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+Handy Bash 'oneliner' commands for tsv file editing
+Symbol for search:
+>> section
+>function
+$bash code
+//comment
+
+
+>> Grep
+> extract text bewteen words (e.g. w1,w2)
+$ grep -o -P '(?<=w1).*(?=w2)'
+
+>grep lines without word (e.g. bbo)
+$ grep -v bbo
+
+>grep and count (e.g. bbo)
+$grep -c bbo filename
+
+>insensitive grep (e.g. bbo/BBO/Bbo)
+$grep -i "bbo" filename 
+
+>count occurrence (e.g. three times a line count three times)
+$grep -o bbo filename 
+
+>COLOR the match (e.g. bbo)!
+$grep --color bbo filename 
+
+>grep search all files in a directory(e.g. bbo)
+$grep -R bbo /path/to/directory or
+$grep -r bbo /path/to/directory 
+
+>search all files in directory, only output file names with matches(e.g. bbo)
+$grep -Rh bbo /path/to/directory or
+$grep -rh bbo /path/to/directory 
+
+>grep OR (e.g. A or B or C or D)
+$grep 'A\|B\|C\|D' 
+
+>grep AND (e.g. A and B)
+$grep 'A.*B' 
+
+>grep all content of a fileA from fileB
+$grep -f fileA fileB 
+
+>grep a tab
+$grep $'\t' 
+
+>>Sed
+>remove lines with word (e.g. bbo)
+$sed "/bbo/d" filename
+
+>edit infile (edit and save)
+$sed -i "/bbo/d" filename
+
+>when using variable (e.g. $i), use double quotes " "
+e.g. add >$i to the first line (to make a FASTA file)
+$sed "1i >$i"  
+//notice the double quotes! in other examples, you can use a single quote, but here, no way! 
+//'1i' means insert to first line
+
+>delete empty lines
+$sed '/^\s*$/d' or
+$sed 's/^$/d' 
+
+>delete last line
+$sed '$d' 
+
+>add \n every nth character (e.g. every 4th character)
+$sed 's/.\{4\}/&\n/g' 
+
+>substitution (e.g. replace A by B)
+$sed 's/A/B/g' filename 
+
+>select lines start with string (e.g. bbo)
+$sed -n '/^@S/p' 
+
+>delete lines with string (e.g. bbo)
+$sed '/bbo/d' filename 
+
+>print every nth lines
+$sed -n '0~3p' filename
+//catch 0: start; 3: step
+
+>print every odd # lines
+$sed -n '1~2p' 
+
+>print every third line including the first line
+$sed -n '1p;0~3p' 
+
+>remove leading whitespace and tabs
+$sed -e 's/^[ \t]*//'
+//notice a whitespace before '\t'!!
+
+>remove only leading whitespace
+$sed 's/ *//'
+//notice a whitespace before '*'!!
+
+>remove ending commas
+$sed 's/,$//g' 
+
+>add a column to the end
+$sed "s/$/\t$i/"
+//$i is the valuable you want to add
+e.g. add the filename to every last column of the file
+$for i in $(ls);do sed -i "s/$/\t$i/" $i;done
+
+>remove newline\ nextline
+$sed ':a;N;$!ba;s/\n//g'
+
+
+>>Awk
+>set tab as field separator
+$awk -F $'\t' 
+
+>output as tab separated (also as field separator)
+$awk -v OFS='\t' 
+
+>pass variable
+a=bbo;b=obb;
+awk -v a="$a" -v b="$b" "$1==a && $10=b' filename 
+
+>print number of characters on each line
+$awk '{print length ($0);}' filename 
+
+>find number of columns
+$awk '{print NF}' 
+
+>reverse column order
+$awk '{print $2, $1}' 
+
+>check if there is a comma in a column (e.g. column $1)
+$awk '$1~/,/ {print}' 
+
+>split and do for loop
+$awk '{split($2, a,",");for (i in a) print $1"\t"a[i]} filename 
+
+>print all lines before nth occurence of a string (e.g stop print lines when bbo appears 7 times)
+$awk -v N=7 '{print}/bbo/&& --N<=0 {exit}'
+
+>add string to the beginning of a column (e.g add "chr" to column $3)
+$awk 'BEGIN{OFS="\t"}$3="chr"$3' 
+
+>remove lines with string (e.g. bbo)
+$awk '!/bbo/' file 
+
+>column subtraction
+$cat file| awk -F '\t' 'BEGIN {SUM=0}{SUM+=$3-$2}END{print SUM}'
+
+>usage and meaning of NR and FNR
+e.g.
