Bash-Oneliner/README.md

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# Bash-Oneliner
Hi bash learners and bioinformaticans, welcome to 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 bash. Not all the code here is oneliner (if the ';' counts..), but i put effort on making them brief and fast.
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This blog will focus on bash commands for parsing biological data for dummies like me, most of which are tsv files (tab-separated values); some of them are for Ubuntu system maintaining (for dummies). I have been recording the bash commands on my notebook, but putting them on web will help others and myself to query. 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.
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English and bash are not my first language, so... correct me anytime, thank you
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In case you would like to check and vote up my questions on Stackoverflow, here's my page:
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http://stackoverflow.com/users/4290753/once
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Here's a more stylish version~
http://onceupon.github.io/Bash-Oneliner/
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##Handy Bash oneliner commands for tsv file editing
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- [Grep](#grep)
- [Sed](#sed)
- [Awk](#awk)
- [Xargs](#xargs)
- [Find](#find)
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- [Loops](#loops)
- [Download](#download)
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- [Random](#random)
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- [Others](#others)
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- [System](#system)
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##Grep
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#####extract text bewteen words (e.g. w1,w2)
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```bash
grep -o -P '(?<=w1).*(?=w2)'
```
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#####grep lines without word (e.g. bbo)
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```bash
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grep -v bbo filename
```
#####grep only one/first match (e.g. bbo)
```bash
grep -m 1 bbo filename
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```
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#####grep and count (e.g. bbo)
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```bash
grep -c bbo filename
```
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#####insensitive grep (e.g. bbo/BBO/Bbo)
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```bash
grep -i "bbo" filename
```
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#####count occurrence (e.g. three times a line count three times)
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```bash
grep -o bbo filename
```
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#####COLOR the match (e.g. bbo)!
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```bash
grep --color bbo filename
```
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#####grep search all files in a directory(e.g. bbo)
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```bash
grep -R bbo /path/to/directory
```
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or
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```bash
grep -r bbo /path/to/directory
```
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#####search all files in directory, only output file names with matches(e.g. bbo)
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```bash
grep -Rh bbo /path/to/directory
```
or
```bash
grep -rh bbo /path/to/directory
```
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#####grep OR (e.g. A or B or C or D)
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```
grep 'A\|B\|C\|D'
```
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#####grep AND (e.g. A and B)
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```bash
grep 'A.*B'
```
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#####grep all content of a fileA from fileB
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```bash
grep -f fileA fileB
```
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#####grep a tab
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```bash
grep $'\t'
```
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#####grep variable from variable
```bash
$echo "$long_str"|grep -q "$short_str"
if [ $? -eq 0 ]; then echo 'found'; fi
```
//grep -q will output 0 if match found
//remember to add space between []!
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#####grep strings between a bracket()
```bash
grep -oP '\(\K[^\)]+'
```
#####grep number of characters with known strings in between(e.g. AAEL000001-RA)
```bash
grep -o -w "\w\{10\}\-R\w\{1\}"
```
// \w word character [0-9a-zA-Z_] \W not word character
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#####a lot examples here
http://www.cyberciti.biz/faq/grep-regular-expressions/
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##Sed
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[[back to top](#handy-bash-oneliner-commands-for-tsv-file-editing)]
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#####remove lines with word (e.g. bbo)
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```bash
sed "/bbo/d" filename
```
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#####edit infile (edit and save)
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```bash
sed -i "/bbo/d" filename
```
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#####when using variable (e.g. $i), use double quotes " "
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e.g. add >$i to the first line (to make a FASTA file)
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```bash
sed "1i >$i"
```
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//notice the double quotes! in other examples, you can use a single quote, but here, no way!
//'1i' means insert to first line
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#####delete empty lines
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```bash
sed '/^\s*$/d'
```
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or
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```bash
sed 's/^$/d'
```
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#####delete last line
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```bash
sed '$d'
```
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#####delete last character from end of file
```bash
sed -i '$ s/.$//' filename
```
#####add string to end of file (e.g. "]")
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```bash
sed '$s/$/]/' filename
```
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#####add string to beginning of every line (e.g. bbo)
```bash
sed -e 's/^/bbo/' file
```
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#####add string to end of each line (e.g. "}")
```bash
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sed -e 's/$/\}\]/' filename
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```
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#####add \n every nth character (e.g. every 4th character)
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```bash
sed 's/.\{4\}/&\n/g'
```
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#####concatenate/combine/join files with a seperator and next line (e.g seperate by ",")
```bash
sed -s '$a,' *.json > all.json
```
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#####substitution (e.g. replace A by B)
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```bash
sed 's/A/B/g' filename
```
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#####select lines start with string (e.g. bbo)
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```bash
sed -n '/^@S/p'
```
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#####delete lines with string (e.g. bbo)
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```bash
sed '/bbo/d' filename
```
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#####print every nth lines
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```bash
sed -n '0~3p' filename
```
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//catch 0: start; 3: step
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#####print every odd # lines
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```bash
sed -n '1~2p'
```
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#####print every third line including the first line
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```bash
sed -n '1p;0~3p'
```
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#####remove leading whitespace and tabs
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```bash
sed -e 's/^[ \t]*//'
```
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//notice a whitespace before '\t'!!
