Bash-Oneliner

Hi bash learners and bioinformaticans, welcome to Bash Oneliner learning station. I started studying bioinformatics data three years ago, and I was amazed by those single-word bash commands which are much faster than my dull scripts, so i started bash. Not all the code here is oneliner (if the ';' counts..), but i put effort on making them brief and fast.

This blog will focus on simple bash commands for parsing biological data, most of which are tsv files (tab-separated values); some of them are for Ubuntu system maintaining. I have been recording the bash commands on my notebook, but putting them on web will help others and myself to query. I apologize that there won't be any citation for the codes, coz i haven't make any record of it, but they are probably from dear Google and Stackoverflow.

English and bash are not my first language, so... correct me anytime, thank you

In case you would like to check and vote up my questions on Stackoverflow, here's my page: http://stackoverflow.com/users/4290753/once

Here's a more stylish version~ http://onceupon.github.io/Bash-Oneliner/

Handy Bash oneliner commands for tsv file editing

• Grep
• Sed
• Awk
• Xargs
• Find
• Loops
• Download
• Random
• Others
• System

Grep

extract text bewteen words (e.g. w1,w2)

grep -o -P '(?<=w1).*(?=w2)'

grep lines without word (e.g. bbo)

grep -v bbo filename

grep only one/first match (e.g. bbo)

grep -m 1 bbo filename

grep and count (e.g. bbo)

grep -c bbo filename

insensitive grep (e.g. bbo/BBO/Bbo)

grep -i "bbo" filename 

count occurrence (e.g. three times a line count three times)

grep -o bbo filename 

COLOR the match (e.g. bbo)!

grep --color bbo filename 

grep search all files in a directory(e.g. bbo)

grep -R bbo /path/to/directory 

or

grep -r bbo /path/to/directory 

search all files in directory, only output file names with matches(e.g. bbo)

grep -Rh bbo /path/to/directory 

or

grep -rh bbo /path/to/directory 

grep OR (e.g. A or B or C or D)

grep 'A\|B\|C\|D' 

grep AND (e.g. A and B)

grep 'A.*B' 

grep all content of a fileA from fileB

grep -f fileA fileB 

grep a tab

grep $'\t' 

grep variable from variable

$echo "$long_str"|grep -q "$short_str"
if [ $? -eq 0 ]; then echo 'found'; fi

//grep -q will output 0 if match found
//remember to add space between []!

grep strings between a bracket()

grep -oP '\(\K[^\)]+'

grep number of characters with known strings in between(e.g. AAEL000001-RA)

grep -o -w "\w\{10\}\-R\w\{1\}"

// \w word character [0-9a-zA-Z_] \W not word character

a lot examples here

http://www.cyberciti.biz/faq/grep-regular-expressions/

Sed

[back to top]

remove lines with word (e.g. bbo)

sed "/bbo/d" filename

edit infile (edit and save)

sed -i "/bbo/d" filename

when using variable (e.g. $i), use double quotes " "

e.g. add >$i to the first line (to make a FASTA file)

sed "1i >$i"  

//notice the double quotes! in other examples, you can use a single quote, but here, no way!
//'1i' means insert to first line

delete empty lines

sed '/^\s*$/d' 

or

sed 's/^$/d' 

delete last line

sed '$d' 

delete last character from end of file

sed -i '$ s/.$//' filename

add string to end of file (e.g. "]")

sed '$s/$/]/' filename

add string to beginning of every line (e.g. bbo)

sed -e 's/^/bbo/' file

add string to end of each line (e.g. "}")

sed -e 's/$/\}\]/' filename

add \n every nth character (e.g. every 4th character)

sed 's/.\{4\}/&\n/g' 

concatenate/combine/join files with a seperator and next line (e.g seperate by ",")

sed -s '$a,' *.json > all.json

substitution (e.g. replace A by B)

sed 's/A/B/g' filename 

select lines start with string (e.g. bbo)

sed -n '/^@S/p' 

delete lines with string (e.g. bbo)

sed '/bbo/d' filename 

print every nth lines

sed -n '0~3p' filename

//catch 0: start; 3: step

print every odd # lines

sed -n '1~2p' 

print every third line including the first line

sed -n '1p;0~3p' 

remove leading whitespace and tabs

sed -e 's/^[ \t]*//'

