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@ -19,32 +19,32 @@ http://stackoverflow.com/users/4290753/once
- [Others](#others) - [Others](#others)
##Grep ##Grep
extract text bewteen words (e.g. w1,w2) #####extract text bewteen words (e.g. w1,w2)
grep -o -P '(?<=w1).*(?=w2)' grep -o -P '(?<=w1).*(?=w2)'
grep lines without word (e.g. bbo) #####grep lines without word (e.g. bbo)
grep -v bbo grep -v bbo
grep and count (e.g. bbo) #####grep and count (e.g. bbo)
grep -c bbo filename grep -c bbo filename
insensitive grep (e.g. bbo/BBO/Bbo) #####insensitive grep (e.g. bbo/BBO/Bbo)
grep -i "bbo" filename grep -i "bbo" filename
count occurrence (e.g. three times a line count three times) #####count occurrence (e.g. three times a line count three times)
grep -o bbo filename grep -o bbo filename
COLOR the match (e.g. bbo)! #####COLOR the match (e.g. bbo)!
grep --color bbo filename grep --color bbo filename
grep search all files in a directory(e.g. bbo) #####grep search all files in a directory(e.g. bbo)
grep -R bbo /path/to/directory grep -R bbo /path/to/directory
@ -53,40 +53,40 @@ or
grep -r bbo /path/to/directory grep -r bbo /path/to/directory
search all files in directory, only output file names with matches(e.g. bbo) #####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 or
grep -rh bbo /path/to/directory grep -rh bbo /path/to/directory
grep OR (e.g. A or B or C or D) #####grep OR (e.g. A or B or C or D)
grep 'A\|B\|C\|D' grep 'A\|B\|C\|D'
grep AND (e.g. A and B) #####grep AND (e.g. A and B)
grep 'A.*B' grep 'A.*B'
grep all content of a fileA from fileB #####grep all content of a fileA from fileB
grep -f fileA fileB grep -f fileA fileB
grep a tab #####grep a tab
grep $'\t' grep $'\t'
##Sed ##Sed
[[back to top](#handy-bash-oneliner-commands-for-tsv-file-editing)] [[back to top](#handy-bash-oneliner-commands-for-tsv-file-editing)]
remove lines with word (e.g. bbo) #####remove lines with word (e.g. bbo)
sed "/bbo/d" filename sed "/bbo/d" filename
edit infile (edit and save) #####edit infile (edit and save)
sed -i "/bbo/d" filename sed -i "/bbo/d" filename
when using variable (e.g. $i), use double quotes " " #####when using variable (e.g. $i), use double quotes " "
e.g. add >$i to the first line (to make a FASTA file) e.g. add >$i to the first line (to make a FASTA file)
sed "1i >$i" sed "1i >$i"
@ -94,7 +94,7 @@ e.g. add >$i to the first line (to make a FASTA file)
//'1i' means insert to first line //'1i' means insert to first line
delete empty lines #####delete empty lines
sed '/^\s*$/d' sed '/^\s*$/d'
@ -102,57 +102,57 @@ or
sed 's/^$/d' sed 's/^$/d'
delete last line #####delete last line
sed '$d' sed '$d'
add \n every nth character (e.g. every 4th character) #####add \n every nth character (e.g. every 4th character)
sed 's/.\{4\}/&\n/g' sed 's/.\{4\}/&\n/g'
substitution (e.g. replace A by B) #####substitution (e.g. replace A by B)
sed 's/A/B/g' filename sed 's/A/B/g' filename
select lines start with string (e.g. bbo) #####select lines start with string (e.g. bbo)
sed -n '/^@S/p' sed -n '/^@S/p'
delete lines with string (e.g. bbo) #####delete lines with string (e.g. bbo)
sed '/bbo/d' filename sed '/bbo/d' filename
print every nth lines #####print every nth lines
sed -n '0~3p' filename sed -n '0~3p' filename
//catch 0: start; 3: step //catch 0: start; 3: step
print every odd # lines #####print every odd # lines
sed -n '1~2p' sed -n '1~2p'
print every third line including the first line #####print every third line including the first line
sed -n '1p;0~3p' sed -n '1p;0~3p'
remove leading whitespace and tabs #####remove leading whitespace and tabs
sed -e 's/^[ \t]*//' sed -e 's/^[ \t]*//'
//notice a whitespace before '\t'!! //notice a whitespace before '\t'!!
