11 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 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
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
-
unxz filename.tar.xz -
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-=-=-=-=-=-=-=-=-=-