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#####remove only leading whitespace
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```bash
sed 's/ *//'
```
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//notice a whitespace before '*'!!
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#####remove ending commas
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```bash
sed 's/,$//g'
```
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#####add a column to the end
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```bash
sed "s/$/\t$i/"
```
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//$i is the valuable you want to add
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e.g. add the filename to every last column of the file
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```bash
for i in $(ls);do sed -i "s/$/\t$i/" $i;done
```
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#####add extension of filename to last column
```bash
for i in T000086_1.02.n T000086_1.02.p;do sed "s/$/\t${i/*./}/" $i;done >T000086_1.02.np
```
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#####remove newline\ nextline
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```bash
sed ':a;N;$!ba;s/\n//g'
```
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#####print a number of lines (e.g. line 10th to line 33 rd)
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```bash
sed -n '10,33p' <filename
```
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#####change delimiter
```bash
sed 's=/=\\/=g'
```
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#Awk
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[[back to top](#handy-bash-oneliner-commands-for-tsv-file-editing)]
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#####set tab as field separator
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```bash
awk -F $'\t'
```
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#####output as tab separated (also as field separator)
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```bash
awk -v OFS='\t'
```
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#####pass variable
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```bash
a=bbo;b=obb;
awk -v a="$a" -v b="$b" "$1==a && $10=b' filename
```
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#####print number of characters on each line
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```bash
awk '{print length ($0);}' filename
```
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#####find number of columns
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```bash
awk '{print NF}'
```
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#####reverse column order
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```bash
awk '{print $2, $1}'
```
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#####check if there is a comma in a column (e.g. column $1)
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```bash
awk '$1~/,/ {print}'
```
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#####split and do for loop
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```bash
awk '{split($2, a,",");for (i in a) print $1"\t"a[i]} filename
```
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#####print all lines before nth occurence of a string (e.g stop print lines when bbo appears 7 times)
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```bash
awk -v N=7 '{print}/bbo/&& --N<=0 {exit}'
```
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#####print filename and last line of all files in directory
```bash
ls|xargs -n1 -I file awk '{s=$0};END{print FILENAME,s}' file'
```
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#####add string to the beginning of a column (e.g add "chr" to column $3)
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```bash
awk 'BEGIN{OFS="\t"}$3="chr"$3'
```
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#####remove lines with string (e.g. bbo)
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```bash
awk '!/bbo/' file
```
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#####column subtraction
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```bash
cat file| awk -F '\t' 'BEGIN {SUM=0}{SUM+=$3-$2}END{print SUM}'
```
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#####usage and meaning of NR and FNR
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e.g.
fileA:
a
b
c
fileB:
d
e
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```bash
awk 'print FILENAME, NR,FNR,$0}' fileA fileB
```
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fileA 1 1 a
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fileA 2 2 b
fileA 3 3 c
fileB 4 1 d
fileB 5 2 e
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#####and gate
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e.g.
fileA:
1 0
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2 1
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3 1
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4 0
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fileB:
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1 0
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2 1
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3 0
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4 1
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```bash
awk -v OFS='\t' 'NR=FNR{a[$1]=$2;next} NF {print $1,((a[$1]=$2)? $2:"0")}' fileA fileB
```
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1 0
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2 1
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3 0
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4 0
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#####round all numbers of file (e.g. 2 significant figure)
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```bash
awk '{while (match($0, /[0-9]+\[0-9]+/)){
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\printf "%s%.2f", substr($0,0,RSTART-1),substr($0,RSTART,RLENGTH)
\$0=substr($0, RSTART+RLENGTH)
\}
\print
\}'
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```
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#####give number/index to every row
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```bash
awk '{printf("%s\t%s\n",NR,$0)}'
```
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#####break combine column data into rows
e.g.