//notice a whitespace before '\t'!!

remove only leading whitespace

sed 's/ *//'

//notice a whitespace before '*'!!

remove ending commas

sed 's/,$//g' 

add a column to the end

sed "s/$/\t$i/"

//$i is the valuable you want to add
e.g. add the filename to every last column of the file

for i in $(ls);do sed -i "s/$/\t$i/" $i;done

add extension of filename to last column

for i in T000086_1.02.n T000086_1.02.p;do sed "s/$/\t${i/*./}/" $i;done >T000086_1.02.np

remove newline\ nextline

sed ':a;N;$!ba;s/\n//g'

print a number of lines (e.g. line 10th to line 33 rd)

sed -n '10,33p' <filename

change delimiter

sed 's=/=\\/=g'

replace with wildcard (e.g A-1-e or A-2-e or A-3-e....)

sed 's/A-.*-e//g' filename

remove last character of file

```bash`` sed '$ s/.$//'

##### insert character at specified position of file (e.g. AAAAAA --> AAA#AAA)
```bash``
sed -r -e 's/^.{3}/&#/' file

Awk

[back to top]

set tab as field separator

awk -F $'\t'  

output as tab separated (also as field separator)

awk -v OFS='\t' 

pass variable

a=bbo;b=obb;
awk -v a="$a" -v b="$b" "$1==a && $10=b' filename 

print number of characters on each line

awk '{print length ($0);}' filename 

find number of columns

awk '{print NF}' 

reverse column order

awk '{print $2, $1}' 

check if there is a comma in a column (e.g. column $1)

awk '$1~/,/ {print}'  

split and do for loop

awk '{split($2, a,",");for (i in a) print $1"\t"a[i]} filename 

print all lines before nth occurence of a string (e.g stop print lines when bbo appears 7 times)

awk -v N=7 '{print}/bbo/&& --N<=0 {exit}'

print filename and last line of all files in directory

ls|xargs -n1 -I file awk '{s=$0};END{print FILENAME,s}' file'

add string to the beginning of a column (e.g add "chr" to column $3)

awk 'BEGIN{OFS="\t"}$3="chr"$3' 

remove lines with string (e.g. bbo)

awk '!/bbo/' file 

column subtraction

cat file| awk -F '\t' 'BEGIN {SUM=0}{SUM+=$3-$2}END{print SUM}'

usage and meaning of NR and FNR

e.g.
fileA:
a
b
c
fileB:
d
e

awk 'print FILENAME, NR,FNR,$0}' fileA fileB 

fileA 1 1 a
fileA 2 2 b
fileA 3 3 c
fileB 4 1 d
fileB 5 2 e

and gate

e.g.
fileA:
1 0
2 1
3 1
4 0

fileB:
1 0
2 1
3 0
4 1

awk -v OFS='\t' 'NR=FNR{a[$1]=$2;next} NF {print $1,((a[$1]=$2)? $2:"0")}' fileA fileB 

1 0
2 1
3 0
4 0

round all numbers of file (e.g. 2 significant figure)

awk '{while (match($0, /[0-9]+\[0-9]+/)){
    \printf "%s%.2f", substr($0,0,RSTART-1),substr($0,RSTART,RLENGTH)
    \$0=substr($0, RSTART+RLENGTH)
    \}
    \print
    \}'

give number/index to every row

awk '{printf("%s\t%s\n",NR,$0)}'

break combine column data into rows

e.g.
seperate

David cat,dog
into
David cat
David dog

detail here:　http://stackoverflow.com/questions/33408762/bash-turning-single-comma-separated-column-into-multi-line-string

awk '{split($2,a,",");for(i in a)print $1"\t"a[i]}' file

sum up a file (each line in file contains only one number)

awk '{s+=$1} END {print s}' filename

average a file (each line in file contains only one number)

awk '{s+=$1}END{print s/NR}'

print field start with string (e.g Linux)

awk '$1 ~ /^Linux/'

sort a row (e.g. 1 40 35 12 23 --> 1 12 23 35 40)

awk ' {split( $0, a, "\t" ); asort( a ); for( i = 1; i <= length(a); i++ ) printf( "%s\t", a[i] ); printf( "\n" ); }'

