Unix Cheat Sheet

FINDING HELP

`man`	format and display the on-line manual pages
	`man [section] name ...`
	(`q`)uit (`/`) search

SPECIAL KEY (COMBINATIONS)

`<TAB>`	Auto-complete
`<UP>`	Scroll through previous commands
`<CTRL>-C`	Cancel
`<CTRL>-A`	Jump to beginning of line

`ls`	list directory contents
	`ls [-ABCFGHLOPRSTUW@abcdefghiklmnopqrstuwx1] [file ...]`
`cd`	Change the current directory to DIR
	`cd [-L\\|-P] [dir]`
`cp`	copy files
	`cp [-R [-H \\| -L \\| -P]] [-fi \\| -n] [-apvX] source_file target_file`
`mv`	move files
	`mv [-f \\| -i \\| -n] [-v] source target`
`rm`	remove directory entries
	`rm [-dfiPRrvW] file ...`
`mkdir`	make directories
	`mkdir [-pv] [-m mode] directory_name ...`
`.`	Current directory
`..`	Parent directory
`~`	Home directory
`/`	Root directory
`*`	Wildcard

EXPLORE TEXT FILES

`head`	display first lines of a file
	`head [-n count \\| -c bytes] [file ...]`
`less`	program used to view contents of text files one screen at a time
	`less [-...N...S...]`
	(`q`)uit (`/`)search
`wc`	word, line, character, and byte count
	`wc [-clmw] [file ...]`
`grep`	file pattern searcher
	`grep [-...c...vw...] [-A num] [-B num] [-f file] [pattern] [file ...]`
`cut`	cut out selected portions of each line of a file
	`cut -f list [-d delim] [-s] [file ...]`
`sort`	sort lines of text files
	`sort [OPTION]... [FILE]...`
`uniq`	report or filter out repeated lines in a file
	`uniq [-c \\| -d \\| -u] [-i] [-f num] [-s chars] [input_file [output_file]]`

INPUT OUTPUT REDIRECTION

`\|`	send output of one command to another command as input
`>`	save output to a new file
`>>`	append output to an existing file
`<`	use file as input

bash scripts

awk

awk can be used to cat a file, or return all of its contents, but it can also be used to subset and only print parts of a file. Specific lines or specific columns based on some condition.

awk expressions use single quotation marks and curly braces.

Print the whole file:

awk '{print}' input_file

Print specific columns:

This example will print just the 1st, 3rd, and 5th columns of every line of the input file.

awk '{print $1,$3,$5}' input_file

Checking a condition:

If you want to print a line only if a column contains a specific value, then you would use an if conditional statement within the awk expression.

This example will only print a line from the input_file if the value in the first column is “chr21”.

awk '{if ($1 == "chr21") {print}}' input_file

Passing a variable:

If you want to use a variable that is predefined within a script within your awk command, you have to set the identity of that variable with the -v flag. Variables set within a script can’t be referenced within the single parentheses of the awk expression. In the example below, a line will be printed if the first column has “apple” in it.

FRUIT="apple"
awk -v fruit=$FRUIT '{if ($1 == fruit) {print}}' input_file

Specifying the delimiter or field separator of output:

This example sets the output field separator (OFS) to make the printed output tab-delimited (“\t”)

awk 'BEGIN{OFS="\t"} {$1=$1; print}' input_file

This example sets the output field separator (OFS) to make the printed output (only the first 3 columns of the input files) separated by a comma (“,”)

awk 'BEGIN{OFS=","} {print $1,$2,$3}' input_file