seperate
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David cat,dog
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into
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David cat
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David dog
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detail here: http://stackoverflow.com/questions/33408762/bash-turning-single-comma-separated-column-into-multi-line-string
```bash
awk '{split($2,a,",");for(i in a)print $1"\t"a[i]}' file
```
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#####sum up a file (each line in file contains only one number)
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```bash
awk '{s+=$1} END {print s}' filename
```
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#####average a file (each line in file contains only one number)
```bash
awk '{s+=$1}END{print s/NR}'
```
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#####print field start with string (e.g Linux)
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```bash
awk '$1 ~ /^Linux/'
```
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#####sort a row (e.g. 1 40 35 12 23 --> 1 12 23 35 40)
```bash
awk ' {split( $0, a, "\t" ); asort( a ); for( i = 1; i <= length(a); i++ ) printf( "%s\t", a[i] ); printf( "\n" ); }'
```
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##Xargs
[[back to top](#handy-bash-oneliner-commands-for-tsv-file-editing)]
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#####set tab as delimiter (default:space)
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```bash
xargs -d\t
```
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#####display 3 items per line
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```bash
echo 1 2 3 4 5 6| xargs -n 3
```
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//1 2 3
4 5 6
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#####prompt before execution
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```bash
echo a b c |xargs -p -n 3
```
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#####print command along with output
2016-06-14 07:55:08 +00:00
2016-07-01 10:52:19 +00:00
```bash
xargs -t abcd
```
2016-06-14 06:57:38 +00:00
///bin/echo abcd
//abcd
2016-06-14 08:03:32 +00:00
2016-06-14 08:10:45 +00:00
#####with find and rm
2016-06-14 07:55:08 +00:00
2016-07-01 10:52:19 +00:00
```bash
find . -name "*.html"|xargs rm -rf
```
2016-06-14 06:57:38 +00:00
2016-06-14 07:55:08 +00:00
delete fiels with whitespace in filename (e.g. "hello 2001")
2016-07-01 10:52:19 +00:00
```bash
find . -name "*.c" -print0|xargs -0 rm -rf
```
2016-06-14 06:57:38 +00:00
2016-06-14 08:10:45 +00:00
#####show limits
2016-06-14 07:55:08 +00:00
2016-07-01 10:52:19 +00:00
```bash
xargs --show-limits
```
2016-06-14 06:57:38 +00:00
2016-06-14 08:10:45 +00:00
#####move files to folder
2016-06-14 07:55:08 +00:00
2016-07-01 10:52:19 +00:00
```bash
find . -name "*.bak" -print 0|xargs -0 -I {} mv {} ~/old
```
2016-06-14 07:55:08 +00:00
2016-06-14 06:57:38 +00:00
or
2016-06-14 07:55:08 +00:00
2016-07-01 10:52:19 +00:00
```bash
find . -name "*.bak" -print 0|xargs -0 -I file mv file ~/old
```
2016-06-14 06:57:38 +00:00
2016-06-14 08:10:45 +00:00
#####move first 100th files to a directory (e.g. d1)
2016-06-14 07:55:08 +00:00
2016-07-01 10:52:19 +00:00
```bash
ls |head -100|xargs -I {} mv {} d1
```
2016-06-14 06:57:38 +00:00
2016-06-14 08:10:45 +00:00
#####parallel
2016-06-14 07:55:08 +00:00
2016-07-01 10:52:19 +00:00
```bash
time echo {1..5} |xargs -n 1 -P 5 sleep
```
a lot faster than
```bash
time echo {1..5} |xargs -n1 sleep
```
2016-06-14 06:57:38 +00:00
2016-06-14 08:10:45 +00:00
#####copy all files from A to B
2016-06-14 07:55:08 +00:00
2016-07-01 10:52:19 +00:00
```bash
find /dir/to/A -type f -name "*.py" -print 0| xargs -0 -r -I file cp -v -p file --target-directory=/path/to/B
```
2016-06-14 06:57:38 +00:00
//v: verbose|
//p: keep detail (e.g. owner)
2016-06-14 08:03:32 +00:00
2016-06-14 08:10:45 +00:00
#####with sed
2016-06-14 07:55:08 +00:00
2016-07-01 10:52:19 +00:00
```bash
ls |xargs -n1 -I file sed -i '/^Pos/d' filename
```
2016-06-14 06:57:38 +00:00
2016-06-14 08:10:45 +00:00
#####add the file name to the first line of file
2016-06-14 07:55:08 +00:00
2016-07-01 10:52:19 +00:00
```bash
ls |sed 's/.txt//g'|xargs -n1 -I file sed -i -e '1 i\>file\' file.txt
```
2016-06-14 06:57:38 +00:00
2016-06-14 08:10:45 +00:00
#####count all files
2016-06-14 07:55:08 +00:00
2016-07-01 10:52:19 +00:00
```bash
ls |xargs -n1 wc -l
```
2016-06-14 06:57:38 +00:00
2016-06-14 08:10:45 +00:00
#####to filter txt to a single line
2016-06-14 07:55:08 +00:00
2016-07-01 10:52:19 +00:00
```bash
ls -l| xargs
```
2016-06-14 06:57:38 +00:00
2016-06-14 08:10:45 +00:00
#####count files within directories
2016-06-14 07:55:08 +00:00
2016-07-01 10:52:19 +00:00
```bash
echo mso{1..8}|xargs -n1 bash -c 'echo -n "$1:"; ls -la "$1"| grep -w 74 |wc -l' --
```
2016-06-14 06:57:38 +00:00
// "--" signals the end of options and display further option processing
2016-06-14 08:03:32 +00:00
2016-06-14 08:10:45 +00:00
#####download dependencies files and install (e.g. requirements.txt)
2016-06-14 07:55:08 +00:00
2016-07-01 10:52:19 +00:00
```bash
cat requirements.txt| xargs -n1 sudo pip install
```
2016-06-14 06:57:38 +00:00
2016-06-14 08:10:45 +00:00
#####count lines in all file, also count total lines
2016-06-14 07:55:08 +00:00
2016-07-01 10:52:19 +00:00
```bash
ls|xargs wc -l
```
2016-09-29 09:17:45 +00:00
#####xargs and grep
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2016-09-29 09:17:45 +00:00
```bash
cat grep_list |xargs -I{} grep {} filename
```
2016-06-14 06:57:38 +00:00
2016-06-14 07:55:08 +00:00
##Find
[[back to top](#handy-bash-oneliner-commands-for-tsv-file-editing)]
2016-06-14 08:10:45 +00:00
#####list all sub directory/file in the current directory
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2016-07-01 10:52:19 +00:00
```bash
find .