+fileA:
+a
+b
+c
+fileB:
+d
+e
+$awk 'print FILENAME, NR,FNR,$0}' fileA fileB fileA    1    1    a
+fileA    2    2    b
+fileA    3    3    c
+fileB    4    1    d
+fileB    5    2    e
+
+>and gate
+e.g.
+fileA:
+1    0
+2    1
+3    1
+4    0
+fileB:
+1    0
+2    1
+3    0
+4    1
+$awk -v OFS='\t' 'NR=FNR{a[$1]=$2;next} NF {print $1,((a[$1]=$2)? $2:"0")}' fileA fileB 1    0
+2    1
+3    0
+4    0
+
+>round all numbers of file (e.g. 2 significant figure)
+$awk '{while (match($0, /[0-9]+\[0-9]+/)){
+\printf "%s%.2f", substr($0,0,RSTART-1),substr($0,RSTART,RLENGTH)
+\$0=substr($0, RSTART+RLENGTH)
+\}
+\print
+\}'
+
+>give number/index to every row
+$awk '{printf("%s\t%s\n",NR,$0)}'
+
+>>Xargs
+>set tab as delimiter (default:space)
+$xargs -d\t
+
+>display 3 items per line
+$echo 1 2 3 4 5 6| xargs -n 3
+//1 2 3
+  4 5 6
+
+>prompt before execution
+$echo a b c |xargs -p -n 3
+
+>print command along with output
+$xargs -t abcd
+///bin/echo abcd
+//abcd
+
+>with find and rm
+$find . -name "*.html"|xargs rm -rf
+
+>delete fiels with whitespace in filename (e.g. "hello 2001")
+$find . -name "*.c" -print0|xargs -0 rm -rf
+
+>show limits
+$xargs --show-limits
+
+>move files to folder
+$find . -name "*.bak" -print 0|xargs -0 -I {} mv {} ~/old
+or
+$find . -name "*.bak" -print 0|xargs -0 -I file mv file ~/old
+
+>move first 100th files to a directory (e.g. d1)
+$ls |head -100|xargs -I {} mv {} d1
+
+>parallel
+$time echo {1..5} |xargs -n 1 -P 5 sleepa lot faster than
+$time echo {1..5} |xargs -n1 sleep
+
+>copy all files from A to B
+$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)
+
+>with sed
+$ls |xargs -n1 -I file sed -i '/^Pos/d' filename
+
+>add the file name to the first line of file
+$ls |sed 's/.txt//g'|xargs -n1 -I file sed -i -e '1 i\>file\' file.txt
+
+>count all files
+$ls |xargs -n1 wc -l
+
+>to filter txt to a single line
+$ls -l| xargs
+
+>count files within directories
+$echo mso{1..8}|xargs -n1 bash -c 'echo -n "$1:"; ls -la "$1"| grep -w 74 |wc -l' --
+// "--" signals the end of options and display further option processing
+
+>download dependencies files and install (e.g. requirements.txt)
+$cat requirements.txt| xargs -n1 sudo pip install
+
+>count lines in all file, also count total lines
+$ls|xargs wc -l
+
+
+
+>>Find 
+>list all sub directory/file in the current directory
+$find .
