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