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edit all comments to start with '#' instead of '//'

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@ -144,9 +144,9 @@ grep $'\t'
```bash ```bash
$echo "$long_str"|grep -q "$short_str" $echo "$long_str"|grep -q "$short_str"
if [ $? -eq 0 ]; then echo 'found'; fi if [ $? -eq 0 ]; then echo 'found'; fi
#grep -q will output 0 if match found
#remember to add space between []!
``` ```
//grep -q will output 0 if match found
//remember to add space between []!
##### Grep strings between a bracket() ##### Grep strings between a bracket()
```bash ```bash
@ -156,8 +156,9 @@ 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 ```bash
grep -o -w "\w\{10\}\-R\w\{1\}" grep -o -w "\w\{10\}\-R\w\{1\}"
# \w word character [0-9a-zA-Z_] \W not word character
``` ```
// \w word character [0-9a-zA-Z_] \W not word character
##### A lot examples here ##### A lot examples here
@ -197,11 +198,9 @@ e.g. add >$i to the first line (to make a FASTA file)
```bash ```bash
sed "1i >$i" sed "1i >$i"
# notice the double quotes! in other examples, you can use a single quote, but here, no way!
# '1i' means insert to first line
``` ```
//notice the double quotes! in other examples, you can use a single quote, but here, no way!
//'1i' means insert to first line
##### Delete/remove empty lines ##### Delete/remove empty lines
```bash ```bash
@ -289,8 +288,10 @@ sed -n 500,5000p filename
```bash ```bash
sed -n '0~3p' filename sed -n '0~3p' filename
# catch 0: start; 3: step
``` ```
//catch 0: start; 3: step
##### Print every odd # lines ##### Print every odd # lines
@ -315,10 +316,9 @@ sed -e 's/^[ \t]*//'
```bash ```bash
sed 's/ *//' sed 's/ *//'
# notice a whitespace before '*'!!
``` ```
//notice a whitespace before '*'!!
##### Remove ending commas ##### Remove ending commas
```bash ```bash
@ -328,9 +328,11 @@ sed 's/,$//g'
```bash ```bash
sed "s/$/\t$i/" sed "s/$/\t$i/"
# $i is the valuable you want to add
# e.g. add the filename to every last column of the file
``` ```
//$i is the valuable you want to add
e.g. add the filename to every last column of the file
```bash ```bash
for i in $(ls);do sed -i "s/$/\t$i/" $i;done for i in $(ls);do sed -i "s/$/\t$i/" $i;done
@ -565,12 +567,10 @@ xargs -d\t
```bash ```bash
echo 1 2 3 4 5 6| xargs -n 3 echo 1 2 3 4 5 6| xargs -n 3
# 1 2 3
# 4 5 6
``` ```
//1 2 3
4 5 6
##### Prompt before execution ##### Prompt before execution
```bash ```bash
@ -581,12 +581,10 @@ echo a b c |xargs -p -n 3
```bash ```bash
xargs -t abcd xargs -t abcd
# bin/echo abcd
# abcd
``` ```
///bin/echo abcd
//abcd
##### With find and rm ##### With find and rm
```bash ```bash
@ -637,12 +635,12 @@ time echo {1..5} |xargs -n1 sleep
```bash ```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 find /dir/to/A -type f -name "*.py" -print 0| xargs -0 -r -I file cp -v -p file --target-directory=/path/to/B
# v: verbose|
# p: keep detail (e.g. owner)
``` ```
//v: verbose|
//p: keep detail (e.g. owner)
##### With sed ##### With sed
```bash ```bash
@ -671,9 +669,9 @@ ls -l| xargs
```bash ```bash
echo mso{1..8}|xargs -n1 bash -c 'echo -n "$1:"; ls -la "$1"| grep -w 74 |wc -l' -- 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
# "--" 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)
@ -727,10 +725,8 @@ if no subdirectory
```bash ```bash
replace "www" "w" -- * replace "www" "w" -- *
# a space before *
``` ```
//a space before *
##### Find and output only filename (e.g. "mso") ##### Find and output only filename (e.g. "mso")
```bash ```bash
@ -741,8 +737,10 @@ find mso*/ -name M* -printf "%f\n"
```bash ```bash
find . -name "*.mso" -size -74c -delete find . -name "*.mso" -size -74c -delete
# M for MB, etc
``` ```
//M for MB, etc
## Loops ## Loops
@ -751,9 +749,9 @@ find . -name "*.mso" -size -74c -delete
```bash ```bash
while read a b c; do echo $(($c-$b));done < <(head filename) while read a b c; do echo $(($c-$b));done < <(head filename)
```
//there is a space between the two '<'s
#there is a space between the two '<'s
```
##### While loop, sum up column subtraction ##### While loop, sum up column subtraction
```bash ```bash
@ -766,19 +764,17 @@ i=0; while read a b c; do ((i+=$c-$b)); echo $i; done < <(head filename)