```
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2016-06-14 08:10:45 +00:00
#####list all files under the current directory
2016-06-14 07:55:08 +00:00
2016-07-01 10:52:19 +00:00
```bash
find . -type f
```
2016-06-14 06:57:38 +00:00
2016-06-14 08:10:45 +00:00
#####list all directories under the current directory
2016-06-14 07:55:08 +00:00
2016-07-01 10:52:19 +00:00
```bash
find . -type d
```
2016-06-14 06:57:38 +00:00
2016-06-14 08:10:45 +00:00
#####edit all files under current directory (e.g. replace 'www' with 'ww')
2016-06-14 07:55:08 +00:00
2016-07-01 10:52:19 +00:00
```bash
find . name '*.php' -exec sed -i 's/www/w/g' {} \;
```
2016-06-14 07:55:08 +00:00
if no subdirectory
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```bash
replace "www" "w" -- *
```
2016-06-14 06:57:38 +00:00
//a space before *
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2016-06-14 08:10:45 +00:00
#####find and output only filename (e.g. "mso")
2016-06-14 07:55:08 +00:00
2016-07-01 10:52:19 +00:00
```bash
find mso*/ -name M* -printf "%f\n"
```
2016-06-14 06:57:38 +00:00
2016-06-14 08:10:45 +00:00
#####find and delete file with size less than (e.g. 74 byte)
2016-06-14 07:55:08 +00:00
2016-07-01 10:52:19 +00:00
```bash
find . -name "*.mso" -size -74c -delete
```
2016-06-14 06:57:38 +00:00
//M for MB, etc
2016-06-16 06:44:57 +00:00
##Loops
[[back to top](#handy-bash-oneliner-commands-for-tsv-file-editing)]
#####while loop, column subtraction of a file (e.g. a 3 columns file)
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```bash
while read a b c; do echo $(($c-$b));done < <(head filename)
```
2016-06-16 06:44:57 +00:00
//there is a space between the two '<'s
#####while loop, sum up column subtraction
2016-07-01 10:52:19 +00:00
```bash
i=0; while read a b c; do ((i+=$c-$b)); echo $i; done < <(head filename)
```
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#####if loop
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```bash
if (($j==$u+2))
```
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//(( )) use for arithmetic operation
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```bash
if [[$age >21]]
```
2016-06-16 06:44:57 +00:00
//[[ ]] use for comparison
#####for loop
2016-07-01 10:52:19 +00:00
```bash
for i in $(ls); do echo file $i;done
```
2016-06-16 06:44:57 +00:00
##Download
[[back to top](#handy-bash-oneliner-commands-for-tsv-file-editing)]
#####download all from a page
2016-07-01 10:52:19 +00:00
```bash
wget -r -l1 -H -t1 -nd -N -np -A mp3 -e robots=off http://example.com
```
2016-06-16 06:44:57 +00:00
//-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
2016-06-27 05:54:48 +00:00
##Random
[[back to top](#handy-bash-oneliner-commands-for-tsv-file-editing)]
#####random pick 100 lines from a file
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```bash
shuf -n 100 filename
```
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#####random order (lucky draw)
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```bash
for i in a b c d e; do echo $i; done| shuf
```
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#####echo series of random numbers between a range (e.g. generate 15 random numbers from 0-10)
2016-07-01 10:52:19 +00:00
```bash
shuf -i 0-10 -n 15
```
2016-06-27 05:54:48 +00:00
#####echo a random number
2016-07-01 10:52:19 +00:00
```bash
echo $RANDOM
```
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#####random from 0-9
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```bash
echo $((RANDOM % 10))
```
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#####random from 1-10
2016-07-01 10:52:19 +00:00
```bash
echo $(((RANDOM %10)+1))
```
2016-06-27 05:54:48 +00:00
2016-06-14 07:55:08 +00:00
##Others
[[back to top](#handy-bash-oneliner-commands-for-tsv-file-editing)]
2016-06-14 08:10:45 +00:00
#####remove newline / nextline
2016-06-14 07:55:08 +00:00
2016-07-01 10:52:19 +00:00
```bash
tr --delete '\n' <input.txt >output.txt
```
2016-06-14 06:57:38 +00:00
2016-06-14 08:10:45 +00:00
#####replace newline
2016-06-14 07:55:08 +00:00
2016-07-01 10:52:19 +00:00
```bash
tr '\n' ' ' <filename
```
2016-06-14 06:57:38 +00:00
2016-06-14 08:10:45 +00:00
#####compare files (e.g. fileA, fileB)
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2016-07-01 10:52:19 +00:00
```bash
diff fileA fileB
```
2016-06-14 06:57:38 +00:00
