for Loop

ii=(1 4 15 16 32 40 41 58 61 72 73 74 97);
for i in ${ii[@]}; do
    echo $i;
done

for i in {1..12}; do echo $i; done
for i in {1..12..2}; do echo $i; done
for i in `seq 0 12`; do echo $i; done

break, continue

The break command terminates the loop (breaks out of it), while continue causes a jump to the next iteration of the loop, skipping all the remaining commands in that particular loop cycle.

case

case word in
  pattern1) 
    list of command
    ;;
  pattern2)
    list of command
    ;;
esac

bash case

while

    while [ -e $trash_dir/$newfile ]; do
		random_suffix=$RANDOM
		newfile=${file}.${random_suffix}
	done

until

opposite to while, it does something repeatedly until the condition is ture.

If conditional

if COMMANDS ; then 
COMMANDS; 
[ elif COMMANDS; then COMMANDS ; ]... 
[ else COMMANDS; ] 
fi

http://www.thegeekstuff.com/2010/06/bash-conditional-expression/

In the above web page, example 6 explains the difference between [ and [[ (single square bracket and double square bracket). The [[ is an enhanced version of [, normally we do NOT need to use [[ unless we want to use globbing feature and etc. In contrast to [ which is a command like "test", [[ is a keyword, and [[ is only recognized in korn and bash.

http://steve-parker.org/sh/test.shtml

-e      exist file
-d      directory exist 
-eq     equal number
-ne     not equal
-gt     a greater than b
-lt     less than
-nt     newer than
-ot     older than
==      same string
!=      not same string
-z      true if string size is zero
=~      regular expression

ps: == only works in bash, run 'bash script.sh' instead of 'sh script.sh'.

if [ -e chrX.idx ]; then
  echo "index file exist!";
else 
  nohup ./segemehl.x -d chrX.fa -x chrX.idx
fi

if [ ! -d $outdir ]; then mkdir $outdir; fi

for directory:

if [ -d ./doc/ ]; then

Nested If conditionals

	if condition
	then
		if condition
		then
			.....
			..
			do this
		else
			....
			..
			do this
		fi
	else
		...
		.....
		do this
	fi

if [ condition ]
then 
        action
elif [ condition2 ]
then
        action2
.
.
.
elif [ condition3 ]
then

else
        actionx
fi

Condition and string comparison

S1='name'
S2='Name'
if [ $S1 == $S2 ];    # NOTE [with spaces] 
then
   echo "$S1 == $S2";
else
   echo "$S1 != $S2 ";
fi

if [ -e ./tmp.sh ];
then 
  echo "file exist\n";
else
  echo "no file\n";
fi

Array

mm="2 4";
dd="random normal X1 link";
for m in $mm; do
  for d in $dd; do
    echo $m.$d;
  done;
done;

or

mm=(2 4);
dd=(random normal X1 link);
for m in "${mm[@]}"; do
  for d in "${dd[@]}"; do
    echo $m.$d;
  done;
done;

• convert string to array

  str='1 2 3 a b c'
  array=($str)
  

• push array

  array=()
  for i in `seq 1 8`; do 
      array=(${array[@]} $i)
  done
  
  
  
  reference: [http://www.thegeekstuff.com/2010/06/bash-array-tutorial/ The Ultimate Bash Array Tutorial with 15 Examples]