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)
- [Loops](#loops)
- [Download](#download)
- [Others](#others)
- [System](#system)

##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


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