diff --git a/README.md b/README.md index 8820628..cf558a8 100644 --- a/README.md +++ b/README.md @@ -11,7 +11,7 @@ http://stackoverflow.com/users/4290753/once Here's a more stylish version~ http://onceupon.github.io/Bash-Oneliner/ -#Handy Bash oneliner commands for tsv file editing +## Handy Bash oneliner commands for tsv file editing - [Grep](#grep) - [Sed](#sed) @@ -24,50 +24,50 @@ http://onceupon.github.io/Bash-Oneliner/ - [Others](#others) - [System](#system) -##Grep -#####extract text bewteen words (e.g. w1,w2) +## Grep +##### extract text bewteen words (e.g. w1,w2) ```bash grep -o -P '(?<=w1).*(?=w2)' ``` -#####grep lines without word (e.g. bbo) +##### grep lines without word (e.g. bbo) ```bash grep -v bbo filename ``` -#####grep only one/first match (e.g. bbo) +##### grep only one/first match (e.g. bbo) ```bash grep -m 1 bbo filename ``` -#####grep and count (e.g. bbo) +##### grep and count (e.g. bbo) ```bash grep -c bbo filename ``` -#####insensitive grep (e.g. bbo/BBO/Bbo) +##### insensitive grep (e.g. bbo/BBO/Bbo) ```bash grep -i "bbo" filename ``` -#####count occurrence (e.g. three times a line count three times) +##### count occurrence (e.g. three times a line count three times) ```bash grep -o bbo filename ``` -#####COLOR the match (e.g. bbo)! +##### COLOR the match (e.g. bbo)! ```bash grep --color bbo filename ``` -#####grep search all files in a directory(e.g. bbo) +##### grep search all files in a directory(e.g. bbo) ```bash grep -R bbo /path/to/directory @@ -78,7 +78,7 @@ or ```bash grep -r bbo /path/to/directory ``` -#####search all files in directory, only output file names with matches(e.g. bbo) +##### search all files in directory, only output file names with matches(e.g. bbo) ```bash grep -Rh bbo /path/to/directory @@ -88,31 +88,31 @@ or grep -rh bbo /path/to/directory ``` -#####grep OR (e.g. A or B or C or D) +##### grep OR (e.g. A or B or C or D) ``` grep 'A\|B\|C\|D' ``` -#####grep AND (e.g. A and B) +##### grep AND (e.g. A and B) ```bash grep 'A.*B' ``` -#####grep all content of a fileA from fileB +##### grep all content of a fileA from fileB ```bash grep -f fileA fileB ``` -#####grep a tab +##### grep a tab ```bash grep $'\t' ``` -#####grep variable from variable +##### grep variable from variable ```bash $echo "$long_str"|grep -q "$short_str" if [ $? -eq 0 ]; then echo 'found'; fi @@ -120,38 +120,38 @@ if [ $? -eq 0 ]; then echo 'found'; fi //grep -q will output 0 if match found //remember to add space between []! -#####grep strings between a bracket() +##### grep strings between a bracket() ```bash grep -oP '\(\K[^\)]+' ``` -#####grep number of characters with known strings in between(e.g. AAEL000001-RA) +##### grep number of characters with known strings in between(e.g. AAEL000001-RA) ```bash grep -o -w "\w\{10\}\-R\w\{1\}" ``` // \w word character [0-9a-zA-Z_] \W not word character -#####a lot examples here +##### a lot examples here http://www.cyberciti.biz/faq/grep-regular-expressions/ -##Sed +## Sed [[back to top](#handy-bash-oneliner-commands-for-tsv-file-editing)] -#####remove lines with word (e.g. bbo) +##### remove lines with word (e.g. bbo) ```bash sed "/bbo/d" filename ``` -#####edit infile (edit and save) +##### edit infile (edit and save) ```bash sed -i "/bbo/d" filename ``` -#####when using variable (e.g. $i), use double quotes " " +##### when using variable (e.g. $i), use double quotes " " e.g. add >$i to the first line (to make a FASTA file) ```bash @@ -161,7 +161,7 @@ sed "1i >$i" //'1i' means insert to first line -#####delete empty lines +##### delete empty lines ```bash sed '/^\s*$/d' @@ -171,62 +171,62 @@ or ```bash sed 's/^$/d' ``` -#####delete last line +##### delete last line ```bash sed '$d' ``` -#####delete last character from end of file +##### delete last character from end of file ```bash sed -i '$ s/.