using-commands.md

title	layout
Using UNIX commands	default

Using UNIX commands

1 Basic utilities / commands

Earlier we introduced the basics of entering commands in the shell.

Since files are such an essential aspect of Unix and working from the shell is the primary way to work with Unix, there are a large number of useful commands and tools to view and manipulate files.

• cat -- concatenate files and print to standard output
• cp -- copy files and directories
• cut --_remove sections from each line of files
• diff -- find differences between two files
• grep -- print lines matching a pattern
• head -- output the first part of files
• find --  search for files in a directory hierarchy
• less -- opposite of more (and better than more)
• more -- file perusal filter for crt viewing
• mv -- move (rename) files
• nl -- number lines of files
• paste -- merge lines of files
• rm -- remove files or directories
• rmdir -- remove empty directories
• sort -- sort lines of text files.
• split -- split a file into pieces
• tac -- concatenate and print files in reverse
• tail -- output the last part of files
• touch -- change file timestamps
• tr -- translate or delete characters
• uniq -- remove duplicate lines from a sorted file
• wc -- print the number of bytes, words, and lines in files
• wget and curl -- non-interactive internet downloading

Recall that a command consists of the command, optionally one or more flags, and optionally one or more arguments. When there is an argument, it is often the name of a file that the command should operate on.

Thus the general syntax for a Unix program/command/utility is:

$ command -options argument1 argument2 ...

For example, :

$ grep -i graphics file.txt

looks for the literal string graphics (argument 1) in file.txt (argument2) with the option -i, which says to ignore the case of the letters. A simpler invocation is:While :

$ less file.txt

which simply pages through a text file (you can navigate up and down with the space bar and the up/down arrows) so you can get a feel for what's in it. To exit less type q.

Unix programs often take flags (options) that are identified with a minus followed by a letter and then (possibly) followed by the specific option (adding a space before the specific option is fine). Options may also involve two dashes, e.g., R --no-save. A standard two dash option for many commands is --help. For example, try:

$ tail --help

Here are a couple of examples of flags when using the tail command (-n 10 and -f):

$ wget https://raw.githubusercontent.com/berkeley-scf/tutorial-using-bash/master/cpds.csv
$ tail -n 10 cpds.csv   # last 10 lines of cpds.csv
$ tail -f cpds.csv      # shows end of file, continually refreshing

The first line downloads the data from GitHub. The two main tools for downloading network-accessible data from the commandline are wget and curl. I tend to use wget as my commandline downloading tool as it is more convenient, but on a Mac, only curl is generally available.

A few more tidbits about grep (we will see more examples of grep in the section on regular expressions, but it is so useful that it is worth seeing many times):

$ grep ^2001 cpds.csv   # returns lines that start with '2001'
$ grep 0$ cpds.csv      # returns lines that end with '0'
$ grep 19.0 cpds.csv    # returns lines with '19' separated from '0' by a single character
$ grep 19.*0 cpds.csv   # now separated by any number of characters
$ grep -o 19.0 cpds.csv # returns only the content matching the pattern, not entire lines

Note that the first argument to grep is the pattern you are looking for. The syntax is different from that used for wildcards in file names. Also, you can use regular expressions in the pattern, but we defer details until later.

It is sometimes helpful to put the pattern inside double quotes, e.g., if you want spaces in your pattern:

$ grep "George .* Bush" cpds.csv

More generally in Unix, enclosing a string in quotes is often useful to indicate that it is a single argument/value.

If you want to explicitly look for one of the special characters used in creating patterns (such as double quote ("), period (.), etc.), you can "escape" them by preceding with a back-slash. For example to look for "Canada", including the quotes:

$ grep "\"Canada\"" cpds.csv     # look for "Canada" (including quotes)
$ grep "19\.0" cpds.csv              # look for 19.0

If you have a big data file and need to subset it by line (e.g., with grep) or by field (e.g., with cut), then you can do it really fast from the Unix command line, rather than reading it with R, SAS, Python, etc.