//a: added; d:delete; c:changed
2016-06-14 07:55:08 +00:00
2016-06-14 06:57:38 +00:00
or
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2016-07-01 10:52:19 +00:00
```bash
sdiff fileA fileB
```
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//side-to-side merge of file differences
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2016-06-14 08:10:45 +00:00
#####number a file (e.g. fileA)
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2016-07-01 10:52:19 +00:00
```bash
nl fileA
```
2016-06-14 06:57:38 +00:00
or
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2016-07-01 10:52:19 +00:00
```bash
nl -nrz fileA
```
2016-06-14 06:57:38 +00:00
//add leading zeros
2016-06-14 08:03:32 +00:00
2016-06-14 08:10:45 +00:00
#####combine/ paste two files (e.g. fileA, fileB)
2016-06-14 07:55:08 +00:00
2016-07-01 10:52:19 +00:00
```bash
paste fileA fileB
```
2016-06-14 06:57:38 +00:00
//default tab seperated
2016-06-14 08:03:32 +00:00
2016-06-14 08:10:45 +00:00
#####reverse string
2016-06-14 07:55:08 +00:00
2016-07-01 10:52:19 +00:00
```bash
echo 12345| rev
```
2016-06-14 06:57:38 +00:00
2016-06-14 08:10:45 +00:00
#####read .gz file without extracting
2016-06-14 07:55:08 +00:00
2016-07-01 10:52:19 +00:00
```bash
zmore filename
```
2016-06-14 06:57:38 +00:00
or
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2016-07-01 10:52:19 +00:00
```bash
zless filename
```
2016-06-14 06:57:38 +00:00
2016-06-14 08:10:45 +00:00
#####run in background, output error file
2016-06-14 07:55:08 +00:00
2016-07-01 10:52:19 +00:00
```bash
2016-09-08 09:31:55 +00:00
some_commands &>log &
```
or
```bash
some_commands 2>log &
2016-07-01 10:52:19 +00:00
```
2016-06-14 07:55:08 +00:00
2016-06-14 06:57:38 +00:00
or
2016-06-14 07:55:08 +00:00
2016-07-01 10:52:19 +00:00
```bash
2016-09-08 09:31:55 +00:00
some_commands 2>&1| tee logfile
2016-07-01 10:52:19 +00:00
```
2016-06-14 07:55:08 +00:00
2016-06-14 06:57:38 +00:00
or
2016-06-14 07:55:08 +00:00
2016-07-01 10:52:19 +00:00
```bash
2016-09-08 09:31:55 +00:00
some_commands 2>&1 >>outfile
2016-07-01 10:52:19 +00:00
```
2016-06-14 06:57:38 +00:00
//0: standard input; 1: standard output; 2: standard error
2016-06-14 08:03:32 +00:00
2016-06-14 08:10:45 +00:00
#####send mail
2016-06-14 07:55:08 +00:00
2016-07-01 10:52:19 +00:00
```bash
echo 'heres the content'| mail -A 'file.txt' -s 'mail.subject' me@gmail.com
```
2016-06-14 06:57:38 +00:00
//use -a flag to set send from (-a "From: some@mail.tld")
2016-06-14 08:03:32 +00:00
2016-07-01 10:52:19 +00:00
#####.xls to csv
2016-06-14 07:55:08 +00:00
2016-07-01 10:52:19 +00:00
```bash
xls2csv filename
```
2016-06-14 08:10:45 +00:00
#####append to file (e.g. hihi)
2016-06-14 07:55:08 +00:00
2016-07-01 10:52:19 +00:00
```bash
echo 'hihi' >>filename
```
2016-06-14 06:57:38 +00:00
2016-06-16 06:44:57 +00:00
#####make BEEP sound
2016-06-14 07:55:08 +00:00
2016-07-01 10:52:19 +00:00
```bash
speaker-test -t sine -f 1000 -l1
```
#####set beep duration
2016-06-14 07:55:08 +00:00
2016-07-01 10:52:19 +00:00
```bash
(speaker-test -t sine -f 1000) & pid=$!;sleep 0.1s;kill -9 $pid
```
2016-06-14 06:57:38 +00:00
2016-06-14 08:10:45 +00:00
#####history edit/ delete
2016-06-14 07:55:08 +00:00
2016-07-01 10:52:19 +00:00
```bash
~/.bash_history
```
2016-06-14 06:57:38 +00:00
or
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2016-07-01 10:52:19 +00:00
```bash
history -d [line_number]
```
2016-06-14 06:57:38 +00:00
2016-06-14 08:10:45 +00:00
#####get last history/record filename
2016-06-14 07:55:08 +00:00
2016-07-01 10:52:19 +00:00
```bash
head !$
```
2016-06-14 06:57:38 +00:00
2016-06-14 08:10:45 +00:00
#####clean screen
2016-06-14 07:55:08 +00:00
2016-07-01 10:52:19 +00:00
```bash
clear
```
2016-06-14 07:55:08 +00:00
2016-06-14 06:57:38 +00:00
or
2016-06-14 07:55:08 +00:00
2016-07-01 10:52:19 +00:00
```bash
Ctrl+l
```
2016-06-14 06:57:38 +00:00
2016-06-14 08:10:45 +00:00
#####send data to last edited file
2016-06-14 07:55:08 +00:00
2016-07-01 10:52:19 +00:00
```bash
cat /directory/to/file
echo 100>!$
```
2016-06-14 06:57:38 +00:00
2016-06-14 08:10:45 +00:00
#####run history number (e.g. 53)
2016-06-14 07:55:08 +00:00
2016-07-01 10:52:19 +00:00
```bash
!53
```
2016-06-14 06:57:38 +00:00
2016-06-14 08:10:45 +00:00
#####run last command
2016-06-14 07:55:08 +00:00
2016-07-01 10:52:19 +00:00
```bash
!!
