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Update README.md
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README.md
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README.md
@ -117,7 +117,7 @@ grep $'\t'
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$echo "$long_str"|grep -q "$short_str"
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if [ $? -eq 0 ]; then echo 'found'; fi
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```
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//grep -q will output 0 if match found
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//grep -q will output 0 if match found
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//remember to add space between []!
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##### grep strings between a bracket()
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@ -128,7 +128,7 @@ grep -oP '\(\K[^\)]+'
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##### grep number of characters with known strings in between(e.g. AAEL000001-RA)
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```bash
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grep -o -w "\w\{10\}\-R\w\{1\}"
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```
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```
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// \w word character [0-9a-zA-Z_] \W not word character
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@ -152,12 +152,12 @@ sed "/bbo/d" filename
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sed -i "/bbo/d" filename
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```
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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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e.g. add >$i to the first line (to make a FASTA file)
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```bash
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sed "1i >$i"
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```
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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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//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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@ -270,8 +270,8 @@ sed 's/,$//g'
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```bash
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sed "s/$/\t$i/"
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```
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//$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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//$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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```bash
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for i in $(ls);do sed -i "s/$/\t$i/" $i;done
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@ -395,58 +395,48 @@ cat file| awk -F '\t' 'BEGIN {SUM=0}{SUM+=$3-$2}END{print SUM}'
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```
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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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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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```bash
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awk 'print FILENAME, NR,FNR,$0}' fileA fileB
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```
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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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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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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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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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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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```bash
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awk -v OFS='\t' 'NR=FNR{a[$1]=$2;next} NF {print $1,((a[$1]=$2)? $2:"0")}' fileA fileB
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```
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1 0
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2 1
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3 0
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4 0
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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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@ -466,16 +456,13 @@ awk '{printf("%s\t%s\n",NR,$0)}'
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```
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##### break combine column data into rows
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e.g.
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seperate
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e.g.
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seperate
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David cat,dog
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into
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David cat
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David dog
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David cat,dog
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into
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David cat
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David dog
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detail here: http://stackoverflow.com/questions/33408762/bash-turning-single-comma-separated-column-into-multi-line-string
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```bash
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@ -521,7 +508,7 @@ xargs -d\t
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echo 1 2 3 4 5 6| xargs -n 3
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```
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//1 2 3
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//1 2 3
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4 5 6
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@ -537,7 +524,7 @@ echo a b c |xargs -p -n 3
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xargs -t abcd
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```
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///bin/echo abcd
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///bin/echo abcd
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//abcd
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@ -593,7 +580,7 @@ time echo {1..5} |xargs -n1 sleep
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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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```
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//v: verbose|
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//v: verbose|
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//p: keep detail (e.g. owner)
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@ -744,23 +731,15 @@ for i in $(ls); do echo file $i;done
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```bash
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wget -r -l1 -H -t1 -nd -N -np -A mp3 -e robots=off http://example.com
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```
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//-r: recursive and download all links on page
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//-l1: only one level link
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//-H: span host, visit other hosts
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//-t1: numbers of retries
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//-nd: don't make new directories, download to here
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//-N: turn on timestamp
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//-nd: no parent
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//-A: type (seperate by ,)
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//-e robots=off: ignore the robots.txt file which stop wget from crashing the site, sorry example.com
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//-r: recursive and download all links on page
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//-l1: only one level link
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//-H: span host, visit other hosts
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//-t1: numbers of retries
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//-nd: don't make new directories, download to here
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//-N: turn on timestamp
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//-nd: no parent
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//-A: type (seperate by ,)
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//-e robots=off: ignore the robots.txt file which stop wget from crashing the site, sorry example.com
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@ -993,7 +972,7 @@ or
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##### extract .xf
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1.unxz filename.tar.xz
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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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@ -1082,7 +1061,7 @@ rsync -av --update directory directory.bak
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```bash
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mkdir -p project/{lib/ext,bin,src,doc/{html,info,pdf},demo/stat}
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```
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//-p: make parent directory
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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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@ -1294,15 +1273,11 @@ head -c 50 file
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```
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##### group/combine rows into one row
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e.g.
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AAAA
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BBBB
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CCCC
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DDDD
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e.g.
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AAAA
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BBBB
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CCCC
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DDDD
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```bash
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cat filename|paste - -
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-->
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@ -1589,7 +1564,7 @@ getent database_name
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```bash
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getent passwd
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```
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//list all user account (all local and LDAP)
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//list all user account (all local and LDAP)
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(e.g. fetch list of grop accounts)
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```bash
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@ -1735,7 +1710,7 @@ nmap -sT -O localhost
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nproc --all
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```
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##### check status of each core
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1. top
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1. top
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2. press '1'
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##### show jobs and PID
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@ -1770,10 +1745,10 @@ ssh -X user_name@ip_address
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```
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or setting through xhost
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--> Install the following for Centos:
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xorg-x11-xauth
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xorg-x11-fonts-*
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xorg-x11-utils
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--> Install the following for Centos:
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xorg-x11-xauth
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xorg-x11-fonts-*
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xorg-x11-utils
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##### kill all process of a user
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@ -1784,16 +1759,16 @@ pkill -U user_name
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-->you might have to install the following:
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apt-get install libglib2.0-bin;
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apt-get install libglib2.0-bin;
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yum install dconf dconf-editor;
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yum install dbus dbus-x11;
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yum install dconf dconf-editor;
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yum install dbus dbus-x11;
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-->Check list
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-->Check list
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```bash
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gsettings list-recursively
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```
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-->Change setting
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-->Change setting
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e.g.
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```bash
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gsettings set org.gnome.gedit.preferences.editor highlight-current-line true
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