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README.md
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README.md
@ -7,3 +7,464 @@ English and bash are not my first language, so... correct me anytime, sorry
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In case you would like to check up and like my stupid questions on Stackoverflow, here's my page:
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http://stackoverflow.com/users/4290753/once
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Handy Bash 'oneliner' commands for tsv file editing
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Symbol for search:
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>> section
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>function
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$bash code
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//comment
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>> Grep
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> extract text bewteen words (e.g. w1,w2)
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$ 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 and count (e.g. bbo)
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$grep -c bbo filename
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>insensitive grep (e.g. bbo/BBO/Bbo)
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$grep -i "bbo" filename
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>count occurrence (e.g. three times a line count three times)
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$grep -o bbo filename
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>COLOR the match (e.g. bbo)!
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$grep --color bbo filename
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>grep search all files in a directory(e.g. bbo)
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$grep -R bbo /path/to/directory or
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$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 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 'A.*B'
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>grep all content of a fileA from fileB
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$grep -f fileA fileB
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>grep a tab
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$grep $'\t'
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>>Sed
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>remove lines with word (e.g. bbo)
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$sed "/bbo/d" filename
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>edit infile (edit and save)
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$sed -i "/bbo/d" filename
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>when using variable (e.g. $i), use double quotes " "
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e.g. add >$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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>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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$sed 's/.\{4\}/&\n/g'
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>substitution (e.g. replace A by B)
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$sed 's/A/B/g' filename
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>select lines start with string (e.g. bbo)
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$sed -n '/^@S/p'
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>delete lines with string (e.g. bbo)
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$sed '/bbo/d' filename
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>print every nth lines
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$sed -n '0~3p' filename
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//catch 0: start; 3: step
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>print every odd # lines
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$sed -n '1~2p'
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>print every third line including the first line
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$sed -n '1p;0~3p'
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>remove leading whitespace and tabs
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$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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$sed 's/ *//'
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//notice a whitespace before '*'!!
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>remove ending commas
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$sed 's/,$//g'
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>add a column to the end
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$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/" $i;done
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>remove newline\ nextline
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$sed ':a;N;$!ba;s/\n//g'
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>>Awk
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>set tab as field separator
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$awk -F $'\t'
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>output as tab separated (also as field separator)
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$awk -v OFS='\t'
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>pass variable
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a=bbo;b=obb;
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awk -v a="$a" -v b="$b" "$1==a && $10=b' filename
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>print number of characters on each line
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$awk '{print length ($0);}' filename
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>find number of columns
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$awk '{print NF}'
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>reverse column order
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$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 '$1~/,/ {print}'
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>split and do for loop
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$awk '{split($2, a,",");for (i in a) print $1"\t"a[i]} filename
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>print all lines before nth occurence of a string (e.g stop print lines when bbo appears 7 times)
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$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"$3'
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>remove lines with string (e.g. bbo)
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$awk '!/bbo/' file
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>column subtraction
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$cat file| awk -F '\t' 'BEGIN {SUM=0}{SUM+=$3-$2}END{print SUM}'
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>usage and meaning of NR and FNR
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e.g.
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fileA:
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a
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b
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c
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fileB:
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d
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e
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$awk 'print FILENAME, NR,FNR,$0}' fileA fileB fileA 1 1 a
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fileA 2 2 b
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fileA 3 3 c
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fileB 4 1 d
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fileB 5 2 e
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>and gate
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e.g.
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fileA:
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1 0
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2 1
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3 1
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4 0
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fileB:
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1 0
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2 1
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3 0
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4 1
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$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($0, RSTART+RLENGTH)
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\}
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\print
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\}'
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>give number/index to every row
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$awk '{printf("%s\t%s\n",NR,$0)}'
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>>Xargs
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>set tab as delimiter (default:space)
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$xargs -d\t
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>display 3 items per line
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$echo 1 2 3 4 5 6| xargs -n 3
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//1 2 3
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4 5 6
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>prompt before execution
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$echo a b c |xargs -p -n 3
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>print command along with output
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$xargs -t abcd
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///bin/echo abcd
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//abcd
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>with find and rm
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$find . -name "*.html"|xargs rm -rf
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>delete fiels with whitespace in filename (e.g. "hello 2001")
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$find . -name "*.c" -print0|xargs -0 rm -rf
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>show limits
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$xargs --show-limits
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>move files to folder
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$find . -name "*.bak" -print 0|xargs -0 -I {} mv {} ~/old
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or
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$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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$ls |head -100|xargs -I {} mv {} d1
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>parallel
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$time echo {1..5} |xargs -n 1 -P 5 sleepa lot faster than
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$time echo {1..5} |xargs -n1 sleep
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>copy all files from A to B
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$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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$ls |xargs -n1 -I file sed -i '/^Pos/d' filename
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>add the file name to the first line of file
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$ls |sed 's/.txt//g'|xargs -n1 -I file sed -i -e '1 i\>file\' file.txt
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>count all files
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$ls |xargs -n1 wc -l
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>to filter txt to a single line
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$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 "$1"| grep -w 74 |wc -l' --
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// "--" signals the end of options and display further option processing
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>download dependencies files and install (e.g. requirements.txt)
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$cat requirements.txt| xargs -n1 sudo pip install
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>count lines in all file, also count total lines
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$ls|xargs wc -l
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>>Find
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>list all sub directory/file in the current directory
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$find .
