Update README.md

README.md

@@ -24,145 +24,196 @@ extract text bewteen words (e.g. w1,w2)
     grep -o -P '(?<=w1).*(?=w2)'
 
 
->grep lines without word (e.g. bbo)
+grep lines without word (e.g. bbo)
-     grep -v bbo
+     
+    grep -v bbo
+
+grep and count (e.g. bbo)
     
->grep and count (e.g. bbo)
     grep -c bbo filename
 
->insensitive grep (e.g. bbo/BBO/Bbo)
+insensitive grep (e.g. bbo/BBO/Bbo)
+    
     grep -i "bbo" filename 
 
->count occurrence (e.g. three times a line count three times)
+count occurrence (e.g. three times a line count three times)
+    
     grep -o bbo filename 
 
->COLOR the match (e.g. bbo)!
+COLOR the match (e.g. bbo)!
+    
     grep --color bbo filename 
 
->grep search all files in a directory(e.g. bbo)
+grep search all files in a directory(e.g. bbo)
-    grep -R bbo /path/to/directory or
+    
+    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)
+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 OR (e.g. A or B or C or D)
+    
     grep 'A\|B\|C\|D' 
 
->grep AND (e.g. A and B)
+grep AND (e.g. A and B)
+    
     grep 'A.*B' 
 
->grep all content of a fileA from fileB
+grep all content of a fileA from fileB
+    
     grep -f fileA fileB 
 
->grep a tab
+grep a tab
-    grep     '\t' 
+    
+    grep $'\t' 
 
 ##Sed
 [[back to top](#handy-bash-oneliner-commands-for-tsv-file-editing)]
 
->remove lines with word (e.g. bbo)
+remove lines with word (e.g. bbo)
+    
     sed "/bbo/d" filename
 
->edit infile (edit and save)
+edit infile (edit and save)
+    
     sed -i "/bbo/d" filename
 
->when using variable (e.g.     i), use double quotes " "
+when using variable (e.g. $i), use double quotes " "
-e.g. add >    i to the first line (to make a FASTA file)
+e.g. add >$i to the first line (to make a FASTA file)
-    sed "1i >    i"  
+    
+    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
+delete empty lines
-    sed '/^\s*    /d' or
-    sed 's/^    /d' 
     
->delete last line
+    sed '/^\s*$/d' 
-    sed '    d' 
+    
+or
+   
+    sed 's/^$/d' 
+
+delete last line
+   
+    sed '$d' 
+
+add \n every nth character (e.g. every 4th character)
     
->add \n every nth character (e.g. every 4th character)
     sed 's/.\{4\}/&\n/g' 
 
->substitution (e.g. replace A by B)
+substitution (e.g. replace A by B)
+    
     sed 's/A/B/g' filename 
 
->select lines start with string (e.g. bbo)
+select lines start with string (e.g. bbo)
+    
     sed -n '/^@S/p' 
 
->delete lines with string (e.g. bbo)
+delete lines with string (e.g. bbo)
+    
     sed '/bbo/d' filename 
 
->print every nth lines
+print every nth lines
+    
     sed -n '0~3p' filename
 //catch 0: start; 3: step
 
->print every odd # lines
+print every odd # lines
+    
     sed -n '1~2p' 
 
->print every third line including the first line
+print every third line including the first line
+    
     sed -n '1p;0~3p' 
 
->remove leading whitespace and tabs
+remove leading whitespace and tabs
+    
     sed -e 's/^[ \t]*//'
 //notice a whitespace before '\t'!!
 
->remove only leading whitespace
+remove only leading whitespace
+    
     sed 's/ *//'
 //notice a whitespace before '*'!!
 
->remove ending commas
+remove ending commas
-    sed 's/,    //g' 
     
->add a column to the end
+    sed 's/,$//g' 
-    sed "s/    /\t    i/"
+
-//    i is the valuable you want to add
+add a column to the end
+    
+    sed "s/$/\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
+    for i in $(ls);do sed -i "s/$/\t$i/" $i;done
-    sed ':a;N;    !ba;s/\n//g'
+
+remove newline\ nextline
+    
+    sed ':a;N;$!ba;s/\n//g'
 
 
 #Awk
->set tab as field separator
+[[back to top](#handy-bash-oneliner-commands-for-tsv-file-editing)]
-    awk -F     '\t' 
+
+set tab as field separator
+    
+    awk -F $'\t'  
+
+output as tab separated (also as field separator)
    