Xargs

[back to top]

set tab as delimiter (default:space)

xargs -d\t

display 3 items per line

echo 1 2 3 4 5 6| xargs -n 3

//1 2 3
4 5 6

prompt before execution

echo a b c |xargs -p -n 3

print command along with output

xargs -t abcd

///bin/echo abcd
//abcd

with find and rm

find . -name "*.html"|xargs rm -rf

delete fiels with whitespace in filename (e.g. "hello 2001")

find . -name "*.c" -print0|xargs -0 rm -rf

show limits

xargs --show-limits

move files to folder

find . -name "*.bak" -print 0|xargs -0 -I {} mv {} ~/old

or

find . -name "*.bak" -print 0|xargs -0 -I file mv file ~/old

move first 100th files to a directory (e.g. d1)

ls |head -100|xargs -I {} mv {} d1

parallel

time echo {1..5} |xargs -n 1 -P 5 sleep

a lot faster than

time echo {1..5} |xargs -n1 sleep

copy all files from A to B

find /dir/to/A -type f -name "*.py" -print 0| xargs -0 -r -I file cp -v -p file --target-directory=/path/to/B

//v: verbose|
//p: keep detail (e.g. owner)

with sed

ls |xargs -n1 -I file sed -i '/^Pos/d' filename

add the file name to the first line of file

ls |sed 's/.txt//g'|xargs -n1 -I file sed -i -e '1 i\>file\' file.txt

count all files

ls |xargs -n1 wc -l

to filter txt to a single line

ls -l| xargs

count files within directories

echo mso{1..8}|xargs -n1 bash -c 'echo -n "$1:"; ls -la "$1"| grep -w 74 |wc -l' --

// "--" signals the end of options and display further option processing

download dependencies files and install (e.g. requirements.txt)

cat requirements.txt| xargs -n1 sudo pip install

count lines in all file, also count total lines

ls|xargs wc -l

xargs and grep

cat grep_list |xargs -I{} grep {} filename

Find

[back to top]

list all sub directory/file in the current directory

find .

list all files under the current directory

find . -type f

list all directories under the current directory

find . -type d

edit all files under current directory (e.g. replace 'www' with 'ww')

find . name '*.php' -exec sed -i 's/www/w/g' {} \;

if no subdirectory

replace "www" "w" -- *

//a space before *

find and output only filename (e.g. "mso")

find mso*/ -name M* -printf "%f\n"

find and delete file with size less than (e.g. 74 byte)

find . -name "*.mso" -size -74c -delete

//M for MB, etc

Loops

[back to top]

while loop, column subtraction of a file (e.g. a 3 columns file)

while read a b c; do echo $(($c-$b));done < <(head filename)

//there is a space between the two '<'s

while loop, sum up column subtraction

i=0; while read a b c; do ((i+=$c-$b)); echo $i; done < <(head filename)

if loop

if (($j==$u+2))

//(( )) use for arithmetic operation

if [[$age >21]]

// use for comparison

test if file exist

if [ -e $DF ]
then
  echo -e "file exists!"
fi

for loop

for i in $(ls); do echo file $i;done

Download

[back to top]

download all from a page

wget -r -l1 -H -t1 -nd -N -np -A mp3 -e robots=off http://example.com

//-r: recursive and download all links on page
//-l1: only one level link
//-H: span host, visit other hosts
//-t1: numbers of retries
//-nd: don't make new directories, download to here
//-N: turn on timestamp
//-nd: no parent
//-A: type (seperate by ,)
//-e robots=off: ignore the robots.txt file which stop wget from crashing the site, sorry example.com

Random

[back to top]

random pick 100 lines from a file

shuf -n 100 filename

random order (lucky draw)

for i in a b c d e; do echo $i; done| shuf

echo series of random numbers between a range (e.g. generate 15 random numbers from 0-10)

shuf -i 0-10 -n 15

echo a random number

echo $RANDOM

random from 0-9

echo $((RANDOM % 10))

random from 1-10

echo $(((RANDOM %10)+1))

