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

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' 

Sed

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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' 

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

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

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

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

Awk

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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}'

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)}'

Xargs

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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

Find

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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

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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

for loop

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

Download

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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

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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

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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

(command here) 2>log &

or

(command here) 2>&1| tee logfile

or

(command here) 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}

array

declare -A array=()

send a directory

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

System

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snapshot of the current processes

ps 

check graphics card

lspci

show IP address

$ip add show

or

ifconfig

check system version

cat /etc/*-release

Linux Programmer's Manuel: hier- description of the filesystem hierarchy

man hier

list job

jobs -l

export PATH

export PATH=$PATH:~/path/you/want

make file execuable

chmod +x filename

//you can now ./filename to execute it

list screen

screen -d -r

echo screen name

screen -ls

check system (x86-64)

uname -i

surf the net

links www.google.com

add user, set passwd

useradd username
passwd username

edit variable for bash, (e.g. displaying the whole path)

1. joe ~/.bash_profile 
2. export PS1='\u@\h:\w\$' 

//$PS1 is a variable that defines the makeup and style of the command prompt

3. source ~/.bash_profile

edit environment setting (e.g. alias)

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)

$echo $PATH

//list of directories separated by a colon

list all environment variables for current user

$env

show partition format

lsblk

soft link program to bin

ln -s /path/to/program /home/usr/bin

//must be the whole path to the program

show hexadecimal view of data

hexdump -C filename.class

jump to different node

rsh node_name

check port (active internet connection)

netstat -tulpn

find whick link to a file

readlink filename

check where a command link to (e.g. python)

which python

list total size of a directory

du -hs .

or

du -sb

copy directory with permission setting

cp -rp /path/to/directory

store current directory

pushd . $popd ;dirs -l 

show disk usage

df -h 

or

du -h 

or

du -sk /var/log/* |sort -rn |head -10

show current runlevel

runlevel

switch runlevel

init 3 

or

telinit 3 

permanently modify runlevel

1. edit /etc/init/rc-sysinit.conf 
2. env DEFAULT_RUNLEVEL=2 

become root

su

become somebody

su somebody

report user quotes on device

requota -auvs

get entries in a number of important databases

getent database_name

(e.g. the 'passwd' database)

getent passwd

//list all user account (all local and LDAP) (e.g. fetch list of grop accounts)

getent group

//store in database 'group'

little xwindow tools

xclock
xeyes

change owner of file

chown user_name filename
chown -R user_name /path/to/directory/

//chown user:group filename

list current mount detail

df

list current usernames and user-numbers

cat /etc/passwd

get all username

getent passwd| awk '{FS="[:]"; print $1}'

show all users

compgen -u

show all groups

compgen -g

show group of user

group username

show uid, gid, group of user

id username

check if it's root

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

more /proc/cpuinfo

or

lscpu

set quota for user (e.g. disk soft limit: 120586240; hard limit: 125829120)

setquota username 120586240 125829120 0 0 /home

show quota for user

quota -v username

fork bomb

:(){:|:&};:

//dont try this at home

check user login

lastlog

edit path for all users

joe /etc/environment

//edit this file

show running processes

ps aux

find maximum number of processes

cat /proc/sys/kernal/pid_max

show and set user limit

ulimit -u

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