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README.md
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README.md
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@ -11,145 +11,154 @@ http://stackoverflow.com/users/4290753/once
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##Handy Bash 'oneliner' commands for tsv file editing
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- Grep
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- Sed
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- Awk
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- Xargs
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- Find
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- Others
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##Grep
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extract text bewteen words (e.g. w1,w2)
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grep -o -P '(?<=w1).*(?=w2)'
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>grep lines without word (e.g. bbo)
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$ grep -v bbo
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grep -v bbo
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>grep and count (e.g. bbo)
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$grep -c bbo filename
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grep -c bbo filename
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>insensitive grep (e.g. bbo/BBO/Bbo)
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$grep -i "bbo" filename
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grep -i "bbo" filename
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>count occurrence (e.g. three times a line count three times)
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$grep -o bbo filename
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grep -o bbo filename
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>COLOR the match (e.g. bbo)!
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$grep --color bbo filename
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grep --color bbo filename
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>grep search all files in a directory(e.g. bbo)
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$grep -R bbo /path/to/directory or
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$grep -r bbo /path/to/directory
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grep -R bbo /path/to/directory or
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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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$grep -Rh bbo /path/to/directory or
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$grep -rh bbo /path/to/directory
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grep -Rh bbo /path/to/directory or
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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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$grep 'A\|B\|C\|D'
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grep 'A\|B\|C\|D'
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>grep AND (e.g. A and B)
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$grep 'A.*B'
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grep 'A.*B'
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>grep all content of a fileA from fileB
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$grep -f fileA fileB
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grep -f fileA fileB
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>grep a tab
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$grep $'\t'
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grep '\t'
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>>Sed
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#Sed
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>remove lines with word (e.g. bbo)
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$sed "/bbo/d" filename
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sed "/bbo/d" filename
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>edit infile (edit and save)
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$sed -i "/bbo/d" filename
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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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$sed "1i >$i"
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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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sed "1i > i"
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//notice the double quotes! in other examples, you can use a single quote, but here, no way!
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//'1i' means insert to first line
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>delete empty lines
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$sed '/^\s*$/d' or
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$sed 's/^$/d'
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sed '/^\s* /d' or
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sed 's/^ /d'
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>delete last line
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$sed '$d'
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sed ' d'
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>add \n every nth character (e.g. every 4th character)
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$sed 's/.\{4\}/&\n/g'
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sed 's/.\{4\}/&\n/g'
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>substitution (e.g. replace A by B)
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$sed 's/A/B/g' filename
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sed 's/A/B/g' filename
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>select lines start with string (e.g. bbo)
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$sed -n '/^@S/p'
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sed -n '/^@S/p'
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>delete lines with string (e.g. bbo)
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$sed '/bbo/d' filename
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sed '/bbo/d' filename
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>print every nth lines
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$sed -n '0~3p' filename
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sed -n '0~3p' filename
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//catch 0: start; 3: step
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>print every odd # lines
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$sed -n '1~2p'
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sed -n '1~2p'
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>print every third line including the first line
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$sed -n '1p;0~3p'
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sed -n '1p;0~3p'
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>remove leading whitespace and tabs
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$sed -e 's/^[ \t]*//'
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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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$sed 's/ *//'
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sed 's/ *//'
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//notice a whitespace before '*'!!
