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 Symbol for search:

section function $bash code //comment

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 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 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 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 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

Others 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 found $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 "."

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