remove only leading whitespace #####remove only leading whitespace
sed 's/ *//' sed 's/ *//'
//notice a whitespace before '*'!! //notice a whitespace before '*'!!
remove ending commas #####remove ending commas
sed 's/,$//g' sed 's/,$//g'
add a column to the end #####add a column to the end
sed "s/$/\t$i/" sed "s/$/\t$i/"
//$i is the valuable you want to add //$i is the valuable you want to add
@ -160,7 +160,7 @@ e.g. add the filename to every last column of the file
for i in $(ls);do sed -i "s/$/\t$i/" $i;done for i in $(ls);do sed -i "s/$/\t$i/" $i;done
remove newline\ nextline #####remove newline\ nextline
sed ':a;N;$!ba;s/\n//g' sed ':a;N;$!ba;s/\n//g'
@ -168,56 +168,56 @@ remove newline\ nextline
#Awk #Awk
[[back to top](#handy-bash-oneliner-commands-for-tsv-file-editing)] [[back to top](#handy-bash-oneliner-commands-for-tsv-file-editing)]
set tab as field separator #####set tab as field separator
awk -F $'\t' awk -F $'\t'
output as tab separated (also as field separator) #####output as tab separated (also as field separator)
awk -v OFS='\t' awk -v OFS='\t'
pass variable #####pass variable
a=bbo;b=obb; a=bbo;b=obb;
awk -v a="$a" -v b="$b" "$1==a && $10=b' filename awk -v a="$a" -v b="$b" "$1==a && $10=b' filename
print number of characters on each line #####print number of characters on each line
awk '{print length ($0);}' filename awk '{print length ($0);}' filename
find number of columns #####find number of columns
awk '{print NF}' awk '{print NF}'
reverse column order #####reverse column order
awk '{print $2, $1}' awk '{print $2, $1}'
check if there is a comma in a column (e.g. column $1) #####check if there is a comma in a column (e.g. column $1)
awk '$1~/,/ {print}' awk '$1~/,/ {print}'
split and do for loop #####split and do for loop
awk '{split($2, a,",");for (i in a) print $1"\t"a[i]} filename 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) #####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}' awk -v N=7 '{print}/bbo/&& --N<=0 {exit}'
add string to the beginning of a column (e.g add "chr" to column $3) #####add string to the beginning of a column (e.g add "chr" to column $3)
awk 'BEGIN{OFS="\t"}$3="chr"$3' awk 'BEGIN{OFS="\t"}$3="chr"$3'
remove lines with string (e.g. bbo) #####remove lines with string (e.g. bbo)
awk '!/bbo/' file awk '!/bbo/' file
column subtraction #####column subtraction
cat file| awk -F '\t' 'BEGIN {SUM=0}{SUM+=$3-$2}END{print SUM}' cat file| awk -F '\t' 'BEGIN {SUM=0}{SUM+=$3-$2}END{print SUM}'
usage and meaning of NR and FNR #####usage and meaning of NR and FNR
e.g. e.g.
fileA: fileA:
a a
@ -234,7 +234,7 @@ fileA 3 3 c
fileB 4 1 d fileB 4 1 d
fileB 5 2 e fileB 5 2 e
and gate #####and gate
e.g. e.g.
