Bash-Oneliner/README.md

# 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](#grep)
- [Sed](#sed)
- [Awk](#awk)
- [Xargs](#xargs)
- [Find](#find)
- [Others](#others)

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

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

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