->output as tab separated (also as field separator)
     awk -v OFS='\t' 
 
->pass variable
+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
+    a=bbo;b=obb;
-    awk '{print length (    0);}' filename 
+    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
   
->find number of columns
     awk '{print NF}' 
 
->reverse column order
+reverse column order
-    awk '{print     2,     1}' 
     
->check if there is a comma in a column (e.g. column     1)
+    awk '{print $2, $1}' 
-    awk '    1~/,/ {print}' 
 
->split and do for loop
+check if there is a comma in a column (e.g. column $1)
-    awk '{split(    2, a,",");for (i in a) print     1"\t"a[i]} filename 
+    
+    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)
     
->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)
+add string to the beginning of a column (e.g add "chr" to column $3)
-    awk 'BEGIN{OFS="\t"}    3="chr"    3' 
+    
+    awk 'BEGIN{OFS="\t"}$3="chr"$3' 
+
+remove lines with string (e.g. bbo)
     
->remove lines with string (e.g. bbo)
     awk '!/bbo/' file 
 
->column subtraction
+column subtraction
-    cat file| awk -F '\t' 'BEGIN {SUM=0}{SUM+=    3-    2}END{print SUM}'
     
->usage and meaning of NR and FNR
+    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
@@ -171,13 +222,15 @@ c
 fileB:
 d
 e
-    awk 'print FILENAME, NR,FNR,    0}' fileA fileB fileA    1    1    a
+    
+    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
+and gate
 e.g.
 fileA:
 1    0
@@ -189,124 +242,164 @@ fileB:
 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
+    
+    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)
+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 '{while (match($0, /[0-9]+\[0-9]+/)){
-    awk '{printf("%s\t%s\n",NR,    0)}'
+    \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
+[[back to top](#handy-bash-oneliner-commands-for-tsv-file-editing)]
+set tab as delimiter (default:space)
 
-#Xargs
->set tab as delimiter (default:space)
     xargs -d\t
 
->display 3 items per line
+display 3 items per line
+
     echo 1 2 3 4 5 6| xargs -n 3
 //1 2 3
   4 5 6
 
->prompt before execution
+prompt before execution
+
     echo a b c |xargs -p -n 3
 
->print command along with output
+print command along with output
+
     xargs -t abcd
 ///bin/echo abcd
 //abcd
 
->with find and rm
+with find and rm
+
     find . -name "*.html"|xargs rm -rf
 
->delete fiels with whitespace in filename (e.g. "hello 2001")
+delete fiels with whitespace in filename (e.g. "hello 2001")
+
     find . -name "*.c" -print0|xargs -0 rm -rf
 
->show limits
+show limits
+
     xargs --show-limits
 
->move files to folder
+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)
+move first 100th files to a directory (e.g. d1)
+
     ls |head -100|xargs -I {} mv {} d1
 
->parallel
+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
+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
+with sed
+
     ls |xargs -n1 -I file sed -i '/^Pos/d' filename
 
->add the file name to the first line of file
+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
+count all files
+
     ls |xargs -n1 wc -l
 
->to filter txt to a single line
+to filter txt to a single line
+
     ls -l| xargs
 
->count files within directories
+count files within directories
-    echo mso{1..8}|xargs -n1 bash -c 'echo -n "    1:"; ls -la "    1"| grep -w 74 |wc -l' --
+
+    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)
+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
+count lines in all file, also count total lines
+
     ls|xargs wc -l
 
 
 
-#Find 
+##Find 
->list all sub directory/file in the current directory
+[[back to top](#handy-bash-oneliner-commands-for-tsv-file-editing)]
+list all sub directory/file in the current directory
+    
     find .
 
->list all files under the current directory
+list all files under the current directory
+    
     find . -type f
 
->list all directories under the current directory
+list all directories under the current directory
+    
     find . -type d
 
->edit all files under current directory (e.g. replace 'www' with 'ww')
+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
+if no subdirectory
+    
     replace "www" "w" -- *
 //a space before *
 
->find and output only filename (e.g. "mso")
+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 and delete file with size less than (e.g. 74 byte)
+    
     find . -name "*.mso" -size -74c -delete
 //M for MB, etc
 
 
-#Others
+##Others
->remove newline / nextline
+[[back to top](#handy-bash-oneliner-commands-for-tsv-file-editing)]
+remove newline / nextline
+    
     tr --delete '\n' <input.txt >output.txt
 