Others

[back to top]

remove newline / nextline

tr --delete '\n' <input.txt >output.txt

replace newline

tr '\n' ' ' <filename

compare files (e.g. fileA, fileB)

diff fileA fileB

//a: added; d:delete; c:changed

or

sdiff fileA fileB

//side-to-side merge of file differences

number a file (e.g. fileA)

nl fileA

or

nl -nrz fileA

//add leading zeros

combine/ paste two files (e.g. fileA, fileB)

paste fileA fileB

//default tab seperated

reverse string

echo 12345| rev

read .gz file without extracting

zmore filename

or

zless filename

run in background, output error file

some_commands  &>log &

or

some_commands 2>log &

or

some_commands 2>&1| tee logfile

or

some_commands 2>&1 >>outfile

//0: standard input; 1: standard output; 2: standard error

send mail

echo 'heres the content'| mail -A 'file.txt' -s 'mail.subject' me@gmail.com

//use -a flag to set send from (-a "From: some@mail.tld")

.xls to csv

xls2csv filename

append to file (e.g. hihi)

echo 'hihi' >>filename

make BEEP sound

speaker-test -t sine -f 1000 -l1

set beep duration

(speaker-test -t sine -f 1000) & pid=$!;sleep 0.1s;kill -9 $pid

history edit/ delete

~/.bash_history

or

history -d [line_number]

get last history/record filename

head !$

clean screen

clear

or

Ctrl+l

send data to last edited file

cat /directory/to/file
echo 100>!$

run history number (e.g. 53)

!53

run last command

!!

run last command that began with (e.g. cat filename)

!cat

or

!c

//run cat filename again

extract .xf

1.unxz filename.tar.xz  
2.tar -xf filename.tar

install python package

pip install packagename

Download file if necessary

data=file.txt
url=http://www.example.com/$data
if [! -s $data];then
    echo "downloading test data..."
    wget $url
fi

wget to a filename (when a long name)

wget -O filename "http://example.com"

wget files to a folder

wget -P /path/to/directory "http://example.com"

delete current bash command

Ctrl+U

or

Ctrl+C

or

Alt+Shift+#

//to make it to history

add things to history (e.g. "addmetohistory")

#addmetodistory

//just add a "#" before~~

sleep awhile or wait for a moment or schedule a job

sleep 5;echo hi

count the time for executing a command

time echo hi

backup with rsync

rsync -av filename filename.bak
rsync -av directory directory.bak
rsync -av --ignore_existing directory/ directory.bak
rsync -av --update directory directory.bak

//skip files that are newer on receiver (i prefer this one!)

make all directories at one time!

mkdir -p project/{lib/ext,bin,src,doc/{html,info,pdf},demo/stat}

//-p: make parent directory
//this will create project/doc/html/; project/doc/info; project/lib/ext ,etc

run command only if another command returns zero exit status (well done)

cd tmp/ && tar xvf ~/a.tar

run command only if another command returns non-zero exit status (not finish)

cd tmp/a/b/c ||mkdir -p tmp/a/b/c

extract to a path

tar xvf -C /path/to/directory filename.gz

use backslash "" to break long command

cd tmp/a/b/c \
> || \
>mkdir -p tmp/a/b/c

get pwd

VAR=$PWD; cd ~; tar xvf -C $VAR file.tar

//PWD need to be capital letter

list file type of file (e.g. /tmp/)

file /tmp/

//tmp/: directory

bash script

#!/bin/bash
file=${1#*.}

//remove string before a "."

file=${1%.*}

//remove string after a "."

search from history

Ctrl+r

python simple HTTP Server

python -m SimpleHTTPServer

variables

{i/a/,}

e.g. replace all

{i//a/,}

//for variable i, replace all 'a' with a comma

read user input

read input
echo $input

generate sequence 1-10

seq 10

sum up input list (e.g. seq 10)

seq 10|paste -sd+|bc

find average of input list/file

i=`wc -l filename|cut -d ' ' -f1`; cat filename| echo "scale=2;(`paste -sd+`)/"$i|bc

generate all combination (e.g. 1,2)

echo {1,2}{1,2}

//1 1, 1 2, 2 1, 2 2

generate all combination (e.g. A,T,C,G)

set = {A,T,C,G}
group= 5
for ((i=0; i<$group; i++));do
    repetition=$set$repetition;done
    bash -c "echo "$repetition""

read file content to variable

foo=$(<test1)

echo size of variable

echo ${#foo}

echo tab

echo -e ' \t '

array

declare -A array=()

send a directory

scp -r directoryname user@ip:/path/to/send

split file into lines (e.g. 1000 lines/smallfile)

