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