##Handy Bash oneliner commands for tsv file editing

- [Grep](#grep)
- [Sed](#sed)
- [Awk](#awk)
- [Xargs](#xargs)
- [Find](#find)
- [Loops](#loops)
- [Download](#download)
- [Random](#random)
- [Others](#others)
- [System](#system)

##Grep
#####extract text bewteen words (e.g. w1,w2)
    
```bash
grep -o -P '(?<=w1).*(?=w2)'
```

#####grep lines without word (e.g. bbo)
     
```bash
grep -v bbo filename
```

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

```bash
grep -m 1 bbo filename
```

#####grep and count (e.g. bbo)
    
```bash
grep -c bbo filename
```

#####insensitive grep (e.g. bbo/BBO/Bbo)
    
```bash
grep -i "bbo" filename 
```

#####count occurrence (e.g. three times a line count three times)
    
```bash
grep -o bbo filename 
```

#####COLOR the match (e.g. bbo)!
    
```bash
grep --color bbo filename 
```

#####grep search all files in a directory(e.g. bbo)
    
```bash
grep -R bbo /path/to/directory 
```

or
    
```bash
grep -r bbo /path/to/directory 
```
#####search all files in directory, only output file names with matches(e.g. bbo)
    
```bash
grep -Rh bbo /path/to/directory 
```
or
```bash    
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)
    
```bash
grep 'A.*B' 
```

#####grep all content of a fileA from fileB
    
```bash
grep -f fileA fileB 
```

#####grep a tab
    
```bash
grep $'\t' 
```

#####grep variable from variable
```bash
$echo "$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()
```bash
grep -oP '\(\K[^\)]+'
```

#####grep number of characters with known strings in between(e.g. AAEL000001-RA)
```bash
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](#handy-bash-oneliner-commands-for-tsv-file-editing)]

#####remove lines with word (e.g. bbo)
    
```bash
sed "/bbo/d" filename
```

#####edit infile (edit and save)
    
```bash
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)
    
```bash
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
    
```bash
sed '/^\s*$/d' 
```    
or
   
```bash
sed 's/^$/d' 
```
#####delete last line
   
```bash
sed '$d' 
```

#####delete last character from end of file
```bash
sed -i '$ s/.$//' filename
```

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

```bash
sed '$s/$/]/' filename
```

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

#####add \n every nth character (e.g. every 4th character)
    
```bash
sed 's/.\{4\}/&\n/g' 
```

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

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

#####substitution (e.g. replace A by B)
    
```bash
sed 's/A/B/g' filename 
```
#####select lines start with string (e.g. bbo)
    
```bash
sed -n '/^@S/p' 
```
#####delete lines with string (e.g. bbo)
    
```bash
sed '/bbo/d' filename 
```
#####print every nth lines
    
```bash
sed -n '0~3p' filename
```
//catch 0: start; 3: step


#####print every odd # lines
    
```bash
sed -n '1~2p' 
```
#####print every third line including the first line
    
```bash
sed -n '1p;0~3p' 
```
#####remove leading whitespace and tabs
    
```bash
sed -e 's/^[ \t]*//'
```
//notice a whitespace before '\t'!!


#####remove only leading whitespace
    
```bash
sed 's/ *//'
```
//notice a whitespace before '*'!!


#####remove ending commas
    
```bash
sed 's/,$//g' 
```
#####add a column to the end
    
```bash
sed "s/$/\t$i/"
```
//$i is the valuable you want to add
e.g. add the filename to every last column of the file
    
```bash
for i in $(ls);do sed -i "s/$/\t$i/" $i;done
```
#####add extension of filename to last column

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

#####print a number of lines (e.g. line 10th to line 33 rd)
    
```bash
sed -n '10,33p' <filename
```

#####change delimiter 
```bash
sed 's=/=\\/=g'
```


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

#####set tab as field separator
    
```bash
awk -F $'\t'  
```

#####output as tab separated (also as field separator)
   
```bash
awk -v OFS='\t' 
```

#####pass variable

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

#####print number of characters on each line
    
```bash
awk '{print length ($0);}' filename 
```

#####find number of columns
  
```bash
awk '{print NF}' 
```

#####reverse column order
    
```bash
awk '{print $2, $1}' 
```

#####check if there is a comma in a column (e.g. column $1)
    
```bash
awk '$1~/,/ {print}'  
```

#####split and do for loop
    
```bash
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)
    