$ split -d -l 1000 bigfilename

rename all files (e.g. remove ABC from all .gz files)

rename 's/ABC//' *.gz

remove extention (e.g remove .gz from filename.gz)

basename filename.gz .gz

zcat filename.gz> $(basename filename.gz .gz).unpacked

use the squeeze repeat option (e.g. /t/t --> /t)

tr -s "/t" < filename

do not print nextline with echo

echo -e 'text here \c'

use the last argument

!$

check last exit code

echo $?

view first 50 characters of file

head -c 50 file

open pictures/images from ssh server

1. ssh -X user_name@ip_address
2. apt-get install eog
3. eog picture.png

Use gedit on server (GUI editor)

1. ssh -X user_name@ip_address
2. apt-get install gedit
3. gedit filename.txt

open PDF file from ssh server

1. ssh -X user_name@ip_address
2. apt-get install evince
3. evince filename.pdf

group/combine rows into one row

e.g.
AAAA
BBBB
CCCC
DDDD

cat filename|paste - -
-->
AAAABBBB
CCCCDDDD
cat filename|paste - - - -
-->
AAAABBBBCCCCDDDD

fastq to fasta

cat file.fastq | paste - - - - | sed 's/^@/>/g'| cut -f1-2 | tr '\t' '\n' >file.fa

cut and get last column

cat file|rev | cut -d/ -f1 | rev

add one to variable/increment a numeric variable (e.g. $var)

((var++))

some handy environment variables

$0 :name of shell or shell script.
$1, $2, $3, ... :positional parameters.
$# :number of positional parameters.
$? :most recent foreground pipeline exit status.
$- :current options set for the shell.

   :pid of the current shell (not subshell).  
$!   :is the PID of the most recent background command.  


## System
[[back to top](#handy-bash-oneliner-commands-for-tsv-file-editing)]

##### snapshot of the current processes

```bash
ps 
```

##### check graphics card

```bash
lspci
```

##### show IP address
    
```bash
$ip add show
```
or
    
```bash
ifconfig
```

##### check system version
    
```bash
cat /etc/*-release
```

##### Linux Programmer's Manuel: hier- description of the filesystem hierarchy
    
```bash
man hier
```

##### list job
    
```bash
jobs -l
```

##### export PATH
    
```bash
export PATH=$PATH:~/path/you/want
```

##### make file execuable
    
```bash
chmod +x filename
```
//you can now ./filename to execute it

##### list screen
    
```bash
screen -d -r
```

##### echo screen name
    
```bash
screen -ls
```

##### check system (x86-64)
    
```bash
uname -i
```

##### surf the net

```bash
links www.google.com
```

##### add user, set passwd
    
```bash
useradd username
passwd username
```

##### edit variable for bash, (e.g. displaying the whole path)
    
```bash
1. joe ~/.bash_profile 
2. export PS1='\u@\h:\w\$' 
```
//$PS1 is a variable that defines the makeup and style of the command prompt 
```bash
3. source ~/.bash_profile
```

##### edit environment setting (e.g. alias)
    
```bash
1. joe ~/.bash_profile
2. alias pd="pwd" //no more need to type that 'w'!
3. source ~/.bash_profile
```

##### list environment variables (e.g. PATH)
    
```bash
$echo $PATH
```
//list of directories separated by a colon

##### list all environment variables for current user
    
```bash
$env
```

##### show partition format
    
```bash
lsblk
```

##### soft link program to bin
    
```bash
ln -s /path/to/program /home/usr/bin
```
//must be the whole path to the program