+
+>list all files under the current directory
+$find . -type f
+
+>list all directories under the current directory
+$find . -type d
+
+>edit all files under current directory (e.g. replace 'www' with 'ww')
+$find . name '*.php' -exec sed -i 's/www/w/g' {} \;
+>if no subdirectory
+$replace "www" "w" -- *
+//a space before *
+
+>find and output only filename (e.g. "mso")
+$find mso*/ -name M* -printf "%f\n"
+
+>find and delete file with size less than (e.g. 74 byte)
+$find . -name "*.mso" -size -74c -delete
+//M for MB, etc
+
+
+>>Others
+>remove newline / nextline
+$tr --delete '\n' <input.txt >output.txt
+
+>replace newline
+$ tr '\n' ' ' <filename
+
+>compare files (e.g. fileA, fileB)
+$diff fileA fileB
+//a: added; d:delete; c:changed
+or
+$sdiff fileA fileB
+//side-to-side merge of file differences
+
+>number a file (e.g. fileA)
+$nl fileA
+or
+$nl -nrz fileA
+//add leading zeros
+
+>combine/ paste two files (e.g. fileA, fileB)
+$paste fileA fileB
+//default tab seperated
+
+>reverse string
+$echo 12345| rev
+
+>read .gz file without extracting
+$zmore filename
+or
+$zless filename
+
+>run in background, output error file
+$(command here) 2>log &
+or
+$(command here) 2>&1| tee logfile
+or
+$(command here) 2>&1 >>outfile
+//0: standard input; 1: standard output; 2: standard error
+
+>send mail
+$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
+$xls2csv filename
+
+>append to file (e.g. hihi)
+$echo 'hihi' >>filename
+
+>make BEEP found
+$speaker-test -t sine -f 1000 -l1
+>set beep duration
+$(speaker-test -t sine -f 1000) & pid=$!;sleep 0.1s;kill -9 $pid
+
+>history edit/ delete
+$~/.bash_history
+or
+$history -d [line_number]
+
+>get last history/record filename
+$head !$
+
+>clean screen
+$clear
+or
+$Ctrl+l
+
+>send data to last edited file
+$cat /directory/to/file
+$echo 100>!$
+
+>run history number (e.g. 53)
+$!53
+
+>run last command
+$!!
+
+>run last command that began with (e.g. cat filename)
+$!cat
+or
+$!c
+//run cat filename again
+
+>extract .xf
+1. $unxz filename.tar.xz
+2. $tar -xf filename.tar
+
+>install python package
+$pip install packagename
+
+>random order (lucky draw)
+$for i in a b c d e; do echo $i; done| shuf
+
+>echo a random number
+$echo $RANDOM
+
+>Download file if necessary
+$data=file.txt
+url=http://www.example.com/$data
+if [! -s $data];then
+    echo "downloading test data..."
+    wget $url
+fi
+
+>wget to a filename (when a long name)
+$wget -O filename "http://example.com"
+
+>wget files to a folder
+$wget -P /path/to/directory "http://example.com"
+
+>delete current bash command
+$Ctrl+U
+or
+$Ctrl+C
+or
+$Alt+Shift+#
+//to make it to history
+
+>add things to history (e.g. "addmetohistory")
+$#addmetodistory
+//just add a "#" before~~
+
+>sleep awhile or wait for a moment or schedule a job
+$sleep 5;echo hi
+
+>count the time for executing a command
+$time echo hi
+
+>backup with rsync
+$rsync -av filename filename.bak
+$rsync -av directory directory.bak
+$rsync -av --ignore_existing directory/ directory.bak
+$rsync -av --update directory directory.bak
+//skip files that are newer on receiver (i prefer this one!)
+
+>make all directories at one time!
+$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
+
+>run command only if another command returns zero exit status (well done)
+$cd tmp/ && tar xvf ~/a.tar
+
+>run command only if another command returns non-zero exit status (not finish)
+$cd tmp/a/b/c ||mkdir -p tmp/a/b/c
+
+>extract to a path
+$tar xvf -C /path/to/directory filename.gz
+
+>use backslash "\" to break long command
+$cd tmp/a/b/c \
+> || \
+>mkdir -p tmp/a/b/c
+
+>get pwd
+$VAR=$PWD; cd ~; tar xvf -C $VAR file.tar
+//PWD need to be capital letter
+
+>list file type of file (e.g. /tmp/)
+$file /tmp/
+//tmp/: directory
+
+>bash script
+#!/bin/bash
+file=${1#*.}
+//remove string before a "."
+file=${1%.*}
+//remove string after a "."
+
+
+
+
+
+
+
+
+=-=-=-=-=-A lot more coming!! =-=-=-=-=-=-=-=-=-=waitwait-=-=-=-=-=-=-=-=-=-