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>remove ending commas
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$sed 's/,$//g'
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sed 's/, //g'
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>add a column to the end
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$sed "s/$/\t$i/"
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//$i is the valuable you want to add
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sed "s/ /\t i/"
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// i is the valuable you want to add
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e.g. add the filename to every last column of the file
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$for i in $(ls);do sed -i "s/$/\t$i/" $i;done
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for i in (ls);do sed -i "s/ /\t i/" i;done
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>remove newline\ nextline
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$sed ':a;N;$!ba;s/\n//g'
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sed ':a;N; !ba;s/\n//g'
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>>Awk
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#Awk
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>set tab as field separator
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$awk -F $'\t'
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awk -F '\t'
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>output as tab separated (also as field separator)
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$awk -v OFS='\t'
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awk -v OFS='\t'
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>pass variable
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a=bbo;b=obb;
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awk -v a="$a" -v b="$b" "$1==a && $10=b' filename
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awk -v a=" a" -v b=" b" " 1==a && 10=b' filename
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>print number of characters on each line
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$awk '{print length ($0);}' filename
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awk '{print length ( 0);}' filename
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>find number of columns
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$awk '{print NF}'
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awk '{print NF}'
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>reverse column order
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$awk '{print $2, $1}'
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awk '{print 2, 1}'
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>check if there is a comma in a column (e.g. column $1)
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$awk '$1~/,/ {print}'
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>check if there is a comma in a column (e.g. column 1)
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awk ' 1~/,/ {print}'
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>split and do for loop
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$awk '{split($2, a,",");for (i in a) print $1"\t"a[i]} filename
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awk '{split( 2, a,",");for (i in a) print 1"\t"a[i]} filename
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>print all lines before nth occurence of a string (e.g stop print lines when bbo appears 7 times)
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$awk -v N=7 '{print}/bbo/&& --N<=0 {exit}'
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awk -v N=7 '{print}/bbo/&& --N<=0 {exit}'
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>add string to the beginning of a column (e.g add "chr" to column $3)
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$awk 'BEGIN{OFS="\t"}$3="chr"$3'
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>add string to the beginning of a column (e.g add "chr" to column 3)
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awk 'BEGIN{OFS="\t"} 3="chr" 3'
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>remove lines with string (e.g. bbo)
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$awk '!/bbo/' file
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awk '!/bbo/' file
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>column subtraction
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$cat file| awk -F '\t' 'BEGIN {SUM=0}{SUM+=$3-$2}END{print SUM}'
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cat file| awk -F '\t' 'BEGIN {SUM=0}{SUM+= 3- 2}END{print SUM}'
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>usage and meaning of NR and FNR
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e.g.
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@ -160,7 +169,7 @@ c
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fileB:
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d
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e
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$awk 'print FILENAME, NR,FNR,$0}' fileA fileB fileA 1 1 a
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awk 'print FILENAME, NR,FNR, 0}' fileA fileB fileA 1 1 a
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fileA 2 2 b
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fileA 3 3 c
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fileB 4 1 d
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@ -178,281 +187,281 @@ fileB:
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2 1
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3 0
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4 1
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$awk -v OFS='\t' 'NR=FNR{a[$1]=$2;next} NF {print $1,((a[$1]=$2)? $2:"0")}' fileA fileB 1 0
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awk -v OFS='\t' 'NR=FNR{a[ 1]= 2;next} NF {print 1,((a[ 1]= 2)? 2:"0")}' fileA fileB 1 0
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2 1
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3 0
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4 0
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>round all numbers of file (e.g. 2 significant figure)
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$awk '{while (match($0, /[0-9]+\[0-9]+/)){
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\printf "%s%.2f", substr($0,0,RSTART-1),substr($0,RSTART,RLENGTH)
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\$0=substr($0, RSTART+RLENGTH)
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awk '{while (match( 0, /[0-9]+\[0-9]+/)){
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\printf "%s%.2f", substr( 0,0,RSTART-1),substr( 0,RSTART,RLENGTH)
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\ 0=substr( 0, RSTART+RLENGTH)
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\}
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\print
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\}'
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>give number/index to every row
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$awk '{printf("%s\t%s\n",NR,$0)}'
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awk '{printf("%s\t%s\n",NR, 0)}'
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>>Xargs
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#Xargs
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>set tab as delimiter (default:space)
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$xargs -d\t
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xargs -d\t
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>display 3 items per line
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$echo 1 2 3 4 5 6| xargs -n 3
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echo 1 2 3 4 5 6| xargs -n 3
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//1 2 3
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4 5 6
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>prompt before execution
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$echo a b c |xargs -p -n 3
