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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 "."
-
-
-
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-=-=-=-=-=-A lot more coming!! =-=-=-=-=-=-=-=-=-=waitwait-=-=-=-=-=-=-=-=-=-