fileA: fileA:
@ -266,7 +266,7 @@ fileB:
4 0 4 0
round all numbers of file (e.g. 2 significant figure) #####round all numbers of file (e.g. 2 significant figure)
awk '{while (match($0, /[0-9]+\[0-9]+/)){ awk '{while (match($0, /[0-9]+\[0-9]+/)){
\printf "%s%.2f", substr($0,0,RSTART-1),substr($0,RSTART,RLENGTH) \printf "%s%.2f", substr($0,0,RSTART-1),substr($0,RSTART,RLENGTH)
@ -275,7 +275,7 @@ round all numbers of file (e.g. 2 significant figure)
\print \print
\}' \}'
give number/index to every row #####give number/index to every row
awk '{printf("%s\t%s\n",NR,$0)}' awk '{printf("%s\t%s\n",NR,$0)}'
@ -285,25 +285,25 @@ set tab as delimiter (default:space)
xargs -d\t xargs -d\t
display 3 items per line #####display 3 items per line
echo 1 2 3 4 5 6| xargs -n 3 echo 1 2 3 4 5 6| xargs -n 3
//1 2 3 //1 2 3
4 5 6 4 5 6
prompt before execution #####prompt before execution
echo a b c |xargs -p -n 3 echo a b c |xargs -p -n 3
print command along with output #####print command along with output
xargs -t abcd xargs -t abcd
///bin/echo abcd ///bin/echo abcd
//abcd //abcd
with find and rm #####with find and rm
find . -name "*.html"|xargs rm -rf find . -name "*.html"|xargs rm -rf
@ -311,11 +311,11 @@ delete fiels with whitespace in filename (e.g. "hello 2001")
find . -name "*.c" -print0|xargs -0 rm -rf find . -name "*.c" -print0|xargs -0 rm -rf
show limits #####show limits
xargs --show-limits xargs --show-limits
move files to folder #####move files to folder
find . -name "*.bak" -print 0|xargs -0 -I {} mv {} ~/old find . -name "*.bak" -print 0|xargs -0 -I {} mv {} ~/old
@ -323,50 +323,50 @@ or
find . -name "*.bak" -print 0|xargs -0 -I file mv file ~/old find . -name "*.bak" -print 0|xargs -0 -I file mv file ~/old
move first 100th files to a directory (e.g. d1) #####move first 100th files to a directory (e.g. d1)
ls |head -100|xargs -I {} mv {} d1 ls |head -100|xargs -I {} mv {} d1
parallel #####parallel
time echo {1..5} |xargs -n 1 -P 5 sleepa lot faster than time echo {1..5} |xargs -n 1 -P 5 sleepa lot faster than
time echo {1..5} |xargs -n1 sleep time echo {1..5} |xargs -n1 sleep
copy all files from A to B #####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 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| //v: verbose|
//p: keep detail (e.g. owner) //p: keep detail (e.g. owner)
with sed #####with sed
ls |xargs -n1 -I file sed -i '/^Pos/d' filename ls |xargs -n1 -I file sed -i '/^Pos/d' filename
add the file name to the first line of file #####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 ls |sed 's/.txt//g'|xargs -n1 -I file sed -i -e '1 i\>file\' file.txt
count all files #####count all files
ls |xargs -n1 wc -l ls |xargs -n1 wc -l
to filter txt to a single line #####to filter txt to a single line
ls -l| xargs ls -l| xargs
count files within directories #####count files within directories
echo mso{1..8}|xargs -n1 bash -c 'echo -n "$1:"; ls -la "$1"| grep -w 74 |wc -l' -- 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 // "--" signals the end of options and display further option processing
download dependencies files and install (e.g. requirements.txt) #####download dependencies files and install (e.g. requirements.txt)
cat requirements.txt| xargs -n1 sudo pip install cat requirements.txt| xargs -n1 sudo pip install
count lines in all file, also count total lines #####count lines in all file, also count total lines
ls|xargs wc -l ls|xargs wc -l
@ -374,19 +374,19 @@ count lines in all file, also count total lines
##Find ##Find
[[back to top](#handy-bash-oneliner-commands-for-tsv-file-editing)] [[back to top](#handy-bash-oneliner-commands-for-tsv-file-editing)]
list all sub directory/file in the current directory #####list all sub directory/file in the current directory
find . find .