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echo a b c |xargs -p -n 3
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>print command along with output
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$xargs -t abcd
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xargs -t abcd
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///bin/echo abcd
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//abcd
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>with find and rm
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$find . -name "*.html"|xargs rm -rf
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find . -name "*.html"|xargs rm -rf
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>delete fiels with whitespace in filename (e.g. "hello 2001")
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$find . -name "*.c" -print0|xargs -0 rm -rf
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find . -name "*.c" -print0|xargs -0 rm -rf
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>show limits
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$xargs --show-limits
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xargs --show-limits
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>move files to folder
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$find . -name "*.bak" -print 0|xargs -0 -I {} mv {} ~/old
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find . -name "*.bak" -print 0|xargs -0 -I {} mv {} ~/old
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or
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$find . -name "*.bak" -print 0|xargs -0 -I file mv file ~/old
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find . -name "*.bak" -print 0|xargs -0 -I file mv file ~/old
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>move first 100th files to a directory (e.g. d1)
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$ls |head -100|xargs -I {} mv {} d1
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ls |head -100|xargs -I {} mv {} d1
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>parallel
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$time echo {1..5} |xargs -n 1 -P 5 sleepa lot faster than
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$time echo {1..5} |xargs -n1 sleep
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time echo {1..5} |xargs -n 1 -P 5 sleepa lot faster than
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time echo {1..5} |xargs -n1 sleep
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>copy all files from A to B
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$find /dir/to/A -type f -name "*.py" -print 0| xargs -0 -r -I file cp -v -p file --target-directory=/path/to/B
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find /dir/to/A -type f -name "*.py" -print 0| xargs -0 -r -I file cp -v -p file --target-directory=/path/to/B
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//v: verbose|
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//p: keep detail (e.g. owner)
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>with sed
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$ls |xargs -n1 -I file sed -i '/^Pos/d' filename
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ls |xargs -n1 -I file sed -i '/^Pos/d' filename
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>add the file name to the first line of file
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$ls |sed 's/.txt//g'|xargs -n1 -I file sed -i -e '1 i\>file\' file.txt
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ls |sed 's/.txt//g'|xargs -n1 -I file sed -i -e '1 i\>file\' file.txt
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>count all files
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$ls |xargs -n1 wc -l
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ls |xargs -n1 wc -l
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>to filter txt to a single line
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$ls -l| xargs
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ls -l| xargs
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>count files within directories
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$echo mso{1..8}|xargs -n1 bash -c 'echo -n "$1:"; ls -la "$1"| grep -w 74 |wc -l' --
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echo mso{1..8}|xargs -n1 bash -c 'echo -n " 1:"; ls -la " 1"| grep -w 74 |wc -l' --
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// "--" signals the end of options and display further option processing
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>download dependencies files and install (e.g. requirements.txt)
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$cat requirements.txt| xargs -n1 sudo pip install
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cat requirements.txt| xargs -n1 sudo pip install
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>count lines in all file, also count total lines
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$ls|xargs wc -l
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ls|xargs wc -l
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>>Find
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#Find
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>list all sub directory/file in the current directory
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$find .
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find .
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>list all files under the current directory
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$find . -type f
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find . -type f
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>list all directories under the current directory
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$find . -type d
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find . -type d
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>edit all files under current directory (e.g. replace 'www' with 'ww')
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$find . name '*.php' -exec sed -i 's/www/w/g' {} \;
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find . name '*.php' -exec sed -i 's/www/w/g' {} \;
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>if no subdirectory
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$replace "www" "w" -- *
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replace "www" "w" -- *
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//a space before *
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>find and output only filename (e.g. "mso")
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$find mso*/ -name M* -printf "%f\n"
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find mso*/ -name M* -printf "%f\n"
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>find and delete file with size less than (e.g. 74 byte)
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$find . -name "*.mso" -size -74c -delete
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find . -name "*.mso" -size -74c -delete
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//M for MB, etc
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>>Others
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#Others
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>remove newline / nextline
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$tr --delete '\n' <input.txt >output.txt
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tr --delete '\n' <input.txt >output.txt
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>replace newline
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$ tr '\n' ' ' <filename
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tr '\n' ' ' <filename
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>compare files (e.g. fileA, fileB)
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$diff fileA fileB
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diff fileA fileB
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//a: added; d:delete; c:changed
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or
