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@ -1,5 +1,5 @@
# Bash-Oneliner # Bash-Oneliner
I am glad that you are here! I started working on bioinformatics a few years ago (recently switched to cloud computing), and was amazed by those single-word bash commands which are much faster than my dull scripts, time saved through learning command-line shortcuts and scripting. Not all the code here is oneliner, but i put effort on making them brief and swift. I am mainly using Ubuntu, RedHat and Linux Mint and CentOS, sorry if the commands dont work on your system. I am glad that you are here! I started working on bioinformatics a few years ago (recently switched to cloud computing), and was amazed by those single-word bash commands which are much faster than my dull scripts, time saved through learning command-line shortcuts and scripting. Not all the code here is oneliner, but i put effort on making them brief and swift. I am mainly using Ubuntu, RedHat and Linux Mint and CentOS, sorry if the commands don't work on your system.
This blog will focus on simple bash commands for parsing data and Linux system maintenance that i acquired from work and LPIC exam. I apologize that there are no detailed citation for all the commands, but they are probably from dear Google and Stackoverflow. This blog will focus on simple bash commands for parsing data and Linux system maintenance that i acquired from work and LPIC exam. I apologize that there are no detailed citation for all the commands, but they are probably from dear Google and Stackoverflow.
@ -34,8 +34,7 @@ Here's a more stylish version of [Bash-Oneliner](http://onceupon.github.io/Bash-
```bash ```bash
Ctrl + n : same as Down arrow. Ctrl + n : same as Down arrow.
Ctrl + p : same as Up arrow. Ctrl + p : same as Up arrow.
Ctrl + r : begins a backward search through cammand history.(keep pressing Ctrl + r to move backward) Ctrl + r : begins a backward search through command history.(keep pressing Ctrl + r to move backward)
Ctrl + l : Clear the terminal
Ctrl + s : to stop output to terminal. Ctrl + s : to stop output to terminal.
Ctrl + q : to resume output to terminal after Ctrl + s. Ctrl + q : to resume output to terminal after Ctrl + s.
Ctrl + a : move to the beginning of line. Ctrl + a : move to the beginning of line.
@ -44,8 +43,6 @@ Ctrl + d : if you've type something, Ctrl + d deletes the character under the cu
Ctrl + k : delete all text from the cursor to the end of line. Ctrl + k : delete all text from the cursor to the end of line.
Ctrl + x + backspace : delete all text from the beginning of line to the cursor. Ctrl + x + backspace : delete all text from the beginning of line to the cursor.
Ctrl + t : transpose the character before the cursor with the one under the cursor, press Esc + t to transposes the two words before the cursor. Ctrl + t : transpose the character before the cursor with the one under the cursor, press Esc + t to transposes the two words before the cursor.
Ctrl + w : delete the word before the cursor.
Ctrl + u : delete the line before the cursor.
Ctrl + x + Ctrl + e : launch editor define by $EDITOR Ctrl + x + Ctrl + e : launch editor define by $EDITOR
``` ```
##### Change case ##### Change case
@ -158,7 +155,7 @@ grep -C 3 'bbo'
grep -o 'S.*' grep -o 'S.*'
``` ```
##### Extract text bewteen words (e.g. w1,w2) ##### Extract text between words (e.g. w1,w2)
```bash ```bash
grep -o -P '(?<=w1).*(?=w2)' grep -o -P '(?<=w1).*(?=w2)'
@ -582,7 +579,7 @@ awk '$1~/,/ {print}'
awk '{split($2, a,",");for (i in a) print $1"\t"a[i]}' filename 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 occurrence of a string (e.g stop print lines when bbo appears 7 times)
```bash ```bash
awk -v N=7 '{print}/bbo/&& --N<=0 {exit}' awk -v N=7 '{print}/bbo/&& --N<=0 {exit}'
@ -981,7 +978,7 @@ while read a b c; do echo $(($c-$b));done < <(head filename)
# Sum up column subtraction # Sum up column subtraction
i=0; while read a b c; do ((i+=$c-$b)); echo $i; done < <(head filename) i=0; while read a b c; do ((i+=$c-$b)); echo $i; done < <(head filename)
# Keep checking a running process (e.g. perl) and start another new process (e.g. python) immetiately after it. (BETTER use the wait command! Ctrl+F 'wait') # Keep checking a running process (e.g. perl) and start another new process (e.g. python) immediately after it. (BETTER use the wait command! Ctrl+F 'wait')
while [[ $(pidof perl) ]];do echo f;sleep 10;done && python timetorunpython.py while [[ $(pidof perl) ]];do echo f;sleep 10;done && python timetorunpython.py
``` ```
@ -1132,7 +1129,7 @@ TMOUT=10
##### Set how long you want to run a command ##### Set how long you want to run a command
```bash ```bash
#This will run the commmand 'sleep 10' for only 1 second. #This will run the command 'sleep 10' for only 1 second.