```
2016-06-14 06:57:38 +00:00
2016-06-14 08:10:45 +00:00
#####run last command that began with (e.g. cat filename)
2016-06-14 07:55:08 +00:00
2016-07-01 10:52:19 +00:00
```bash
!cat
```
2016-06-14 07:55:08 +00:00
2016-06-14 06:57:38 +00:00
or
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2016-07-01 10:52:19 +00:00
```bash
!c
```
2016-06-14 06:57:38 +00:00
//run cat filename again
2016-06-14 08:03:32 +00:00
2016-06-14 08:10:45 +00:00
#####extract .xf
2016-06-14 07:55:08 +00:00
1.unxz filename.tar.xz
2.tar -xf filename.tar
2016-06-14 06:57:38 +00:00
2016-06-14 08:10:45 +00:00
#####install python package
2016-06-14 07:55:08 +00:00
2016-07-01 10:52:19 +00:00
```bash
pip install packagename
```
2016-06-14 06:57:38 +00:00
2016-06-14 08:10:45 +00:00
#####Download file if necessary
2016-06-14 07:55:08 +00:00
2016-07-01 10:52:19 +00:00
```bash
data=file.txt
url=http://www.example.com/$data
if [! -s $data];then
echo "downloading test data..."
wget $url
fi
```
2016-06-14 06:57:38 +00:00
2016-06-14 08:10:45 +00:00
#####wget to a filename (when a long name)
2016-06-14 07:55:08 +00:00
2016-07-01 10:52:19 +00:00
```bash
wget -O filename "http://example.com"
```
2016-06-14 06:57:38 +00:00
2016-06-14 08:10:45 +00:00
#####wget files to a folder
2016-06-14 07:55:08 +00:00
2016-07-01 10:52:19 +00:00
```bash
wget -P /path/to/directory "http://example.com"
```
2016-06-14 06:57:38 +00:00
2016-06-14 08:10:45 +00:00
#####delete current bash command
2016-06-14 07:55:08 +00:00
2016-07-01 10:52:19 +00:00
```bash
Ctrl+U
```
2016-06-14 07:55:08 +00:00
2016-06-14 06:57:38 +00:00
or
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2016-07-01 10:52:19 +00:00
```bash
Ctrl+C
```
2016-06-14 07:55:08 +00:00
2016-06-14 06:57:38 +00:00
or
2016-06-14 07:55:08 +00:00
2016-07-01 10:52:19 +00:00
```bash
Alt+Shift+#
```
2016-06-14 06:57:38 +00:00
//to make it to history
2016-06-14 08:03:32 +00:00
2016-06-14 08:10:45 +00:00
#####add things to history (e.g. "addmetohistory")
2016-06-14 07:55:08 +00:00
2016-07-01 10:52:19 +00:00
```bash
#addmetodistory
```
2016-06-14 06:57:38 +00:00
//just add a "#" before~~
2016-06-14 08:03:32 +00:00
2016-06-14 08:10:45 +00:00
#####sleep awhile or wait for a moment or schedule a job
2016-06-14 07:55:08 +00:00
2016-07-01 10:52:19 +00:00
```bash
sleep 5;echo hi
```
2016-06-14 06:57:38 +00:00
2016-06-14 08:10:45 +00:00
#####count the time for executing a command
2016-06-14 07:55:08 +00:00
2016-07-01 10:52:19 +00:00
```bash
time echo hi
```
2016-06-14 06:57:38 +00:00
2016-06-14 08:10:45 +00:00
#####backup with rsync
2016-06-14 07:55:08 +00:00
2016-07-01 10:52:19 +00:00
```bash
rsync -av filename filename.bak
rsync -av directory directory.bak
rsync -av --ignore_existing directory/ directory.bak
rsync -av --update directory directory.bak
```
2016-06-14 06:57:38 +00:00
//skip files that are newer on receiver (i prefer this one!)
2016-06-14 08:03:32 +00:00
2016-06-14 08:10:45 +00:00
#####make all directories at one time!