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$sdiff fileA fileB
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sdiff fileA fileB
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//side-to-side merge of file differences
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>number a file (e.g. fileA)
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$nl fileA
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nl fileA
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or
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$nl -nrz fileA
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nl -nrz fileA
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//add leading zeros
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>combine/ paste two files (e.g. fileA, fileB)
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$paste fileA fileB
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paste fileA fileB
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//default tab seperated
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>reverse string
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$echo 12345| rev
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echo 12345| rev
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>read .gz file without extracting
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$zmore filename
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zmore filename
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or
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$zless filename
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zless filename
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>run in background, output error file
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$(command here) 2>log &
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(command here) 2>log &
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or
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$(command here) 2>&1| tee logfile
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(command here) 2>&1| tee logfile
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or
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$(command here) 2>&1 >>outfile
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(command here) 2>&1 >>outfile
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//0: standard input; 1: standard output; 2: standard error
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>send mail
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$echo 'heres the content'| mail -A 'file.txt' -s 'mail.subject' me@gmail.com
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echo 'heres the content'| mail -A 'file.txt' -s 'mail.subject' me@gmail.com
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//use -a flag to set send from (-a "From: some@mail.tld")
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>.xls to csv
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$xls2csv filename
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xls2csv filename
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>append to file (e.g. hihi)
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$echo 'hihi' >>filename
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echo 'hihi' >>filename
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|
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>make BEEP found
|
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$speaker-test -t sine -f 1000 -l1
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speaker-test -t sine -f 1000 -l1
|
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>set beep duration
|
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$(speaker-test -t sine -f 1000) & pid=$!;sleep 0.1s;kill -9 $pid
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(speaker-test -t sine -f 1000) & pid= !;sleep 0.1s;kill -9 pid
|
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|
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>history edit/ delete
|
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$~/.bash_history
|
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~/.bash_history
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or
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$history -d [line_number]
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history -d [line_number]
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|
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>get last history/record filename
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$head !$
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head !
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>clean screen
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||||
$clear
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clear
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or
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||||
$Ctrl+l
|
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Ctrl+l
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>send data to last edited file
|
||||
$cat /directory/to/file
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$echo 100>!$
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cat /directory/to/file
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echo 100>!
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>run history number (e.g. 53)
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$!53
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!53
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>run last command
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$!!
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!!
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||||
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||||
>run last command that began with (e.g. cat filename)
|
||||
$!cat
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!cat
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||||
or
|
||||
$!c
|
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!c
|
||||
//run cat filename again
|
||||
|
||||
>extract .xf
|
||||
1. $unxz filename.tar.xz
|
||||
2. $tar -xf filename.tar
|
||||
1. unxz filename.tar.xz
|
||||
2. tar -xf filename.tar
|
||||
|
||||
>install python package
|
||||
$pip install packagename
|
||||
pip install packagename
|
||||
|
||||
>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 $RANDOM
|
||||
echo RANDOM
|
||||
|
||||
>Download file if necessary
|
||||
$data=file.txt
|
||||
url=http://www.example.com/$data
|
||||
if [! -s $data];then
|
||||
data=file.txt
|
||||
url=http://www.example.com/ data
|
||||
if [! -s data];then
|
||||
echo "downloading test data..."
|
||||
wget $url
|
||||
wget url
|
||||
fi
|
||||
|
||||
>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 -P /path/to/directory "http://example.com"
|
||||
wget -P /path/to/directory "http://example.com"
|
||||
|
||||
>delete current bash command
|
||||
$Ctrl+U
|
||||
Ctrl+U
|
||||
or
|
||||
$Ctrl+C
|
||||
Ctrl+C
|
||||
or
|
||||
$Alt+Shift+#
|
||||
Alt+Shift+#
|
||||
//to make it to history
|
||||
|
||||
>add things to history (e.g. "addmetohistory")
|
||||
$#addmetodistory
|
||||
#addmetodistory
|
||||
//just add a "#" before~~
|
||||
|
||||
>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
|
||||
$time echo hi
|
||||
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
|
||||
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}
|
||||
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
|
||||
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
|
||||
cd tmp/a/b/c ||mkdir -p tmp/a/b/c
|
||||
|
||||
>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
|
||||
$cd tmp/a/b/c \
|
||||
cd tmp/a/b/c \
|
||||
> || \
|
||||
>mkdir -p tmp/a/b/c
|
||||
|
||||
>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
|
||||
|
||||
>list file type of file (e.g. /tmp/)
|
||||
$file /tmp/
|
||||
file /tmp/
|
||||
//tmp/: directory
|
||||
|
||||
>bash script
|
||||
#!/bin/bash
|
||||
file=${1#*.}
|
||||
file= {1#*.}
|
||||
//remove string before a "."
|
||||
file=${1%.*}
|
||||
file= {1%.*}
|
||||
//remove string after a "."
|
||||
|
||||
|
||||
|
|
|
|||
Loading…
Reference in a new issue