```bash
awk -v N=7 '{print}/bbo/&& --N<=0 {exit}'
```

#####print filename and last line of all files in directory
```bash
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)
    
```bash
awk 'BEGIN{OFS="\t"}$3="chr"$3' 
```

#####remove lines with string (e.g. bbo)
    
```bash
awk '!/bbo/' file 
```

#####column subtraction
    
```bash
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
    
```bash
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
    
```bash
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)
    
```bash
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
    
```bash
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
```bash
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)

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

#####average a file (each line in file contains only one number)
```bash
awk '{s+=$1}END{print s/NR}'
```

#####print field start with string (e.g Linux)

```bash
awk '$1 ~ /^Linux/'
```

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

```bash
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](#handy-bash-oneliner-commands-for-tsv-file-editing)]

#####set tab as delimiter (default:space)

```bash
xargs -d\t
```

#####display 3 items per line

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

//1 2 3
  4 5 6


#####prompt before execution

```bash
echo a b c |xargs -p -n 3
```

#####print command along with output

```bash
xargs -t abcd
```

///bin/echo abcd
//abcd


#####with find and rm

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

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

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

#####show limits

```bash
xargs --show-limits
```

#####move files to folder

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

or

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

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

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

#####parallel

```bash
time echo {1..5} |xargs -n 1 -P 5 sleep
```
a lot faster than
```bash
time echo {1..5} |xargs -n1 sleep
```

#####copy all files from A to B

```bash
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

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

#####add the file name to the first line of file

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

#####count all files

```bash
ls |xargs -n1 wc -l
```

#####to filter txt to a single line

```bash
ls -l| xargs
```

#####count files within directories

```bash
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)
 
```bash
cat requirements.txt| xargs -n1 sudo pip install
```

#####count lines in all file, also count total lines

```bash
ls|xargs wc -l
```



##Find 
[[back to top](#handy-bash-oneliner-commands-for-tsv-file-editing)]
#####list all sub directory/file in the current directory
    
```bash
find .
```

#####list all files under the current directory
    
```bash
find . -type f
```

#####list all directories under the current directory
    
```bash
find . -type d
```

#####edit all files under current directory (e.g. replace 'www' with 'ww')
    
```bash
find . name '*.php' -exec sed -i 's/www/w/g' {} \;
```
if no subdirectory
    
```bash
replace "www" "w" -- *
```
//a space before *


#####find and output only filename (e.g. "mso")
    
```bash
find mso*/ -name M* -printf "%f\n"
```

#####find and delete file with size less than (e.g. 74 byte)
    
```bash
find . -name "*.mso" -size -74c -delete
```
//M for MB, etc


##Loops
[[back to top](#handy-bash-oneliner-commands-for-tsv-file-editing)]
#####while loop, column subtraction of a file (e.g. a 3 columns file)
    
```bash
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
    
```bash
i=0; while read a b c; do ((i+=$c-$b)); echo $i; done < <(head filename)
```

#####if loop
    
```bash
if (($j==$u+2))
```
//(( )) use for arithmetic operation
    
```bash
if [[$age >21]]
```
//[[ ]] use for comparison

#####for loop
    
```bash
for i in $(ls); do echo file $i;done
```


##Download
[[back to top](#handy-bash-oneliner-commands-for-tsv-file-editing)]
#####download all from a page
    
```bash
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](#handy-bash-oneliner-commands-for-tsv-file-editing)]
#####random pick 100 lines from a file
    
```bash
shuf -n 100 filename
```

#####random order (lucky draw)
    
```bash
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)
    
```bash
shuf -i 0-10 -n 15
```

#####echo a random number
    
```bash
echo $RANDOM
```

#####random from 0-9
    
```bash
echo $((RANDOM % 10))
```

#####random from 1-10
    
```bash
echo $(((RANDOM %10)+1))
```



##Others
[[back to top](#handy-bash-oneliner-commands-for-tsv-file-editing)]
#####remove newline / nextline
    
```bash
tr --delete '\n' <input.txt >output.txt
```

#####replace newline
     
```bash
tr '\n' ' ' <filename
```

#####compare files (e.g. fileA, fileB)
    
```bash
diff fileA fileB
```
//a: added; d:delete; c:changed

or

```bash
sdiff fileA fileB
```
//side-to-side merge of file differences


#####number a file (e.g. fileA)