timeout 1 sleep 10 timeout 1 sleep 10
``` ```
@ -1366,7 +1363,7 @@ jobs -l
export PATH=$PATH:~/path/you/want export PATH=$PATH:~/path/you/want
``` ```
##### Make file execuable ##### Make file executable
```bash ```bash
chmod +x filename chmod +x filename
@ -1650,7 +1647,7 @@ quota -v username
``` ```
##### Fork bomb ##### Fork bomb
# dont try this at home # don't try this at home
```bash ```bash
:(){:|:&};: :(){:|:&};:
``` ```
@ -1688,7 +1685,7 @@ ulimit -u
```bash ```bash
nmap -sT -O localhost nmap -sT -O localhost
#notice that some commpanies might not like you using nmap #notice that some companies might not like you using nmap
``` ```
##### Print out number of cores/ processors ##### Print out number of cores/ processors
@ -1721,7 +1718,7 @@ shutdown -r +5 "Server will restart in 5 minutes. Please save your work."
shutdown -c shutdown -c
``` ```
##### Boardcast to all users ##### Broadcast to all users
```bash ```bash
wall -n hihi wall -n hihi
``` ```
@ -1898,7 +1895,7 @@ ssh -f -L 9000:targetservername:8088 root@192.168.14.72 -N
#pidof #pidof
pidof sublime_text pidof sublime_text
#pgrep, you dont have to type the whole program name #pgrep, you don't have to type the whole program name
pgrep sublim pgrep sublim
#top, takes longer time #top, takes longer time
@ -1920,7 +1917,7 @@ top|grep sublime_text
[ioblazer](https://labs.vmware.com/flings/ioblazer) - multi-platform storage stack micro-benchmark. [ioblazer](https://labs.vmware.com/flings/ioblazer) - multi-platform storage stack micro-benchmark.
[iozone](http://www.iozone.org/) - filesystem benchmark. [iozone](http://www.iozone.org/) - filesystem benchmark.
[iperf3](https://iperf.fr/iperf-download.php) - measure TCP/UDP/SCTP performance. [iperf3](https://iperf.fr/iperf-download.php) - measure TCP/UDP/SCTP performance.
[kcbench](https://github.com/knurd/kcbench) - kernel compile benchmark, compiles a kernel and messures the time it takes. [kcbench](https://github.com/knurd/kcbench) - kernel compile benchmark, compiles a kernel and measures the time it takes.
[lmbench](http://www.bitmover.com/lmbench/) - Suite of simple, portable benchmarks. [lmbench](http://www.bitmover.com/lmbench/) - Suite of simple, portable benchmarks.
[netperf](https://github.com/HewlettPackard/netperf) - measure network performance, test unidirectional throughput, and end-to-end latency. [netperf](https://github.com/HewlettPackard/netperf) - measure network performance, test unidirectional throughput, and end-to-end latency.
[netpipe](https://linux.die.net/man/1/netpipe) - network protocol independent performance evaluator. [netpipe](https://linux.die.net/man/1/netpipe) - network protocol independent performance evaluator.
@ -2064,7 +2061,7 @@ ip a
ip r ip r
``` ```
##### Display ARP cache (ARP cache displays the MAC addresses of deveice in the same network that you have connected to) ##### Display ARP cache (ARP cache displays the MAC addresses of device in the same network that you have connected to)
```bash ```bash
ip n ip n
``` ```
@ -2685,7 +2682,7 @@ example:
q -d "," "select c3,c4,c5 from /path/to/file.txt where c3='foo' and c5='boo'" q -d "," "select c3,c4,c5 from /path/to/file.txt where c3='foo' and c5='boo'"
``` ```
##### Sreen and tmux ##### Screen and tmux
create session and attach: create session and attach:
```bash ```bash
screen screen
@ -2735,7 +2732,7 @@ or
tmux kill-session -t foo tmux kill-session -t foo
``` ```
scroll: scroll:
(screeen) (screen)
Hit your screen prefix combination (C-a / control+A), then hit Escape. Hit your screen prefix combination (C-a / control+A), then hit Escape.
Move up/down with the arrow keys (↑ and ↓). Move up/down with the arrow keys (↑ and ↓).
@ -2828,7 +2825,7 @@ tree
```bash ```bash
#1. install virtualenv. #1. install virtualenv.
sudo apt-get install virtualenv sudo apt-get install virtualenv
#2. Creat a directory (name it .venv or whatever name your want) for your new shiny isolated environment. #2. Create a directory (name it .venv or whatever name your want) for your new shiny isolated environment.
virtualenv .venv virtualenv .venv
#3. source virtual bin #3. source virtual bin
source .venv/bin/activate source .venv/bin/activate