list all files under the current directory #####list all files under the current directory
find . -type f find . -type f
list all directories under the current directory #####list all directories under the current directory
find . -type d find . -type d
edit all files under current directory (e.g. replace 'www' with 'ww') #####edit all files under current directory (e.g. replace 'www' with 'ww')
find . name '*.php' -exec sed -i 's/www/w/g' {} \; find . name '*.php' -exec sed -i 's/www/w/g' {} \;
if no subdirectory if no subdirectory
@ -395,11 +395,11 @@ if no subdirectory
//a space before * //a space before *
find and output only filename (e.g. "mso") #####find and output only filename (e.g. "mso")
find mso*/ -name M* -printf "%f\n" find mso*/ -name M* -printf "%f\n"
find and delete file with size less than (e.g. 74 byte) #####find and delete file with size less than (e.g. 74 byte)
find . -name "*.mso" -size -74c -delete find . -name "*.mso" -size -74c -delete
//M for MB, etc //M for MB, etc
@ -407,15 +407,15 @@ find and delete file with size less than (e.g. 74 byte)
##Others ##Others
[[back to top](#handy-bash-oneliner-commands-for-tsv-file-editing)] [[back to top](#handy-bash-oneliner-commands-for-tsv-file-editing)]
remove newline / nextline #####remove newline / nextline
tr --delete '\n' <input.txt >output.txt tr --delete '\n' <input.txt >output.txt
replace newline #####replace newline
tr '\n' ' ' <filename tr '\n' ' ' <filename
compare files (e.g. fileA, fileB) #####compare files (e.g. fileA, fileB)
diff fileA fileB diff fileA fileB
//a: added; d:delete; c:changed //a: added; d:delete; c:changed
@ -426,7 +426,7 @@ or
//side-to-side merge of file differences //side-to-side merge of file differences
number a file (e.g. fileA) #####number a file (e.g. fileA)
nl fileA nl fileA
@ -437,17 +437,17 @@ or
//add leading zeros //add leading zeros
combine/ paste two files (e.g. fileA, fileB) #####combine/ paste two files (e.g. fileA, fileB)
paste fileA fileB paste fileA fileB
//default tab seperated //default tab seperated
reverse string #####reverse string
echo 12345| rev echo 12345| rev
read .gz file without extracting #####read .gz file without extracting
zmore filename zmore filename
@ -455,7 +455,7 @@ or
zless filename zless filename
run in background, output error file #####run in background, output error file
(command here) 2>log & (command here) 2>log &
@ -469,7 +469,7 @@ or
//0: standard input; 1: standard output; 2: standard error //0: standard input; 1: standard output; 2: standard error
send mail #####send mail
echo 'heres the content'| mail -A 'file.txt' -s 'mail.subject' me@gmail.com 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") //use -a flag to set send from (-a "From: some@mail.tld")
@ -479,18 +479,18 @@ send mail
xls2csv filename xls2csv filename
append to file (e.g. hihi) #####append to file (e.g. hihi)
echo 'hihi' >>filename echo 'hihi' >>filename
make BEEP found #####make BEEP found
speaker-test -t sine -f 1000 -l1 speaker-test -t sine -f 1000 -l1
set beep duration set beep duration
(speaker-test -t sine -f 1000) & pid=$!;sleep 0.1s;kill -9 $pid (speaker-test -t sine -f 1000) & pid=$!;sleep 0.1s;kill -9 $pid
history edit/ delete #####history edit/ delete
~/.bash_history ~/.bash_history
@ -498,11 +498,11 @@ or
history -d [line_number] history -d [line_number]
get last history/record filename #####get last history/record filename
head !$ head !$
clean screen #####clean screen
clear clear
@ -510,20 +510,20 @@ or
Ctrl+l Ctrl+l
send data to last edited file #####send data to last edited file
cat /directory/to/file cat /directory/to/file
echo 100>!$ echo 100>!$
run history number (e.g. 53) #####run history number (e.g. 53)
!53 !53
run last command #####run last command
!! !!