```bash
nl fileA
```
or

```bash
nl -nrz fileA
```
//add leading zeros


#####combine/ paste two files (e.g. fileA, fileB)
    
```bash
paste fileA fileB
```
//default tab seperated


#####reverse string
    
```bash
echo 12345| rev
```

#####read .gz file without extracting
    
```bash
zmore filename
```
or
    
```bash
zless filename
```

#####run in background, output error file
    
```bash
(command here) 2>log &
```

or

```bash
(command here) 2>&1| tee logfile
```

or

```bash
(command here) 2>&1 >>outfile
```
//0: standard input; 1: standard output; 2: standard error


#####send mail
    
```bash
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
    
```bash
xls2csv filename
```
#####append to file (e.g. hihi)
    
```bash
echo 'hihi' >>filename
```

#####make BEEP sound
    
```bash
speaker-test -t sine -f 1000 -l1
```

#####set beep duration
    
```bash
(speaker-test -t sine -f 1000) & pid=$!;sleep 0.1s;kill -9 $pid
```

#####history edit/ delete
    
```bash
~/.bash_history
```
or

```bash
history -d [line_number]
```

#####get last history/record filename
    
```bash
head !$
```

#####clean screen
    
```bash
clear
```

or

```bash
Ctrl+l
```

#####send data to last edited file
    
```bash
cat /directory/to/file
echo 100>!$
```

#####run history number (e.g. 53)
    
```bash
!53
```

#####run last command
    
```bash
!!
```

#####run last command that began with (e.g. cat filename)
    
```bash
!cat
```

or

```bash
!c
```
//run cat filename again


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

#####install python package
    
```bash
pip install packagename
```


#####Download file if necessary
    
```bash
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)
    
```bash
wget -O filename "http://example.com"
```

#####wget files to a folder

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

#####delete current bash command
    
```bash
Ctrl+U
```

or

```bash
Ctrl+C
```

or

```bash
Alt+Shift+#
```
//to make it to history


#####add things to history (e.g. "addmetohistory")
    
```bash
#addmetodistory
```
//just add a "#" before~~


#####sleep awhile or wait for a moment or schedule a job
    
```bash
sleep 5;echo hi
```

#####count the time for executing a command
    
```bash
time echo hi
```

#####backup with rsync
    
```bash
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!
    
```bash
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)
    
```bash
cd tmp/ && tar xvf ~/a.tar
```

#####run command only if another command returns non-zero exit status (not finish)
    
```bash
cd tmp/a/b/c ||mkdir -p tmp/a/b/c
```

#####extract to a path
    
```bash
tar xvf -C /path/to/directory filename.gz
```

#####use backslash "\" to break long command
    
```bash
cd tmp/a/b/c \
> || \
>mkdir -p tmp/a/b/c
```

#####get pwd
    
```bash
VAR=$PWD; cd ~; tar xvf -C $VAR file.tar
```
//PWD need to be capital letter

#####list file type of file (e.g. /tmp/)
    
```bash
file /tmp/
```
//tmp/: directory


#####bash script
    
```bash
#!/bin/bash
file=${1#*.}
```
//remove string before a "."

```bash
file=${1%.*}
```
//remove string after a "."

#####search from history
    
```bash
Ctrl+r
```

#####python simple HTTP Server
    
```bash
python -m SimpleHTTPServer
```

#####variables
    
```bash
{i/a/,}
```
e.g. replace all
```bash
{i//a/,}
```
//for variable i, replace all 'a' with a comma

#####read user input
    
```bash
read input
echo $input
```

#####generate sequence 1-10
    
```bash
seq 10
```

#####sum up input list (e.g. seq 10)
    
```bash
seq 10|paste -sd+|bc
```

#####find average of input list/file
    
```bash
i=`wc -l filename|cut -d ' ' -f1`; cat filename| echo "scale=2;(`paste -sd+`)/"$i|bc
```

#####generate all combination (e.g. 1,2)
    
```bash
echo {1,2}{1,2}
```
//1 1, 1 2, 2 1, 2 2

#####generate all combination (e.g. A,T,C,G)
    
```bash
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
```bash
foo=$(<test1)
```

#####echo size of variable

```bash
echo ${#foo}
```

#####echo tab

```bash
echo -e ' \t '
```

#####array
```bash
declare -A array=()
```

#####send a directory

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

#####split file into lines (e.g. 1000 lines/smallfile)
```bash
$ split -d -l 1000 bigfilename
```


##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'



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