while [[ $(pidof perl) ]];do echo f;sleep 10;done && python timetorunpython.py while [[ $(pidof perl) ]];do echo f;sleep 10;done && python timetorunpython.py
``` ```
##### If loop ##### If loop
```bash ```bash
if (($j==$u+2)) if (($j==$u+2))
#(( )) use for arithmetic operation
``` ```
//(( )) use for arithmetic operation
```bash ```bash
if [[$age >21]] if [[$age >21]]
#[[ ]] use for comparison
``` ```
//[[ ]] use for comparison
##### Test if file exist ##### Test if file exist
```bash ```bash
@ -864,24 +860,23 @@ echo "var=5;--var"| bc
``` ```
## Download ## Download
[[back to top](#handy-bash-oneliner-commands-for-tsv-file-editing)] [[back to top](#handy-bash-oneliner-commands-for-tsv-file-editing)]
##### Download all from a page ##### Download all from a page
```bash ```bash
wget -r -l1 -H -t1 -nd -N -np -A mp3 -e robots=off http://example.com wget -r -l1 -H -t1 -nd -N -np -A mp3 -e robots=off http://example.com
# -r: recursive and download all links on page
# -l1: only one level link
# -H: span host, visit other hosts
# -t1: numbers of retries
# -nd: don't make new directories, download to here
# -N: turn on timestamp
# -nd: no parent
# -A: type (seperate by ,)
# -e robots=off: ignore the robots.txt file which stop wget from crashing the site, sorry example.com
``` ```
//-r: recursive and download all links on page
//-l1: only one level link
//-H: span host, visit other hosts
//-t1: numbers of retries
//-nd: don't make new directories, download to here
//-N: turn on timestamp
//-nd: no parent
//-A: type (seperate by ,)
//-e robots=off: ignore the robots.txt file which stop wget from crashing the site, sorry example.com
##### Upload a file to web and download (https://transfer.sh/) ##### Upload a file to web and download (https://transfer.sh/)
--> upload: --> upload:
@ -1041,16 +1036,15 @@ tr /a-z/ /A-Z/
```bash ```bash
diff fileA fileB diff fileA fileB
# a: added; d:delete; c:changed
``` ```
//a: added; d:delete; c:changed
or or
```bash ```bash
sdiff fileA fileB sdiff fileA fileB
# side-to-side merge of file differences
``` ```
//side-to-side merge of file differences
##### Number a file (e.g. fileA) ##### Number a file (e.g. fileA)
@ -1061,23 +1055,19 @@ or
```bash ```bash
nl -nrz fileA nl -nrz fileA
# add leading zeros
``` ```
//add leading zeros
or or
```bash ```bash
nl -w1 -s ' ' nl -w1 -s ' '
# making it simple, blank seperated
``` ```
//making it simple, blank seperated
##### Combine/ paste two files (e.g. fileA, fileB) ##### Combine/ paste two files (e.g. fileA, fileB)
```bash ```bash
paste fileA fileB paste fileA fileB
# default tab seperated
``` ```
//default tab seperated
##### Reverse string ##### Reverse string
```bash ```bash
@ -1118,17 +1108,15 @@ or
```bash ```bash
some_commands 2>&1 >>outfile some_commands 2>&1 >>outfile
#0: standard input; 1: standard output; 2: standard error
``` ```
//0: standard input; 1: standard output; 2: standard error
##### Send mail ##### Send mail
```bash ```bash
echo 'heres the content'| mail -a /path/to/attach_file.txt -s 'mail.subject' me@gmail.com echo 'heres the content'| mail -a /path/to/attach_file.txt -s 'mail.subject' me@gmail.com
# use -a flag to set send from (-a "From: some@mail.tld")
``` ```
//use -a flag to set send from (-a "From: some@mail.tld")
##### .xls to csv ##### .xls to csv
@ -1211,9 +1199,8 @@ or
```bash ```bash
!c !c
# run cat filename again
``` ```
//run cat filename again
##### Extract .xf ##### Extract .xf
@ -1242,17 +1229,15 @@ or
```bash ```bash
Alt+Shift+# Alt+Shift+#
# to make it to history
``` ```
//to make it to history
##### Add something to history (e.g. "addmetohistory") ##### Add something to history (e.g. "addmetohistory")
```bash ```bash
#addmetodistory #addmetodistory
#just add a "#" before~~
``` ```
//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
@ -1282,10 +1267,9 @@ rsync -av directory user@ip_address:/path/to/directory.bak
```bash ```bash
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
``` ```
//-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)
@ -1317,15 +1301,16 @@ cd tmp/a/b/c \
```bash ```bash
VAR=$PWD; cd ~; tar xvf -C $VAR file.tar VAR=$PWD; cd ~; tar xvf -C $VAR file.tar