Much of the power of these utilities comes in piping between them (see the next section) and using wildcards to operate on groups of files. The utilities can also be used in shell scripts to do more complicated things.

We'll see further examples of how to use these utilities later.

Exercise

You've already seen some of the above commands. Use the --help syntax to view the abbreviated man pages for some commands you're not familiar with and consider how you might use these commands.

3 Streams, pipes, and redirects

3.1 Streams (stdin/stdout/stderr)

Unix programs that involve input and/or output often operate by reading input from a stream known as standard input (stdin), and writing their results to a stream known as standard output (stdout). In addition, a third stream known as standard error (stderr) receives error messages and other information that's not part of the program's results. In the usual interactive session, standard output and standard error default to your screen, and standard input defaults to your keyboard.

3.2 Overview of redirection

You can change the place from which programs read and write through redirection. The shell provides this service, not the individual programs, so redirection will work for all programs. The following table shows some examples of redirection.

Table. Common Redirection Operators

Redirection Syntax	Function
$ cmd > file	Send stdout to file
$ cmd 1> file	Same as above
$ cmd 2> file	Send stderr to file
$ cmd > file 2>&1	Send both stdout and stderr to file
$ cmd < file	Receive stdin from file
$ cmd >> file	Append stdout to file
$ cmd 1>> file	Same as above
$ cmd 2>> file	Append stderr to file
$ cmd >> file 2>&1	Append both stdout and stderr to file
$ cmd1 | cmd2	Pipe stdout from cmd1 to cmd2
$ cmd1 2>&1 | cmd2	Pipe stdout and stderr from cmd1 to cmd2
$ cmd1 | tee file1 | cmd2	Pipe stdout from cmd1 to cmd2 while simultaneously writing it to file1
	using tee

Note that cmd may include options and arguments as seen in the previous section.

3.3 Standard redirection (pipes)

Operations where output from one command is used as input to another command (via the | operator) are known as pipes; they are made especially useful by the convention that many UNIX commands will accept their input through the standard input stream when no file name is provided to them.

A simple pipe to wc to count the number of words in a string:

$ echo "hey there" | wc -w
2

Translating lowercase to UPPERCASE with tr:

$ echo 'user1'  | tr 'a-z' 'A-Z'
USER1

Here's an example of finding out how many unique entries there are in the 2nd column of a data file whose fields are separated by commas:

$ cut -d',' -f2 cpds.csv | sort | uniq | wc
$ cut -d',' -f2 cpds.csv | sort | uniq > countries.txt

Here are the piecies of what is going on in the commands above:

• We use the cut utility to extract the second field (-f2) or column of the file cpds.csv where the fields (or columns) are split or delimited by a comma (-d',').
• The standard output of the cut command [is then piped (via |) to the standard input of the sort command.
• Then the output of sort is sent to the input of uniq to remove duplicate entries in the sorted list provided by sort. (Rather than using sort | uniq, you could also use sort -u.)
• Finally, the first of the cut commands prints a word count summary using wc; while the second saving the sorted information with duplicates removed in the file countries.txt.

As another example of checking for anomalies in a set of files, with the , to see if there are any "S" values in certain fields (based on fixed width using -b) of a set of files (USC*dly), one can do this:

$ cut -b29,37,45,53,61,69,77,85,93,101,109,117,125,133,141,149, \ 
            157,165,173,181,189,197,205,213,221,229,237,245,253, \
            261,269 USC*.dly | grep S | less

(Note I did that on 22,000 files (5 Gb or so) in about 5 minutes on my desktop; it would have taken much more time to read the data into a program like R or Python.)