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>list all files under the current directory
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$find . -type f
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>list all directories under the current directory
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$find . -type d
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>edit all files under current directory (e.g. replace 'www' with 'ww')
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$find . name '*.php' -exec sed -i 's/www/w/g' {} \;
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>if no subdirectory
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$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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$find mso*/ -name M* -printf "%f\n"
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>find and delete file with size less than (e.g. 74 byte)
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$find . -name "*.mso" -size -74c -delete
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//M for MB, etc
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>>Others
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>remove newline / nextline
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$tr --delete '\n' <input.txt >output.txt
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>replace newline
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$ tr '\n' ' ' <filename
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>compare files (e.g. fileA, fileB)
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$diff fileA fileB
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//a: added; d:delete; c:changed
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or
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$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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$nl fileA
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or
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$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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$paste fileA fileB
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//default tab seperated
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>reverse string
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$echo 12345| rev
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>read .gz file without extracting
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$zmore filename
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or
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$zless filename
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>run in background, output error file
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$(command here) 2>log &
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or
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$(command here) 2>&1| tee logfile
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or
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$(command here) 2>&1 >>outfile
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//0: standard input; 1: standard output; 2: standard error
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>send mail
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$echo 'heres the content'| mail -A 'file.txt' -s 'mail.subject' me@gmail.com
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//use -a flag to set send from (-a "From: some@mail.tld")
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>.xls to csv
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$xls2csv filename
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>append to file (e.g. hihi)
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$echo 'hihi' >>filename
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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 $pid
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>history edit/ delete
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$~/.bash_history
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or
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$history -d [line_number]
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>get last history/record filename
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$head !$
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>clean screen
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$clear
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or
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$Ctrl+l
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>send data to last edited file
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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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$!53
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>run last command
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$!!
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>run last command that began with (e.g. cat filename)
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$!cat
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or
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$!c
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//run cat filename again
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>extract .xf
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1. $unxz filename.tar.xz
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2. $tar -xf filename.tar
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>install python package
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$pip install packagename
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>random order (lucky draw)
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$for i in a b c d e; do echo $i; done| shuf
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>echo a random number
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$echo $RANDOM
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>Download file if necessary
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$data=file.txt
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url=http://www.example.com/$data
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if [! -s $data];then
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echo "downloading test data..."
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wget $url
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fi
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>wget to a filename (when a long name)
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$wget -O filename "http://example.com"
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>wget files to a folder
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$wget -P /path/to/directory "http://example.com"
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>delete current bash command
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$Ctrl+U
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or
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$Ctrl+C
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or
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$Alt+Shift+#
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//to make it to history
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>add things to history (e.g. "addmetohistory")
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$#addmetodistory
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//just add a "#" before~~
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>sleep awhile or wait for a moment or schedule a job
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$sleep 5;echo hi
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>count the time for executing a command
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$time echo hi
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>backup with rsync
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$rsync -av filename filename.bak
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$rsync -av directory directory.bak
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$rsync -av --ignore_existing directory/ directory.bak
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$rsync -av --update directory directory.bak
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//skip files that are newer on receiver (i prefer this one!)
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>make all directories at one time!
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$mkdir -p project/{lib/ext,bin,src,doc/{html,info,pdf},demo/stat}
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//-p: make parent directory
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//this will create project/doc/html/; project/doc/info; project/lib/ext ,etc
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>run command only if another command returns zero exit status (well done)
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$cd tmp/ && tar xvf ~/a.tar
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>run command only if another command returns non-zero exit status (not finish)
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$cd tmp/a/b/c ||mkdir -p tmp/a/b/c
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>extract to a path
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$tar xvf -C /path/to/directory filename.gz
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>use backslash "\" to break long command
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$cd tmp/a/b/c \
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> || \
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>mkdir -p tmp/a/b/c
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>get pwd
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$VAR=$PWD; cd ~; tar xvf -C $VAR file.tar
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//PWD need to be capital letter
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>list file type of file (e.g. /tmp/)
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$file /tmp/
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//tmp/: directory
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>bash script
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#!/bin/bash
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file=${1#*.}
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//remove string before a "."
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file=${1%.*}
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//remove string after a "."
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=-=-=-=-=-A lot more coming!! =-=-=-=-=-=-=-=-=-=waitwait-=-=-=-=-=-=-=-=-=-
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Reference in New Issue
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