A collection of handy Bash One-Liners and terminal tricks for data processing and Linux system maintenance.
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2016-06-16 14:44:57 +08:00
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BBO-Bioinformatics-Bash-Oneliner

Hi bioinformaticans and bash learner, welcome to BBO, Bioinformatics Bash Oneliner learning station. I started studying bioinformatics data three years ago, and my cs friend install Ubuntu on my lab computer. I was amazed by those single-word bash commands which are much faster than my dull scripts, so i started and insist using 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 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 'Ctrl +F '. 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, sorry

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

##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

#####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 [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' 

#####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'

#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}'

#####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 [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 sleepa 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

##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

#####random order (lucky draw)

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

#####echo a random number

echo $RANDOM

#####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

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