2016-06-14 07:55:08 +00:00
2016-07-01 10:52:19 +00:00
```bash
mkdir -p project/{lib/ext,bin,src,doc/{html,info,pdf},demo/stat}
```
2016-06-14 06:57:38 +00:00
//-p: make parent directory
//this will create project/doc/html/; project/doc/info; project/lib/ext ,etc
2016-06-14 08:03:32 +00:00
2016-06-14 08:10:45 +00:00
#####run command only if another command returns zero exit status (well done)
2016-06-14 07:55:08 +00:00
2016-07-01 10:52:19 +00:00
```bash
cd tmp/ && tar xvf ~/a.tar
```
2016-06-14 06:57:38 +00:00
2016-06-14 08:10:45 +00:00
#####run command only if another command returns non-zero exit status (not finish)
2016-06-14 07:55:08 +00:00
2016-07-01 10:52:19 +00:00
```bash
cd tmp/a/b/c ||mkdir -p tmp/a/b/c
```
2016-06-14 06:57:38 +00:00
2016-06-14 08:10:45 +00:00
#####extract to a path
2016-06-14 07:55:08 +00:00
2016-07-01 10:52:19 +00:00
```bash
tar xvf -C /path/to/directory filename.gz
```
2016-06-14 06:57:38 +00:00
2016-06-14 08:10:45 +00:00
#####use backslash "\" to break long command
2016-06-14 07:55:08 +00:00
2016-07-01 10:52:19 +00:00
```bash
cd tmp/a/b/c \
> || \
>mkdir -p tmp/a/b/c
```
2016-06-14 06:57:38 +00:00
2016-06-14 08:10:45 +00:00
#####get pwd
2016-06-14 08:03:32 +00:00
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```bash
VAR=$PWD; cd ~; tar xvf -C $VAR file.tar
```
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//PWD need to be capital letter
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#####list file type of file (e.g. /tmp/)
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```bash
file /tmp/
```
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//tmp/: directory
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#####bash script
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```bash
#!/bin/bash
file=${1#*.}
```
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//remove string before a "."
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```bash
file=${1%.*}
```
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//remove string after a "."
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#####search from history
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```bash
Ctrl+r
```
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#####python simple HTTP Server
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```bash
python -m SimpleHTTPServer
```
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#####variables
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```bash
{i/a/,}
```
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e.g. replace all
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```bash
{i//a/,}
```
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//for variable i, replace all 'a' with a comma
#####read user input
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```bash
read input
echo $input
```
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#####generate sequence 1-10
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```bash
seq 10
```
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#####sum up input list (e.g. seq 10)
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```bash
seq 10|paste -sd+|bc
```
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#####find average of input list/file
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```bash
i=`wc -l filename|cut -d ' ' -f1`; cat filename| echo "scale=2;(`paste -sd+`)/"$i|bc
```
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#####generate all combination (e.g. 1,2)
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```bash
echo {1,2}{1,2}
```
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//1 1, 1 2, 2 1, 2 2
#####generate all combination (e.g. A,T,C,G)
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```bash
set = {A,T,C,G}
group= 5
for ((i=0; i<$group; i++));do
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repetition=$set$repetition;done
bash -c "echo "$repetition""
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```
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#####read file content to variable
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```bash
foo=$(<test1)
```
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#####echo size of variable
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```bash
echo ${#foo}
```
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2016-08-25 11:57:18 +00:00
#####echo tab
```bash
echo -e ' \t '
```
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#####array
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```bash
declare -A array=()
```
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#####send a directory
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```bash
scp -r directoryname user@ip:/path/to/send
```
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#####split file into lines (e.g. 1000 lines/smallfile)
```bash
$ split -d -l 1000 bigfilename
```
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2016-09-23 03:15:49 +00:00
#####rename all files (e.g. remove ABC from all .gz files)
```bash
rename 's/ABC//' *.gz
```
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#####remove extention (e.g remove .gz from filename.gz)
```bash
basename filename.gz .gz
zcat filename.gz> $(basename filename.gz .gz).unpacked
```
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##System
[[back to top](#handy-bash-oneliner-commands-for-tsv-file-editing)]
#####snapshot of the current processes
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```bash
ps
```
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#####check graphics card
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```bash
lspci
```
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#####show IP address
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```bash
$ip add show
```
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or
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```bash
ifconfig
```
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#####check system version
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```bash
cat /etc/*-release
```
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#####Linux Programmer's Manuel: hier- description of the filesystem hierarchy
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```bash
man hier
```
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#####list job
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```bash
jobs -l
```
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#####export PATH
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```bash
export PATH=$PATH:~/path/you/want
```
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#####make file execuable
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```bash
chmod +x filename
```
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//you can now ./filename to execute it
#####list screen
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```bash
screen -d -r
```
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#####echo screen name
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```bash
screen -ls
```
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#####check system (x86-64)
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```bash
uname -i
```
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#####surf the net
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```bash
links www.google.com
```
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#####add user, set passwd
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```bash
useradd username
passwd username
```
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#####edit variable for bash, (e.g. displaying the whole path)
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```bash
1. joe ~/.bash_profile
2. export PS1='\u@\h:\w\$'
```
//$PS1 is a variable that defines the makeup and style of the command prompt
```bash
3. source ~/.bash_profile
```
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#####edit environment setting (e.g. alias)
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```bash
1. joe ~/.bash_profile
2. alias pd="pwd" //no more need to type that 'w'!