##### show hexadecimal view of data
    
```bash
hexdump -C filename.class
```

##### jump to different node
    
```bash
rsh node_name
```

##### check port (active internet connection)
    
```bash
netstat -tulpn
```

##### find whick link to a file
    
```bash
readlink filename
```

##### check where a command link to (e.g. python)
    
```bash
which python
```

##### list total size of a directory
    
```bash
du -hs .
```
or
    
```bash
du -sb
```

##### copy directory with permission setting
    
```bash
cp -rp /path/to/directory
```

##### store current directory
    
```bash
pushd . $popd ;dirs -l 
```

##### show disk usage
    
```bash
df -h 
```
or
   
```bash
du -h 
```
or
    
```bash
du -sk /var/log/* |sort -rn |head -10
```

##### show current runlevel
    
```bash
runlevel
```

##### switch runlevel
    
```bash
init 3 
```
or
```bash
telinit 3 
```
##### permanently modify runlevel
    
```bash
1. edit /etc/init/rc-sysinit.conf 
2. env DEFAULT_RUNLEVEL=2 
```

##### become root
    
```bash
su
```

##### become somebody
    
```bash
su somebody
```

##### report user quotes on device
    
```bash
requota -auvs
```

##### get entries in a number of important databases
    
```bash
getent database_name
```
(e.g. the 'passwd' database)
    
```bash
getent passwd
```
//list all user account (all local and LDAP)  
(e.g. fetch list of grop accounts)
    
```bash
getent group
```
//store in database 'group'

##### little xwindow tools
    
```bash
xclock
xeyes
```

##### change owner of file
    
```bash
chown user_name filename
chown -R user_name /path/to/directory/
```
//chown user:group filename

##### list current mount detail
    
```bash
df
```

##### list current usernames and user-numbers
    
```bash
cat /etc/passwd
```
##### get all username
    
```bash
getent passwd| awk '{FS="[:]"; print $1}'
```

##### show all users
    
```bash
compgen -u
```

##### show all groups
    
```bash
compgen -g
```

##### show group of user
    
```bash
group username
```

##### show uid, gid, group of user
    
```bash
id username
```

##### check if it's root
    
```bash
if [$(id -u) -ne 0];then
    echo "You are not root!"
    exit;
fi
```
//'id -u' output 0 if it's not root

##### find out CPU information
    
```bash
more /proc/cpuinfo
```
or
    
```bash
lscpu
```

##### set quota for user (e.g. disk soft limit: 120586240; hard limit: 125829120)
    
```bash
setquota username 120586240 125829120 0 0 /home
```

##### show quota for user
    
```bash
quota -v username
```

##### fork bomb
    
```bash
:(){:|:&};:
```
//dont try this at home

##### check user login
    
```bash
lastlog
```

##### edit path for all users
    
```bash
joe /etc/environment
```
//edit this file

##### show running processes
    
```bash
ps aux
```

##### find maximum number of processes
    
```bash
cat /proc/sys/kernal/pid_max
```

##### show and set user limit
    
```bash
ulimit -u
```
##### which ports are listening for TCP connections from the network

```bash
nmap -sT -O localhost
```

##### print out number of cores/ processors

```bash
nproc --all
```
##### check status of each core
1. top  
2. press '1'

##### show jobs and PID

```bash
jobs -l
```

##### list all running services

```bash
service --status-all
```

##### schedule shutdown server
```bash
shutdown -r +5 "Server will restart in 5 minutes. Please save your work."
```
##### cancel scheduled shutdown
```bash
shutdown -c
```

##### boardcast to all users
```bash
wall -n hihi
```

##### enable X11 forwarding,in order to use graphical application on servers
```bash
ssh -X user_name@ip_address
```
or setting through xhost

--> Install the following for Centos:  
xorg-x11-xauth  
xorg-x11-fonts-*  
xorg-x11-utils  


##### kill all process of a user
```bash
pkill -U user_name
```
##### set gedit preference on server

-->you might have to install the following:

apt-get install libglib2.0-bin;  

yum install dconf dconf-editor;  
yum install dbus dbus-x11;  

-->Check list  
```bash
gsettings list-recursively
```
-->Change setting  
e.g.
```bash
gsettings set org.gnome.gedit.preferences.editor highlight-current-line true
gsettings set org.gnome.gedit.preferences.editor scheme 'cobalt'
gsettings set org.gnome.gedit.preferences.editor use-default-font false
gsettings set org.gnome.gedit.preferences.editor editor-font 'Cantarell Regular 12'
```


=-=-=-=-=-A lot more coming!! =-=-=-=-=-=-=-=-=-=waitwait-=-=-=-=-=-=-=-=-=-