

Relative Path Resolution

Solution

ls Reading Comprehension

Solution

Nelle’s Pipeline: Organizing Files

Using dates in filenames

TAB-completion

Lesson Keypoints:

The `ls` command

The `--help` flag

The `man` command

`ls` Reading Comprehension