3. source ~/.bash_profile
```
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#####list environment variables (e.g. PATH)
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```bash
$echo $PATH
```
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//list of directories separated by a colon
#####list all environment variables for current user
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```bash
$env
```
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#####show partition format
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```bash
lsblk
```
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#####soft link program to bin
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```bash
ln -s /path/to/program /home/usr/bin
```
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//must be the whole path to the program
#####show hexadecimal view of data
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```bash
hexdump -C filename.class
```
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#####jump to different node
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```bash
rsh node_name
```
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#####check port (active internet connection)
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```bash
netstat -tulpn
```
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#####find whick link to a file
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```bash
readlink filename
```
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#####check where a command link to (e.g. python)
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```bash
which python
```
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#####list total size of a directory
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```bash
du -hs .
```
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or
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```bash
du -sb
```
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#####copy directory with permission setting
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```bash
cp -rp /path/to/directory
```
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#####store current directory
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```bash
pushd . $popd ;dirs -l
```
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#####show disk usage
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```bash
df -h
```
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or
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```bash
du -h
```
2016-06-16 06:52:03 +00:00
or
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```bash
du -sk /var/log/* |sort -rn |head -10
```
2016-06-16 06:52:03 +00:00
#####show current runlevel
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```bash
runlevel
```
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#####switch runlevel
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```bash
init 3
```
or
```bash
telinit 3
```
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#####permanently modify runlevel
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```bash
1. edit /etc/init/rc-sysinit.conf
2. env DEFAULT_RUNLEVEL=2
```
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#####become root
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```bash
su
```
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#####become somebody
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```bash
su somebody
```
2016-06-14 06:57:38 +00:00
2016-06-17 10:55:54 +00:00
#####report user quotes on device
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```bash
requota -auvs
```
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#####get entries in a number of important databases
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```bash
getent database_name
```
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(e.g. the 'passwd' database)
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```bash
getent passwd
```
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//list all user account (all local and LDAP)
(e.g. fetch list of grop accounts)
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```bash
getent group
```
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//store in database 'group'
#####little xwindow tools
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```bash
xclock
xeyes
```
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#####change owner of file
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```bash
chown user_name filename
chown -R user_name /path/to/directory/
```
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//chown user:group filename
#####list current mount detail
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```bash
df
```
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#####list current usernames and user-numbers
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```bash
cat /etc/passwd
```
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#####get all username
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```bash
getent passwd| awk '{FS="[:]"; print $1}'
```
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#####show all users
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```bash
compgen -u
```
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#####show all groups
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```bash
compgen -g
```
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#####show group of user
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```bash
group username
```
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#####show uid, gid, group of user
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```bash
id username
```
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#####check if it's root
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```bash
if [$(id -u) -ne 0];then
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echo "You are not root!"
exit;
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fi
```
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//'id -u' output 0 if it's not root
#####find out CPU information
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```bash
more /proc/cpuinfo
```
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or
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```bash
lscpu
```
2016-06-17 10:55:54 +00:00
#####set quota for user (e.g. disk soft limit: 120586240; hard limit: 125829120)
2016-07-01 10:52:19 +00:00
```bash
setquota username 120586240 125829120 0 0 /home
```
2016-06-17 10:55:54 +00:00
#####show quota for user
2016-07-01 10:52:19 +00:00
```bash
quota -v username
```
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#####fork bomb
2016-07-01 10:52:19 +00:00
```bash
:(){:|:&};:
```
2016-06-17 10:55:54 +00:00
//dont try this at home
#####check user login
2016-07-01 10:52:19 +00:00
```bash
lastlog
```
2016-06-17 10:55:54 +00:00
#####edit path for all users
2016-07-01 10:52:19 +00:00
```bash
joe /etc/environment
```
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//edit this file
#####show running processes
2016-07-01 10:52:19 +00:00
```bash
ps aux
```
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#####find maximum number of processes
2016-07-01 10:52:19 +00:00
```bash
cat /proc/sys/kernal/pid_max
```
2016-06-17 10:55:54 +00:00
#####show and set user limit
2016-07-01 10:52:19 +00:00
```bash
ulimit -u
```
2016-09-01 09:24:27 +00:00
#####which ports are listening for TCP connections from the network
2016-06-14 06:57:38 +00:00
2016-09-01 09:24:27 +00:00
```bash
nmap -sT -O localhost
```
2016-06-14 06:57:38 +00:00
2016-09-02 07:40:41 +00:00
#####print out number of cores/ processors
```bash
nproc --all
```
#####check status of each core
1. top
2. press '1'
2016-09-10 09:39:01 +00:00
#####show jobs and PID
2016-09-02 07:40:41 +00:00
2016-09-10 09:39:01 +00:00
```bash
jobs -l
```
2016-09-02 07:40:41 +00:00
2016-09-10 09:46:30 +00:00
#####list all running services
```bash
service --status-all
```
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=-=-=-=-=-A lot more coming!! =-=-=-=-=-=-=-=-=-=waitwait-=-=-=-=-=-=-=-=-=-