-

-Handy Bash oneliner commands for tsv file editing

- - - -

-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/$/]/' filename
- -
-add string to end of each line (e.g. "}")
- -
sed -e 's/$/\}\]/' 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'
- -

-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
- -

-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

- -
-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
- -
(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}
- -
-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
- -

-System

- -

[back to top]

- -
-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
- -
-which ports are listening for TCP connections from the network
- -
nmap -sT -O localhost
- -
-print out number of cores/ processors
- -
nproc --all
- -
-check status of each core
- -
    -
  1. top
    2. -
  2. press '1'
    3. -
- -

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

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