Appndix: Command Line Commands

File Tree Navigation

ls lists all files and directories in the working directory.

• ls -a lists all contents in working directory, includes hidden files and directories.
• ls -l lists all contents of a directory in long format.
• ls -t orders files and directories by the time they were last modified.
• pwd “print working directory”
• rm deletes files.
  • rm -r deletes a directory and all its child directories.
• touch creates a new empty file in the working directory.

Input/Output Redirection

• > takes the standard output of the command on the left and redirects it to the file on the right.
• >> takes the standard output of the command on the left and appends it to the file on the right.
• < takes the standard input from the file on the right and inputs it into the program on the left.
• | is a “pipe”. It takes the standard output of the command on the left, and pipes it as standard input to the command on the right.

Alias

• alias allows you to create keyboard shortcuts (aliases).

Grep

grep stands for “global regular expression print”. It searches files for lines that match a pattern and returns the results. Case sensitive. Grep Documentation located here.

Syntax of grep command:

grep [option...] [patterns] [file...]

There can be zero or more options and zero or more files. Typically, patterns should be quoted.

• grep -i for case insensitive grep.
• grep -R (“Recursive”) searches all files in a directory and outputs filenames and lines containing matched results.
• grep -Rl (“Recursive” and “files with matches”) searches all files in a directory and outputs only filenames with matched results.

Uniq

uniq “unique”. Takes a filename or standard input and prints out every line, removing any exact duplicates.

Syntax of uniq command:

uniq [option] [INPUT[OUTPUT]]

Options for uniq command:

• -c or --count to prefix lines by the number of occurrences.
• -d or --repeated only prints the repeated lines, not lines which aren’t repeated.
• -D or --all-repeated[=METHOD] prints all duplicate lines.
• -u or --unique to print only unique lines (non-duplicate lines).
• -i or --ignore-case to ignore the case sensitivity of characters when comparing.
• -f or --skip-fields=N skip fields to filter duplicate lines (for example, skip one column to filter for uniqueness in the next column). Avoid comparing the first N fields.
• -s or --skip-char=Nskip characters (like the skip fields option). Avoid comparing the first N characters.
• -w or --check-chars=N to consider characters (like checking characters, but only consider certain characters. For example, -w 2 will consider only the first two characters for uniqueness).

Note: sort the input first to filter all unique lines, not just contiguous ones.

Sort

Sort documentation found here. Tool to sort, merge, or compare all the lines from the files given (or standard input).

Sort command syntax:

sort [options] [file...]
sort [options] ... --files0-from=F

Sort command ordering options:

• -b, --ignore-leading-blanks to ignore leading blanks.
• -d, --dictionary-order to consider only blanks and alphanumeric characters.
• -f, --ignore-case to fold lower case to upper case characters.
• -g, --general-numeric-sort to compare according to general numerical value.
• -i, --ignore-nonprinting to consider only printable characters.
• -M, --month-sort to compare (unknown) < ‘JAN’ < … < ‘DEC’
• -h, --human-numeric-sort to compare human readable numbers (e.g., 2K 1G)
• -n, --numeric-sort to compare according to string numerical value.
• -R, --random-sort to sort by random hash of keys.
• -random-source=FILE to get random bytes from FILE.
• -r, --reverse to reverse the result of comparisons.
• -sort=WORD to sort according to WORD (word can be general-numeric, human-numeric, month, numeric, random, version)
• -V, --version-sort for natural sort of (version) numbers within text.

Other options given in sort man page (linked above). Descriptions of how lines are compared and sorted given in man page. Examples of sort command also given in man page.

Misc.

• sed “stream editor”. Accepts standard input and modifies it based on an expression before displaying it as output data.
• sort takes a file name or standard input and orders each line alphabetically, printing it to standard output.
• source activates changes in bash profile for current session.

Background Commands and Persistent Sessions

To run a command in the background, add ampersand to the end of the command:

command &

To suppress the stdout and stderr messages, use:

command > /dev/null 2>&1 &

To display the status of all stoped and background jobs in the current shell session:

jobs -l

To bring a background process to the foreground, use the fg command (or fg %1 if you have multiple background jobs.

To terminate the background process, use the kill command followed by the process ID (which can be obtained through the jobs -l command, above. In this example it’s 12928):

kill -9 12928

Generally, if connection drops or you exit the shell session, the background process terminates. To keep the process running, use the disown command or start the process with the nohup command.

Alternatively, use Tmux (“terminal multiplexer”) to switch between multiple programs in one terminal. Tmux sessions are persistent; programs will continue to run even if you exit the shell or are disconnected.