Bash-Oneliner/bashoneliner
2016-06-14 14:55:29 +08:00

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Handy Bash 'oneliner' commands for tsv file editing
Symbol for search:
>> section
>function
$bash code
//comment
>> 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
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-=-=-=-=-=-=-=-=-=-