| 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 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 "$1"| grep -w 74 |wc -l' --
// "--" signals the end of options and display further option processing
download dependencies files and install (e.g. requirements.txt)
cat requirements.txt| xargs -n1 sudo pip install
count lines in all file, also count total lines
ls|xargs wc -l
##Find [back to top] list all sub directory/file in the current directory
find .
list all files under the current directory
find . -type f
list all directories under the current directory
find . -type d
edit all files under current directory (e.g. replace 'www' with 'ww')
find . name '*.php' -exec sed -i 's/www/w/g' {} \;
if no subdirectory
replace "www" "w" -- *
//a space before *
find and output only filename (e.g. "mso")
find mso*/ -name M* -printf "%f\n"
find and delete file with size less than (e.g. 74 byte)
find . -name "*.mso" -size -74c -delete
//M for MB, etc
##Others [back to top] remove newline / nextline
tr --delete '\n' <input.txt >output.txt
replace newline
tr '\n' ' ' <filename
compare files (e.g. fileA, fileB)
diff fileA fileB
//a: added; d:delete; c:changed
or
sdiff fileA fileB
//side-to-side merge of file differences
number a file (e.g. fileA)
nl fileA
or
nl -nrz fileA
//add leading zeros
combine/ paste two files (e.g. fileA, fileB)
paste fileA fileB
//default tab seperated
reverse string
echo 12345| rev
read .gz file without extracting
zmore filename
or
zless filename
run in background, output error file
(command here) 2>log &
or
(command here) 2>&1| tee logfile
or
(command here) 2>&1 >>outfile
//0: standard input; 1: standard output; 2: standard error
send mail
echo 'heres the content'| mail -A 'file.txt' -s 'mail.subject' me@gmail.com
//use -a flag to set send from (-a "From: some@mail.tld")
.xls to csv
xls2csv filename
append to file (e.g. hihi)
echo 'hihi' >>filename
make BEEP found
speaker-test -t sine -f 1000 -l1
set beep duration
(speaker-test -t sine -f 1000) & pid=$!;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-=-=-=-=-=-=-=-=-=-