run last command that began with (e.g. cat filename) #####run last command that began with (e.g. cat filename)
!cat !cat
@ -533,24 +533,24 @@ or
//run cat filename again //run cat filename again
extract .xf #####extract .xf
1.unxz filename.tar.xz 1.unxz filename.tar.xz
2.tar -xf filename.tar 2.tar -xf filename.tar
install python package #####install python package
pip install packagename pip install packagename
random order (lucky draw) #####random order (lucky draw)
for i in a b c d e; do echo $i; done| shuf for i in a b c d e; do echo $i; done| shuf
echo a random number #####echo a random number
echo $RANDOM echo $RANDOM
Download file if necessary #####Download file if necessary
data=file.txt data=file.txt
url=http://www.example.com/$data url=http://www.example.com/$data
@ -559,15 +559,15 @@ Download file if necessary
wget $url wget $url
fi fi
wget to a filename (when a long name) #####wget to a filename (when a long name)
wget -O filename "http://example.com" wget -O filename "http://example.com"
wget files to a folder #####wget files to a folder
wget -P /path/to/directory "http://example.com" wget -P /path/to/directory "http://example.com"
delete current bash command #####delete current bash command
Ctrl+U Ctrl+U
@ -581,21 +581,21 @@ or
//to make it to history //to make it to history
add things to history (e.g. "addmetohistory") #####add things to history (e.g. "addmetohistory")
#addmetodistory #addmetodistory
//just add a "#" before~~ //just add a "#" before~~
sleep awhile or wait for a moment or schedule a job #####sleep awhile or wait for a moment or schedule a job
sleep 5;echo hi sleep 5;echo hi
count the time for executing a command #####count the time for executing a command
time echo hi time echo hi
backup with rsync #####backup with rsync
rsync -av filename filename.bak rsync -av filename filename.bak
rsync -av directory directory.bak rsync -av directory directory.bak
@ -604,43 +604,43 @@ backup with rsync
//skip files that are newer on receiver (i prefer this one!) //skip files that are newer on receiver (i prefer this one!)
make all directories at one time! #####make all directories at one time!
mkdir -p project/{lib/ext,bin,src,doc/{html,info,pdf},demo/stat} mkdir -p project/{lib/ext,bin,src,doc/{html,info,pdf},demo/stat}
//-p: make parent directory //-p: make parent directory
//this will create project/doc/html/; project/doc/info; project/lib/ext ,etc //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) #####run command only if another command returns zero exit status (well done)
cd tmp/ && tar xvf ~/a.tar cd tmp/ && tar xvf ~/a.tar
run command only if another command returns non-zero exit status (not finish) #####run command only if another command returns non-zero exit status (not finish)
cd tmp/a/b/c ||mkdir -p tmp/a/b/c cd tmp/a/b/c ||mkdir -p tmp/a/b/c
extract to a path #####extract to a path
tar xvf -C /path/to/directory filename.gz tar xvf -C /path/to/directory filename.gz
use backslash "\" to break long command #####use backslash "\" to break long command
cd tmp/a/b/c \ cd tmp/a/b/c \
> || \ > || \
>mkdir -p tmp/a/b/c >mkdir -p tmp/a/b/c
get pwd #####get pwd
VAR=$PWD; cd ~; tar xvf -C $VAR file.tar VAR=$PWD; cd ~; tar xvf -C $VAR file.tar
//PWD need to be capital letter //PWD need to be capital letter
list file type of file (e.g. /tmp/) #####list file type of file (e.g. /tmp/)
file /tmp/ file /tmp/
//tmp/: directory //tmp/: directory
bash script #####bash script
#!/bin/bash #!/bin/bash
file=${1#*.} file=${1#*.}