->replace newline
+replace newline
+     
      tr '\n' ' ' <filename
 
->compare files (e.g. fileA, fileB)
+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
 
@@ -316,154 +409,203 @@ or
     nl -nrz fileA
 //add leading zeros
 
->combine/ paste two files (e.g. fileA, fileB)
+combine/ paste two files (e.g. fileA, fileB)
+    
     paste fileA fileB
 //default tab seperated
 
->reverse string
+reverse string
+    
     echo 12345| rev
 
->read .gz file without extracting
+read .gz file without extracting
+    
     zmore filename
+
 or
+    
     zless filename
 
->run in background, output error file
+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
+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
+.xls to csv
+    
     xls2csv filename
 
->append to file (e.g. hihi)
+append to file (e.g. hihi)
+    
     echo 'hihi' >>filename
 
->make BEEP found
+make BEEP found
-    speaker-test -t sine -f 1000 -l1
+    
->set beep duration
+    speaker-test -t sine -f 1000 -l1
-    (speaker-test -t sine -f 1000) & pid=    !;sleep 0.1s;kill -9     pid
+set beep duration
+    
+    (speaker-test -t sine -f 1000) & pid=$!;sleep 0.1s;kill -9 $pid
+
+history edit/ delete
     
->history edit/ delete
     ~/.bash_history
+
 or
+
     history -d [line_number]
 
->get last history/record filename
+get last history/record filename
-    head !    
+    
+    head !$
+
+clean screen
     
->clean screen
     clear
+
 or
+
     Ctrl+l
 
->send data to last edited file
+send data to last edited file
-    cat /directory/to/file
+    
-    echo 100>!    
+    cat /directory/to/file
+    echo 100>!$
+
+run history number (e.g. 53)
     
->run history number (e.g. 53)
     !53
 
->run last command
+run last command
+    
     !!
 
->run last command that began with (e.g. cat filename)
+run last command that began with (e.g. cat filename)
+    
     !cat
+
 or
+
     !c
 //run cat filename again
 
->extract .xf
+extract .xf
-1.     unxz filename.tar.xz
+    
-2.     tar -xf filename.tar
+    1.unxz filename.tar.xz
+    2.tar -xf filename.tar
+
+install python package
     
->install python package
     pip install packagename
 
->random order (lucky draw)
+random order (lucky draw)
-    for i in a b c d e; do echo     i; done| shuf
     
->echo a random number
+    for i in a b c d e; do echo $i; done| shuf
-    echo     RANDOM
+
+echo a random number
+    
+    echo $RANDOM
+
+Download file if necessary
     
->Download file if necessary
     data=file.txt
-url=http://www.example.com/    data
+    url=http://www.example.com/$data
-if [! -s     data];then
+    if [! -s $data];then
-    echo "downloading test data..."
+        echo "downloading test data..."
-    wget     url
+        wget $url
-fi
+    fi
+
+wget to a filename (when a long name)
     
->wget to a filename (when a long name)
     wget -O filename "http://example.com"
 
->wget files to a folder
+wget files to a folder
+
     wget -P /path/to/directory "http://example.com"
 
->delete current bash command
+delete current bash command
+    
     Ctrl+U
+
 or
+
     Ctrl+C
+
 or
+
     Alt+Shift+#
 //to make it to history
 
->add things to history (e.g. "addmetohistory")
+add things to history (e.g. "addmetohistory")
+    
     #addmetodistory
 //just add a "#" before~~
 
->sleep awhile or wait for a moment or schedule a job
+sleep awhile or wait for a moment or schedule a job
+    
     sleep 5;echo hi
 
->count the time for executing a command
+count the time for executing a command
+    
     time echo hi
 
->backup with rsync
+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!
+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)
+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)
+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
+extract to a path
+    
     tar xvf -C /path/to/directory filename.gz
 
->use backslash "\" to break long command
+use backslash "\" to break long command
-    cd tmp/a/b/c \
-> || \
->mkdir -p tmp/a/b/c
     
->get pwd
+    cd tmp/a/b/c \
-    VAR=    PWD; cd ~; tar xvf -C     VAR file.tar
+    > || \
+    >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/)
+list file type of file (e.g. /tmp/)
     file /tmp/
 //tmp/: directory
 
->bash script
+bash script
-#!/bin/bash
+    #!/bin/bash
-file=    {1#*.}
+    file=${1#*.}
 //remove string before a "."
-file=    {1%.*}
+    file=${1%.*}
 //remove string after a "."