17 KiB
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 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, thank you
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 And if you want to check out stylish BBO: http://bbonut.blogspot.tw/#system
##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]]
#####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
##System [back to top]
#####snapshot of the current processes
ps
#####check graphics card
lspci
#####show IP address
$ip add show
or
ifconfig
#####check system version
cat /etc/*-release
#####Linux Programmer's Manuel: hier- description of the filesystem hierarchy
man hier
#####list job
jobs -l
#####export PATH
export PATH=$PATH:~/path/you/want
#####make file execuable
chmod +x filename
//you can now ./filename to execute it
#####list screen
screen -d -r
#####echo screen name
screen -ls
#####check system (x86-64)
uname -i
#####surf the net
links www.google.com
#####add user, set passwd
useradd username
passwd username
#####edit variable for bash, (e.g. displaying the whole path)
1. joe ~/.bash_profile
2. export PS1='\u@\h:\w\$'
//$PS1 is a variable that defines the makeup and style of the command prompt
3. source ~/.bash_profile
#####edit environment setting (e.g. alias)
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)
$echo $PATH
//list of directories separated by a colon
#####list all environment variables for current user
$env
#####show partition format
lsblk
#####soft link program to bin
ln -s /path/to/program /home/usr/bin
//must be the whole path to the program
#####show hexadecimal view of data
hexdump -C filename.class
#####jump to different node
rsh node_name
#####check port (active internet connection)
netstat -tulpn
#####find whick link to a file
readlink filename
#####check where a command link to (e.g. python)
which python
#####list total size of a directory
du -hs .
or
du -sb
#####copy directory with permission setting
cp -rp /path/to/directory
#####store current directory
pushd . $popd ;dirs -l
#####show disk usage
df -h
or
du -h
or
du -sk /var/log/* |sort -rn |head -10
#####show current runlevel
runlevel
#####switch runlevel
init 3 or
telinit 3
#####permanently modify runlevel
1. edit /etc/init/rc-sysinit.conf
2. env DEFAULT_RUNLEVEL=2
#####become root
su
#####become somebody
su somebody
=-=-=-=-=-A lot more coming!! =-=-=-=-=-=-=-=-=-=waitwait-=-=-=-=-=-=-=-=-=-