$//' filename ``` -#####add string to end of file (e.g. "]") +##### add string to end of file (e.g. "]") ```bash sed '$s/$/]/' filename ``` -#####add string to beginning of every line (e.g. bbo) +##### add string to beginning of every line (e.g. bbo) ```bash sed -e 's/^/bbo/' file ``` -#####add string to end of each line (e.g. "}") +##### add string to end of each line (e.g. "}") ```bash sed -e 's/$/\}\]/' filename ``` -#####add \n every nth character (e.g. every 4th character) +##### add \n every nth character (e.g. every 4th character) ```bash sed 's/.\{4\}/&\n/g' ``` -#####concatenate/combine/join files with a seperator and next line (e.g seperate by ",") +##### concatenate/combine/join files with a seperator and next line (e.g seperate by ",") ```bash sed -s '$a,' *.json > all.json ``` -#####substitution (e.g. replace A by B) +##### substitution (e.g. replace A by B) ```bash sed 's/A/B/g' filename ``` -#####select lines start with string (e.g. bbo) +##### select lines start with string (e.g. bbo) ```bash sed -n '/^@S/p' ``` -#####delete lines with string (e.g. bbo) +##### delete lines with string (e.g. bbo) ```bash sed '/bbo/d' filename ``` -#####print every nth lines +##### print every nth lines ```bash sed -n '0~3p' filename @@ -234,17 +234,17 @@ sed -n '0~3p' filename //catch 0: start; 3: step -#####print every odd # lines +##### print every odd # lines ```bash sed -n '1~2p' ``` -#####print every third line including the first line +##### print every third line including the first line ```bash sed -n '1p;0~3p' ``` -#####remove leading whitespace and tabs +##### remove leading whitespace and tabs ```bash sed -e 's/^[ \t]*//' @@ -252,7 +252,7 @@ sed -e 's/^[ \t]*//' //notice a whitespace before '\t'!! -#####remove only leading whitespace +##### remove only leading whitespace ```bash sed 's/ *//' @@ -260,12 +260,12 @@ sed 's/ *//' //notice a whitespace before '*'!! -#####remove ending commas +##### remove ending commas ```bash sed 's/,$//g' ``` -#####add a column to the end +##### add a column to the end ```bash sed "s/$/\t$i/" @@ -276,125 +276,125 @@ e.g. add the filename to every last column of the file ```bash for i in $(ls);do sed -i "s/$/\t$i/" $i;done ``` -#####add extension of filename to last column +##### add extension of filename to last column ```bash for i in T000086_1.02.n T000086_1.02.p;do sed "s/$/\t${i/*./}/" $i;done >T000086_1.02.np ``` -#####remove newline\ nextline +##### remove newline\ nextline ```bash sed ':a;N;$!ba;s/\n//g' ``` -#####print a number of lines (e.g. line 10th to line 33 rd) +##### print a number of lines (e.g. line 10th to line 33 rd) ```bash sed -n '10,33p' AAA#AAA) +##### insert character at specified position of file (e.g. AAAAAA --> AAA#AAA) ```bash`` sed -r -e 's/^.{3}/&#/' file ``` -#Awk +## Awk [[back to top](#handy-bash-oneliner-commands-for-tsv-file-editing)] -#####set tab as field separator +##### set tab as field separator ```bash awk -F $'\t' ``` -#####output as tab separated (also as field separator) +##### output as tab separated (also as field separator) ```bash awk -v OFS='\t' ``` -#####pass variable +##### pass variable ```bash a=bbo;b=obb; awk -v a="$a" -v b="$b" "$1==a && $10=b' filename ``` -#####print number of characters on each line +##### print number of characters on each line ```bash awk '{print length ($0);}' filename ``` -#####find number of columns +##### find number of columns ```bash awk '{print NF}' ``` -#####reverse column order +##### reverse column order ```bash awk '{print $2, $1}' ``` -#####check if there is a comma in a column (e.g. column $1) +##### check if there is a comma in a column (e.g. column $1) ```bash awk '$1~/,/ {print}' ``` -#####split and do for loop +##### split and do for loop ```bash awk '{split($2, a,",");for (i in a) print $1"\t"a[i]} filename ``` -#####print all lines before nth occurence of a string (e.g stop print lines when bbo appears 7 times) +##### print all lines before nth occurence of a string (e.g stop print lines when bbo appears 7 times) ```bash awk -v N=7 '{print}/bbo/&& --N<=0 {exit}' ``` -#####print filename and last line of all files in directory +##### print filename and last line of all files in directory ```bash ls|xargs -n1 -I file awk '{s=$0};END{print FILENAME,s}' file' ``` -#####add string to the beginning of a column (e.g add "chr" to column $3) +##### add string to the beginning of a column (e.g add "chr" to column $3) ```bash awk 'BEGIN{OFS="\t"}$3="chr"$3' ``` -#####remove lines with string (e.g. bbo) +##### remove lines with string (e.g. bbo) ```bash awk '!/bbo/' file ``` -#####column subtraction +##### column subtraction ```bash cat file| awk -F '\t' 'BEGIN {SUM=0}{SUM+=$3-$2}END{print SUM}' ``` -#####usage and meaning of NR and FNR +##### usage and meaning of NR and FNR e.g. fileA: a @@ -414,7 +414,7 @@ fileA 3 3 c fileB 4 1 d fileB 5 2 e -#####and gate +##### and gate e.g. fileA: @@ -448,7 +448,7 @@ awk -v OFS='\t' 'NR=FNR{a[$1]=$2;next} NF {print $1,((a[$1]=$2)? $2:"0")}' fileA 4 0 -#####round all numbers of file (e.g. 2 significant figure) +##### round all numbers of file (e.g. 2 significant figure) ```bash awk '{while (match($0, /[0-9]+\[0-9]+/)){ @@ -459,12 +459,12 @@ awk '{while (match($0, /[0-9]+\[0-9]+/)){ \}' ``` -#####give number/index to every row +##### give number/index to every row ```bash awk '{printf("%s\t%s\n",NR,$0)}' ``` -#####break combine column data into rows +##### break combine column data into rows e.g. seperate @@ -482,40 +482,40 @@ detail here:　http://stackoverflow.com/questions/33408762/bash-turning-single-c awk '{split($2,a,",");for(i in a)print $1"\t"a[i]}' file ``` -#####sum up a file (each line in file contains only one number) +##### sum up a file (each line in file contains only one number) ```bash awk '{s+=$1} END {print s}' filename ``` -#####average a file (each line in file contains only one number) +##### average a file (each line in file contains only one number) ```bash awk '{s+=$1}END{print s/NR}' ``` -#####print field start with string (e.g Linux) +##### print field start with string (e.g Linux) ```bash awk '$1 ~ /^Linux/' ``` -#####sort a row (e.g. 1 40 35 12 23 --> 1 12 23 35 40) +##### sort a row (e.g. 1 40 35 12 23 --> 1 12 23 35 40) ```bash awk ' {split( $0, a, "\t" ); asort( a ); for( i = 1; i <= length(a); i++ ) printf( "%s\t", a[i] ); printf( "\n" ); }' ``` -##Xargs +## Xargs [[back to top](#handy-bash-oneliner-commands-for-tsv-file-editing)] -#####set tab as delimiter (default:space) +##### set tab as delimiter (default:space) ```bash xargs -d\t ``` -#####display 3 items per line +##### display 3 items per line ```bash echo 1 2 3 4 5 6| xargs -n 3 @@ -525,13 +525,13 @@ echo 1 2 3 4 5 6| xargs -n 3 4 5 6 -#####prompt before execution +##### prompt before execution ```bash echo a b c |xargs -p -n 3 ``` -#####print command along with output +##### print command along with output ```bash xargs -t abcd @@ -541,7 +541,7 @@ xargs -t abcd //abcd -#####with find and rm +##### with find and rm ```bash find . -name "*.html"|xargs rm -rf @@ -553,13 +553,13 @@ delete fiels with whitespace in filename (e.g. "hello 2001") find . -name "*.c" -print0|xargs -0 rm -rf ``` -#####show limits +##### show limits ```bash xargs --show-limits ``` -#####move files to folder +##### move files to folder ```bash find . -name "*.bak" -print 0|xargs -0 -I {} mv {} ~/old @@ -571,13 +571,13 @@ or find . -name "*.bak" -print 0|xargs -0 -I file mv file ~/old ``` -#####move first 100th files to a directory (e.g. d1) +##### move first 100th files to a directory (e.g. d1) ```bash ls |head -100|xargs -I {} mv {} d1 ``` -#####parallel +##### parallel ```bash time echo {1..5} |xargs -n 1 -P 5 sleep @@ -587,7 +587,7 @@ a lot faster than time echo {1..5} |xargs -n1 sleep ``` -#####copy all files from A to B +##### copy all files from A to B ```bash find /dir/to/A -type f -name "*.py" -print 0| xargs -0 -r -I file cp -v -p file --target-directory=/path/to/B @@ -597,31 +597,31 @@ find /dir/to/A -type f -name "*.py" -print 0| xargs -0 -r -I file cp -v -p file //p: keep detail (e.g. owner) -#####with sed +##### with sed ```bash ls |xargs -n1 -I file sed -i '/^Pos/d' filename ``` -#####add the file name to the first line of file +##### add the file name to the first line of file ```bash ls |sed 's/.txt//g'|xargs -n1 -I file sed -i -e '1 i\>file\' file.txt ``` -#####count all files +##### count all files ```bash ls |xargs -n1 wc -l ``` -#####to filter txt to a single line +##### to filter txt to a single line ```bash ls -l| xargs ``` -#####count files within directories +##### count files within directories ```bash echo mso{1..8}|xargs -n1 bash -c 'echo -n "$1:"; ls -la "$1"| grep -w 74 |wc -l' -- @@ -629,44 +629,44 @@ echo mso{1..8}|xargs -n1 bash -c 'echo -n "$1:"; ls -la "$1"| grep -w 74 |wc -l' // "--" signals the end of options and display further option processing -#####download dependencies files and install (e.g. requirements.txt) +##### download dependencies files and install (e.g. requirements.txt) ```bash cat requirements.txt| xargs -n1 sudo pip install ``` -#####count lines in all file, also count total lines +##### count lines in all file, also count total lines ```bash ls|xargs wc -l ``` -#####xargs and grep +##### xargs and grep ```bash cat grep_list |xargs -I{} grep {} filename ``` -##Find +## Find [[back to top](#handy-bash-oneliner-commands-for-tsv-file-editing)] -#####list all sub directory/file in the current directory +##### list all sub directory/file in the current directory ```bash find . ``` -#####list all files under the current directory +##### list all files under the current directory ```bash find . -type f ``` -#####list all directories under the current directory +##### list all directories under the current directory ```bash find . -type d ``` -#####edit all files under current directory (e.g. replace 'www' with 'ww') +##### edit all files under current directory (e.g. replace 'www' with 'ww') ```bash find . name '*.php' -exec sed -i 's/www/w/g' {} \; @@ -679,13 +679,13 @@ replace "www" "w" -- * //a space before * -#####find and output only filename (e.g. "mso") +##### find and output only filename (e.g. "mso") ```bash find mso*/ -name M* -printf "%f\n" ``` -#####find and delete file with size less than (e.g. 74 byte) +##### find and delete file with size less than (e.g. 74 byte) ```bash find . -name "*.mso" -size -74c -delete @@ -693,22 +693,22 @@ find . -name "*.mso" -size -74c -delete //M for MB, etc -##Loops +## Loops [[back to top](#handy-bash-oneliner-commands-for-tsv-file-editing)] -#####while loop, column subtraction of a file (e.g. a 3 columns file) +##### while loop, column subtraction of a file (e.g. a 3 columns file) ```bash while read a b c; do echo $(($c-$b));done < <(head filename) ``` //there is a space between the two '<'s -#####while loop, sum up column subtraction +##### while loop, sum up column subtraction ```bash i=0; while read a b c; do ((i+=$c-$b)); echo $i; done < <(head filename) ``` -#####if loop +##### if loop ```bash if (($j==$u+2)) @@ -721,7 +721,7 @@ if [[$age >21]] //[[ ]] use for comparison -#####test if file exist +##### test if file exist ```bash if [ -e $DF ] then @@ -730,16 +730,16 @@ fi ``` -#####for loop +##### for loop ```bash for i in $(ls); do echo file $i;done ``` -##Download +## Download [[back to top](#handy-bash-oneliner-commands-for-tsv-file-editing)] -#####download all from a page +##### download all from a page ```bash wget -r -l1 -H -t1 -nd -N -np -A mp3 -e robots=off http://example.com @@ -764,39 +764,39 @@ wget -r -l1 -H -t1 -nd -N -np -A mp3 -e robots=off http://example.com -##Random +## Random [[back to top](#handy-bash-oneliner-commands-for-tsv-file-editing)] -#####random pick 100 lines from a file +##### random pick 100 lines from a file ```bash shuf -n 100 filename ``` -#####random order (lucky draw) +##### random order (lucky draw) ```bash for i in a b c d e; do echo $i; done| shuf ``` -#####echo series of random numbers between a range (e.g. generate 15 random numbers from 0-10) +##### echo series of random numbers between a range (e.g. generate 15 random numbers from 0-10) ```bash shuf -i 0-10 -n 15 ``` -#####echo a random number +##### echo a random number ```bash echo $RANDOM ``` -#####random from 0-9 +##### random from 0-9 ```bash echo $((RANDOM % 10)) ``` -#####random from 1-10 +##### random from 1-10 ```bash echo $(((RANDOM %10)+1)) @@ -804,21 +804,21 @@ echo $(((RANDOM %10)+1)) -##Others +## Others [[back to top](#handy-bash-oneliner-commands-for-tsv-file-editing)] -#####remove newline / nextline +##### remove newline / nextline ```bash tr --delete '\n' output.txt ``` -#####replace newline +##### replace newline ```bash tr '\n' ' ' log & @@ -898,7 +898,7 @@ some_commands 2>&1 >>outfile //0: standard input; 1: standard output; 2: standard error -#####send mail +##### send mail ```bash echo 'heres the content'| mail -A 'file.txt' -s 'mail.subject' me@gmail.com @@ -906,30 +906,30 @@ echo 'heres the content'| mail -A 'file.txt' -s 'mail.subject' me@gmail.com //use -a flag to set send from (-a "From: some@mail.tld") -#####.xls to csv +##### .xls to csv ```bash xls2csv filename ``` -#####append to file (e.g. hihi) +##### append to file (e.g. hihi) ```bash echo 'hihi' >>filename ``` -#####make BEEP sound +##### make BEEP sound ```bash speaker-test -t sine -f 1000 -l1 ``` -#####set beep duration +##### set beep duration ```bash (speaker-test -t sine -f 1000) & pid=$!;sleep 0.1s;kill -9 $pid ``` -#####history edit/ delete +##### history edit/ delete ```bash ~/.bash_history @@ -940,13 +940,13 @@ or history -d [line_number] ``` -#####get last history/record filename +##### get last history/record filename ```bash head !$ ``` -#####clean screen +##### clean screen ```bash clear @@ -958,26 +958,26 @@ or Ctrl+l ``` -#####send data to last edited file +##### send data to last edited file ```bash cat /directory/to/file echo 100>!$ ``` -#####run history number (e.g. 53) +##### run history number (e.g. 53) ```bash !53 ``` -#####run last command +##### run last command ```bash !! ``` -#####run last command that began with (e.g. cat filename) +##### run last command that began with (e.g. cat filename) ```bash !cat @@ -991,19 +991,19 @@ or //run cat filename again -#####extract .xf +##### extract .xf 1.unxz filename.tar.xz 2.tar -xf filename.tar -#####install python package +##### install python package ```bash pip install packagename ``` -#####Download file if necessary +##### Download file if necessary ```bash data=file.txt @@ -1014,19 +1014,19 @@ if [! -s $data];then fi ``` -#####wget to a filename (when a long name) +##### wget to a filename (when a long name) ```bash wget -O filename "http://example.com" ``` -#####wget files to a folder +##### wget files to a folder ```bash wget -P /path/to/directory "http://example.com" ``` -#####delete current bash command +##### delete current bash command ```bash Ctrl+U @@ -1046,7 +1046,7 @@ Alt+Shift+# //to make it to history -#####add things to history (e.g. "addmetohistory") +##### add things to history (e.g. "addmetohistory") ```bash #addmetodistory @@ -1054,19 +1054,19 @@ Alt+Shift+# //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 ```bash sleep 5;echo hi ``` -#####count the time for executing a command +##### count the time for executing a command ```bash time echo hi ``` -#####backup with rsync +##### backup with rsync ```bash rsync -av filename filename.bak @@ -1077,7 +1077,7 @@ rsync -av --update directory directory.bak //skip files that are newer on receiver (i prefer this one!) -#####make all directories at one time! +##### make all directories at one time! ```bash mkdir -p project/{lib/ext,bin,src,doc/{html,info,pdf},demo/stat} @@ -1086,25 +1086,25 @@ mkdir -p project/{lib/ext,bin,src,doc/{html,info,pdf},demo/stat} //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) ```bash 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) ```bash cd tmp/a/b/c ||mkdir -p tmp/a/b/c ``` -#####extract to a path +##### extract to a path ```bash tar xvf -C /path/to/directory filename.gz ``` -#####use backslash "\" to break long command +##### use backslash "\" to break long command ```bash cd tmp/a/b/c \ @@ -1112,14 +1112,14 @@ cd tmp/a/b/c \ >mkdir -p tmp/a/b/c ``` -#####get pwd +##### get pwd ```bash VAR=$PWD; cd ~; tar xvf -C $VAR file.tar ``` //PWD need to be capital letter -#####list file type of file (e.g. /tmp/) +##### list file type of file (e.g. /tmp/) ```bash file /tmp/ @@ -1127,7 +1127,7 @@ file /tmp/ //tmp/: directory -#####bash script +##### bash script ```bash #!/bin/bash @@ -1140,19 +1140,19 @@ file=${1%.*} ``` //remove string after a "." -#####search from history +##### search from history ```bash Ctrl+r ``` -#####python simple HTTP Server +##### python simple HTTP Server ```bash python -m SimpleHTTPServer ``` -#####variables +##### variables ```bash {i/a/,} @@ -1163,39 +1163,39 @@ e.g. replace all ``` //for variable i, replace all 'a' with a comma -#####read user input +##### read user input ```bash read input echo $input ``` -#####generate sequence 1-10 +##### generate sequence 1-10 ```bash seq 10 ``` -#####sum up input list (e.g. seq 10) +##### sum up input list (e.g. seq 10) ```bash seq 10|paste -sd+|bc ``` -#####find average of input list/file +##### find average of input list/file ```bash i=`wc -l filename|cut -d ' ' -f1`; cat filename| echo "scale=2;(`paste -sd+`)/"$i|bc ``` -#####generate all combination (e.g. 1,2) +##### generate all combination (e.g. 1,2) ```bash echo {1,2}{1,2} ``` //1 1, 1 2, 2 1, 2 2 -#####generate all combination (e.g. A,T,C,G) +##### generate all combination (e.g. A,T,C,G) ```bash set = {A,T,C,G} @@ -1205,94 +1205,94 @@ for ((i=0; i<$group; i++));do bash -c "echo "$repetition"" ``` -#####read file content to variable +##### read file content to variable ```bash foo=$( $(basename filename.gz .gz).unpacked ``` -#####use the squeeze repeat option (e.g. /t/t --> /t) +##### use the squeeze repeat option (e.g. /t/t --> /t) ```bash tr -s "/t" < filename ``` -#####do not print nextline with echo +##### do not print nextline with echo ```bash echo -e 'text here \c' ``` -#####use the last argument +##### use the last argument ```bash !$ ``` -#####check last exit code +##### check last exit code ```bash echo $? ``` -#####view first 50 characters of file +##### view first 50 characters of file ```bash head -c 50 file ``` -#####open pictures/images from ssh server +##### open pictures/images from ssh server ```bash 1. ssh -X user_name@ip_address 2. apt-get install eog 3. eog picture.png ``` -#####Use gedit on server (GUI editor) +##### Use gedit on server (GUI editor) ```bash 1. ssh -X user_name@ip_address 2. apt-get install gedit 3. gedit filename.txt ``` -#####open PDF file from ssh server +##### open PDF file from ssh server ```bash 1. ssh -X user_name@ip_address 2. apt-get install evince 3. evince filename.pdf ``` -#####group/combine rows into one row +##### group/combine rows into one row e.g. @@ -1313,37 +1313,37 @@ cat filename|paste - - - - AAAABBBBCCCCDDDD ``` -#####fastq to fasta +##### fastq to fasta ```bash