3.4 The tee command

The tee command lets you create two streams from one. For example, consider the case where you want the results of this command:

$ cut -d',' -f2 cpds.csv | sort | uniq 

to both be output to the terminal screen you are working in as well as being saved to a file. You could issue the command twice:

$ cut -d',' -f2 cpds.csv | sort | uniq
$ cut -d',' -f2 cpds.csv | sort | uniq > countries.txt

Instead of repeating the command and wasting computing time, you could use tee command:

$ cut -d',' -f2 cpds.csv | sort | uniq | tee countries.txt

4 Command substitution and the xargs command

4.1 Command substitution

A closely related, but subtly different, capability to piping is command substitution. You may sometimes need to substitute the results of a command for use by another command. For example, if you wanted to use the directory listing returned by ls as the argument to another command, you would type $(ls) in the location you want the result of ls to appear.

When the shell encounters a command surrounded by $(), it runs the command and replaces the expression with the output from the command. This allows something similar to a pipe, but it is appropriate when a command reads its arguments directly from the command line instead of through standard input.

For example, suppose we are interested in searching for the text pdf in the last 4 R code files (those with suffix .r or .R) that were modified in the current directory. We can find the names of the four most recently modified files ending in .R or .r using:

$ ls -t *.{R,r} | head -4

and we can search for the required pattern using grep . Putting these together with command substitution, we can solve the problem using:

$ grep pdf $(ls -t *.{R,r} | head -4)

Suppose that the four R code file names produced by the ls command above were: test.R, run.R, analysis.R , and process.R. Then the result of the command substitution above is to run the following command:

$ grep pdf test.R run.R analysis.R process.R

Note

An older notation for command substitution is to use backticks (e.g., `ls` rather than $(ls)). It is generally preferable to use the new notation, since there are many annoyances with the backtick notation. For example, backslashes (\) inside of backticks behave in a non-intuitive way, nested quoting is more cumbersome inside backticks, nested substitution is more difficult inside of backticks, and it is easy to visually mistake backticks for a single quote.

Note that piping the output of the ls command into grep would not achieve the desired goal, since grep reads its filenames as arguments from the command line, not standard input.

4.2 The xargs command

While it doesn't work to directly use pipes to redirect output from one program as arguments to another program, you can redirect output as the arguments to another program using the xargs utility. Here's an example:

$ ls -t *.{R,r} | head -4 | xargs grep pdf

where the result is equivalent to the use of command substitution we saw in the previous section.

Exercise

Try the following commands:

$ ls -l tr
$ type -p tr
$ ls -l type -p tr
$ ls -l $(type -p tr)

Make sure you understand why each command behaves as it does.

5 Brace expansion

We saw brace expansion when discussing file wildcards. For example, we can rename a file with a long name easily like this:

$ mv my_long_filename.{txt,csv}
$ ls my_long_filename*
my_long_filename.csv
$ mv my_long_filename.csv{,-old}
$ ls my_long_filename*
my_long_filename.csv-old

This works because the shell expands the braces before passing the result on to the command. So with the mv calls above, the shell expands the braces to produce

mv my_long_filename.txt my_long_filename.csv
mv my_long_filename.csv my_long_filename.csv-old

Brace expansion is quite useful and more flexible than I've indicated. Above we saw how to use brace expansion using a comma-separated list of items inside the curly braces (e.g., {txt,csv}), but they can also be used with a sequence specification. A sequence is indicated with a start and end item separated by two periods (..). Try typing the following examples at the command line and try to figure out how they work:

$ echo {1..15}
$ echo c{c..e}
$ echo {d..a}
$ echo {1..5..2}
$ echo {z..a..-2}

This can be used for filename wildcards but also anywhere else it would be useful. For example to kill a bunch of sequentially-numbered processes:

$ kill 1397{62..81}

6 Quoting

A note about using single vs. double quotes in shell code. In general, variables inside double quotes will be evaluated, but variables not inside double quotes will not be:

$ echo "My home directory is $HOME"
My home directory is /home/jarrod
$ echo 'My home directory is $HOME'
My home directory is $HOME

Table. Quotes

Types of Quoting	Description
' '	hard quote - no substitution allowed
" "	soft quote - allow substitution

This can be useful, for example, when you have a directory with a space in its name (of course, it is better to avoid spaces in file and directory names). For example, suppose you have a directory named "with space" within the /home/jarrod home directory. Since bash uses spaces to parse the elements of the command line, you might try escaping any spaces with a backslash:

$ ls $HOME/with\ space
file1.txt

However that can be a pain and may not work in all circumstances. A cleaner approach is to use soft (or double) quotes:

$ ls "$HOME/with space"
file1.txt

If you used hard quotes, you will get this error:

$ ls '$HOME/with space'
ls: cannot access $HOME/with space: No such file or directory

What if you have double quotes in your file or directory name, such as a directory "with"quote (again, it is better to avoid using double quotes in file and directory names)? In this case, you will need to escape the quote:

$ ls "$HOME/\"with\"quote"

So we'll generally use double quotes. We can always work with a literal double quote by escaping it as seen above.

7 Powerful tools for text manipulation: grep, sed, and awk

Before the text editor, there was the line editor. Rather than presenting you with the entire text as a text editor does, a line editor only displays lines of text when it is requested to. The original Unix line editor is called ed. You will likely never use ed directly, but you will very likely use commands that are its descendants. For example, the commands grep, sed, awk, and vim are all based directly on ed (e.g., grep is a ed command that is now available as a standalone command, while sed is a streaming version of ed) or inherit much of its syntax (e.g., awk and vim both heavily borrow from the ed syntax). Since ed was written when computing resources were very constrained compared to today, this means that the syntax of these commands can be terse. However, it also means that learning the syntax for one of these tools will be rewarded when you need to learn the syntax of another of these tools.

An important benefit of these tools, particularly when working with large files, is that by operating line by line they don't incur the memory use that would be involved in reading an entire file into memory in a program like Python or R and then operating on the file's contents in memory.

You may not need to learn much sed or awk, but it is good to know about them since you can search the internet for awk or sed one-liners. If you have some file munging task, it can be helpful to do a quick search before writing code to perform the task yourself.

7.1 grep

The simplest of these tools is grep. As I mentioned, ed only displays lines of text when requested. One common task was to print all the lines in a file matching a specific regular expression. The command in ed that does this is g/<re>/p, which stands for globally match all lines containing the regular express <re> and print them out.

One often uses grep with regular expressions, covered later, so we'll just show some basic usage here.

To start you will need to create a file called testfile.txt with the following content:

This is the first line.
Followed by this line.
And then ...

To print all the lines containing is:

$ grep is testfile.txt
This is the first line.
Followed by this line.

To print all the lines not containing is:

$ grep -v is testfile.txt 
And then ...

To print only the matches, one can use the -o flag, though this would generally only be interesting when used with a regular expression pattern since in this case, we know "is" is what will be returned:

$ grep -o is testfile.txt
is
is
is

One could also use --color so that the matches are highlighed in color.

7.2 sed

Here are some useful things you can do with sed. Note that as with other UNIX tools, sed will not generally directly alter a file (unless you use the -i flag); instead it will print the modified version of the file to stdout.

Printing lines of text with sed:

$ sed -n '1,9p' file.txt       # prints out lines 1-9 from file.txt
$ sed -n '/^#/p' file.txt      # prints out lines starting with # from file.txt 

The first command prints out lines 1-9, while the second one prints out lines starting with #.

Deleting lines of text with sed:

$ sed -e '1,9d' file.txt
$ sed -e '/^;/d' -e '/^$/d' file.txt

The first line deletes lines 1-9 of file.txt, printing the remaining lines to stdout. What do you think the second line does?

Note that the -e flag is only necessary if you want to have more than one expression, so it's not actually needed in the first line.

Text substitution with sed:

$ sed 's/old_pattern/new_pattern/' file.txt > new_file.txt
$ sed 's/old_pattern/new_pattern/g' file.txt > new_file.txt
$ sed -i 's/old_pattern/new_pattern/g' file.txt 

The first line replaces only the first instance in a line, while the second line replaces all instances in a line (i.e., globally). The use of the -i flag in the third line replaces the pattern in place in the file, thereby altering file.txt. Use the -i flag carefully as there is no way to easily restore the original version of the file.

7.3 awk

Awk is a general purpose programming language typically used in data extraction tasks and particularly well-suited to one-liners (although it is possible to write long programs in it, it is rare). For our purposes, we will just look at a few common one-liners to get a sense of how it works. Basically, awk will go through a file line by line and perform some action for each line.

For example, to select a given column from some text (here getting the PIDs of some processes, which are in the second ($2) column of the output of ps -f:

ps -f | awk '{ print $2 }'

To double space a file, you would read each line, print it, and then print a blank line:

$ awk '{ print } { print "" }' file.txt 

Print every line of a file that is longer than 80 characters:

$ awk 'length($0) > 80' file.txt

Print the home directory of every user defined in the file /etc/passwd:

$ awk -F: '{ print $6 }' /etc/passwd

To see what that does, let's look at the first line of /etc/passwd:

$ head -n 1 /etc/passwd
root:x:0:0:root:/root:/bin/bash

As you can see the entries are separated by colons (:) and the sixth field contains the root user's home directory (/root). The option -F: specifies that the colon : is the field delimiter (instead of the default space delmiter) and print $6 prints the 6th field of each line.

Summing columns:

$ awk '{print $1 + $2}' file.txt

This will sum columns 1 and 2 of file.txt.

8 Aliases (command shortcuts) and .bashrc

Aliases allow you to use an abbreviation for a command, to create new functionality or to insure that certain options are always used when you call an existing command. For example, I'm lazy and would rather type q instead of exit to terminate a shell window. You could create the alias as follow:

$ alias q=exit

As another example, suppose you find the -F option of ls (which displays / after directories, \ after executable files and @ after links) to be very useful. The command :

$ alias ls="ls -F"

will ensure that the -F option will be used whenever you use ls. If you need to use the unaliased version of something for which you've created an alias, precede the name with a backslash (\). For example, to use the normal version of ls after you've created the alias described above:

$ \ls

The real power of aliases is only achieved when they are automatically set up whenever you log in to the computer or open a new shell window. To achieve that goal with aliases (or any other bash shell commands), simply insert the commands in the file .bashrc in your home directory. For example, here is an excerpt from my .bashrc:

    # .bashrc

    # Source global definitions
    if [ -f /etc/bashrc ]; then
            . /etc/bashrc
    fi

    # User specific aliases and functions
    pushdp () {
     pushd "$(python -c "import os.path as _, ${1}; \
       print _.dirname(_.realpath(${1}.__file__[:-1]))"
     )"
    }

    export EDITOR=vim
    source /usr/share/git-core/contrib/completion/git-prompt.sh
    export PS1='[\u@\h \W$(__git_ps1 " (%s)")]\$ '

    # history settings
    export HISTCONTROL=ignoredups   # no duplicate entries
    shopt -s histappend             # append, don't overwrite

    # R settings
    export R_LIBS=$HOME/usr/lib64/R/library
    alias R="/usr/bin/R --quiet --no-save"

    # Set path
    mybin=$HOME/usr/bin
    export PATH=$mybin:$HOME/.local/bin:$HOME/usr/local/bin:$PATH:
    export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HOME/usr/local/lib

    # Additional aliases  
    alias grep='grep --color=auto'
    alias hgrep='history | grep'
    alias l.='ls -d .* --color=auto'
    alias ll='ls -l --color=auto'
    alias ls='ls --color=auto'
    alias more=less
    alias vi=vim

Exercise

Look over the content of the example .bashrc and make sure you understand what each line does. For instance, use man grep to see what the option --color=auto does. Use man which to figure out what the various options passed to it do.