# PWD need to be capital letter
``` ```
//PWD need to be capital letter
##### List file type of file (e.g. /tmp/) ##### List file type of file (e.g. /tmp/)
```bash ```bash
file /tmp/ file /tmp/
# tmp/: directory
``` ```
//tmp/: directory
##### Bash script ##### Bash script
@ -1333,13 +1318,13 @@ file /tmp/
```bash ```bash
#!/bin/bash #!/bin/bash
file=${1#*.} file=${1#*.}
# remove string before a "."
``` ```
//remove string before a "."
```bash ```bash
file=${1%.*} file=${1%.*}
# remove string after a "."
``` ```
//remove string after a "."
##### Search from history ##### Search from history
@ -1367,7 +1352,7 @@ e.g. with grep
```bash ```bash
test="god the father" test="god the father"
grep ${test// /\\\|} file.txt grep ${test// /\\\|} file.txt
#turning the space into 'or' (\|) in grep # turning the space into 'or' (\|) in grep
``` ```
##### Read user input ##### Read user input
@ -1393,9 +1378,8 @@ i=`wc -l filename|cut -d ' ' -f1`; cat filename| echo "scale=2;(`paste -sd+`)/"$
```bash ```bash
echo {1,2}{1,2} echo {1,2}{1,2}
# 1 1, 1 2, 2 1, 2 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 ```bash
@ -1750,8 +1734,8 @@ export PATH=$PATH:~/path/you/want
```bash ```bash
chmod +x filename chmod +x filename
# you can now ./filename to execute it
``` ```
//you can now ./filename to execute it
##### List screen ##### List screen
@ -1789,8 +1773,9 @@ passwd username
```bash ```bash
1. joe ~/.bash_profile 1. joe ~/.bash_profile
2. export PS1='\u@\h:\w\$' 2. export PS1='\u@\h:\w\$'
# $PS1 is a variable that defines the makeup and style of the command prompt
``` ```
//$PS1 is a variable that defines the makeup and style of the command prompt
```bash ```bash
3. source ~/.bash_profile 3. source ~/.bash_profile
``` ```
@ -1807,9 +1792,8 @@ passwd username
```bash ```bash
$echo $PATH $echo $PATH
# list of directories separated by a colon
``` ```
//list of directories separated by a colon
##### List all environment variables for current user ##### List all environment variables for current user
```bash ```bash
@ -1826,8 +1810,8 @@ lsblk
```bash ```bash
ln -s /path/to/program /home/usr/bin ln -s /path/to/program /home/usr/bin
# must be the whole path to the program
``` ```
//must be the whole path to the program
##### Show hexadecimal view of data ##### Show hexadecimal view of data
@ -1947,22 +1931,22 @@ getent database_name
```bash ```bash
getent passwd getent passwd
# list all user account (all local and LDAP)
# (e.g. fetch list of grop accounts)
``` ```
//list all user account (all local and LDAP)
(e.g. fetch list of grop accounts)
```bash ```bash
getent group getent group
# store in database 'group'
``` ```
//store in database 'group'
##### Change owner of file ##### Change owner of file
```bash ```bash
chown user_name filename chown user_name filename
chown -R user_name /path/to/directory/ chown -R user_name /path/to/directory/
# chown user:group filename
``` ```
//chown user:group filename
##### List current mount detail ##### List current mount detail
@ -2012,9 +1996,8 @@ if [$(id -u) -ne 0];then
echo "You are not root!" echo "You are not root!"
exit; exit;
fi fi
# 'id -u' output 0 if it's not root
``` ```
//'id -u' output 0 if it's not root
##### Find out CPU information ##### Find out CPU information
```bash ```bash
@ -2039,11 +2022,10 @@ quota -v username
``` ```
##### Fork bomb ##### Fork bomb
# dont try this at home
```bash ```bash
:(){:|:&};: :(){:|:&};:
``` ```
//dont try this at home
##### Check user login ##### Check user login
@ -2055,9 +2037,8 @@ lastlog
```bash ```bash
joe /etc/environment joe /etc/environment
# edit this file
``` ```
//edit this file
##### Show running processes ##### Show running processes
```bash ```bash