cat file.fastq | paste - - - - | sed 's/^@/>/g'| cut -f1-2 | tr '\t' '\n' >file.fa ``` -#####cut and get last column +##### cut and get last column ```bash cat file|rev | cut -d/ -f1 | rev ``` -#####add one to variable/increment a numeric variable (e.g. $var) +##### add one to variable/increment a numeric variable (e.g. $var) ```bash ((var++)) ``` -##System +## System [[back to top](#handy-bash-oneliner-commands-for-tsv-file-editing)] -#####snapshot of the current processes +##### snapshot of the current processes ```bash ps ``` -#####check graphics card +##### check graphics card ```bash lspci ``` -#####show IP address +##### show IP address ```bash $ip add show @@ -1354,69 +1354,69 @@ or ifconfig ``` -#####check system version +##### check system version ```bash cat /etc/*-release ``` -#####Linux Programmer's Manuel: hier- description of the filesystem hierarchy +##### Linux Programmer's Manuel: hier- description of the filesystem hierarchy ```bash man hier ``` -#####list job +##### list job ```bash jobs -l ``` -#####export PATH +##### export PATH ```bash export PATH=$PATH:~/path/you/want ``` -#####make file execuable +##### make file execuable ```bash chmod +x filename ``` //you can now ./filename to execute it -#####list screen +##### list screen ```bash screen -d -r ``` -#####echo screen name +##### echo screen name ```bash screen -ls ``` -#####check system (x86-64) +##### check system (x86-64) ```bash uname -i ``` -#####surf the net +##### surf the net ```bash links www.google.com ``` -#####add user, set passwd +##### add user, set passwd ```bash useradd username passwd username ``` -#####edit variable for bash, (e.g. displaying the whole path) +##### edit variable for bash, (e.g. displaying the whole path) ```bash 1. joe ~/.bash_profile @@ -1427,7 +1427,7 @@ passwd username 3. source ~/.bash_profile ``` -#####edit environment setting (e.g. alias) +##### edit environment setting (e.g. alias) ```bash 1. joe ~/.bash_profile @@ -1435,63 +1435,63 @@ passwd username 3. source ~/.bash_profile ``` -#####list environment variables (e.g. PATH) +##### list environment variables (e.g. PATH) ```bash $echo $PATH ``` //list of directories separated by a colon -#####list all environment variables for current user +##### list all environment variables for current user ```bash $env ``` -#####show partition format +##### show partition format ```bash lsblk ``` -#####soft link program to bin +##### soft link program to bin ```bash ln -s /path/to/program /home/usr/bin ``` //must be the whole path to the program -#####show hexadecimal view of data +##### show hexadecimal view of data ```bash hexdump -C filename.class ``` -#####jump to different node +##### jump to different node ```bash rsh node_name ``` -#####check port (active internet connection) +##### check port (active internet connection) ```bash netstat -tulpn ``` -#####find whick link to a file +##### find whick link to a file ```bash readlink filename ``` -#####check where a command link to (e.g. python) +##### check where a command link to (e.g. python) ```bash which python ``` -#####list total size of a directory +##### list total size of a directory ```bash du -hs . @@ -1502,19 +1502,19 @@ or du -sb ``` -#####copy directory with permission setting +##### copy directory with permission setting ```bash cp -rp /path/to/directory ``` -#####store current directory +##### store current directory ```bash pushd . $popd ;dirs -l ``` -#####show disk usage +##### show disk usage ```bash df -h @@ -1530,13 +1530,13 @@ or du -sk /var/log/* |sort -rn |head -10 ``` -#####show current runlevel +##### show current runlevel ```bash runlevel ``` -#####switch runlevel +##### switch runlevel ```bash init 3 @@ -1545,32 +1545,32 @@ or ```bash telinit 3 ``` -#####permanently modify runlevel +##### permanently modify runlevel ```bash 1. edit /etc/init/rc-sysinit.conf 2. env DEFAULT_RUNLEVEL=2 ``` -#####become root +##### become root ```bash su ``` -#####become somebody +##### become somebody ```bash su somebody ``` -#####report user quotes on device +##### report user quotes on device ```bash requota -auvs ``` -#####get entries in a number of important databases +##### get entries in a number of important databases ```bash getent database_name @@ -1588,14 +1588,14 @@ getent group ``` //store in database 'group' -#####little xwindow tools +##### little xwindow tools ```bash xclock xeyes ``` -#####change owner of file +##### change owner of file ```bash chown user_name filename @@ -1603,48 +1603,48 @@ chown -R user_name /path/to/directory/ ``` //chown user:group filename -#####list current mount detail +##### list current mount detail ```bash df ``` -#####list current usernames and user-numbers +##### list current usernames and user-numbers ```bash cat /etc/passwd ``` -#####get all username +##### get all username ```bash getent passwd| awk '{FS="[:]"; print $1}' ``` -#####show all users +##### show all users ```bash compgen -u ``` -#####show all groups +##### show all groups ```bash compgen -g ``` -#####show group of user +##### show group of user ```bash group username ``` -#####show uid, gid, group of user +##### show uid, gid, group of user ```bash id username ``` -#####check if it's root +##### check if it's root ```bash if [$(id -u) -ne 0];then @@ -1654,7 +1654,7 @@ fi ``` //'id -u' output 0 if it's not root -#####find out CPU information +##### find out CPU information ```bash more /proc/cpuinfo @@ -1665,97 +1665,97 @@ or lscpu ``` -#####set quota for user (e.g. disk soft limit: 120586240; hard limit: 125829120) +##### set quota for user (e.g. disk soft limit: 120586240; hard limit: 125829120) ```bash setquota username 120586240 125829120 0 0 /home ``` -#####show quota for user +##### show quota for user ```bash quota -v username ``` -#####fork bomb +##### fork bomb ```bash :(){:|:&};: ``` //dont try this at home -#####check user login +##### check user login ```bash lastlog ``` -#####edit path for all users +##### edit path for all users ```bash joe /etc/environment ``` //edit this file -#####show running processes +##### show running processes ```bash ps aux ``` -#####find maximum number of processes +##### find maximum number of processes ```bash cat /proc/sys/kernal/pid_max ``` -#####show and set user limit +##### show and set user limit ```bash ulimit -u ``` -#####which ports are listening for TCP connections from the network +##### which ports are listening for TCP connections from the network ```bash nmap -sT -O localhost ``` -#####print out number of cores/ processors +##### print out number of cores/ processors ```bash nproc --all ``` -#####check status of each core +##### check status of each core 1. top 2. press '1' -#####show jobs and PID +##### show jobs and PID ```bash jobs -l ``` -#####list all running services +##### list all running services ```bash service --status-all ``` -#####schedule shutdown server +##### schedule shutdown server ```bash shutdown -r +5 "Server will restart in 5 minutes. Please save your work." ``` -#####cancel scheduled shutdown +##### cancel scheduled shutdown ```bash shutdown -c ``` -#####boardcast to all users +##### boardcast to all users ```bash wall -n hihi ``` -#####enable X11 forwarding,in order to use graphical application on servers +##### enable X11 forwarding,in order to use graphical application on servers ```bash ssh -X user_name@ip_address ``` @@ -1767,11 +1767,11 @@ xorg-x11-fonts-* xorg-x11-utils -#####kill all process of a user +##### kill all process of a user ```bash pkill -U user_name ``` -#####set gedit preference on server +##### set gedit preference on server -->you might have to install the following: