Shell_Programming.md

Shell Programming

 

Step 1: Assigning Variable

v=`ls | grep -E '*.fa$|*.fasta$'`          # using ` `
v=$(ls | grep -E '*.fa$|*.fasta$')         # using $( )

echo $v

Note: There will be no space before and after equal sign.

   

Step 2: Conditional Operation (if-else)

• Step 1: Check Numbers

  if [ 2 -lt 3 ]; then # 2 < 3
      echo 'action, if works.'
  else
      echo 'action, else works.'
  fi

  Note-1: We can't use [2 -lt 3]; use proper space.

  Note-2: Documentation.

   

Step 3: Iteration (Loop)

• Step 1: Simple Print Number

  for i in {1..9..2}; do
      echo $i
  done
  
  # Output (Like): 1, 3, 5, 7, 9

• Step 2: Simple Print (Itemized)

  for i in 1 9 2; do
      echo $i
  done
  
  # Output (Like): 1, 9, 2

• Step 3: Show file name one-by-one

  v=`ls | grep -E '*.fa$|*.fasta$'`
  
  for i in $v; do
      echo $i
  done

• Step 4: Check whether it is file or directory

  v=`ls`
  
  for i in $v; do
      if [ -d $i ]; then
          echo $i '->' 'is a directory.'
      else
          echo $i '->' 'is a file.'
      fi
  done

   

Step 3: Array

• Step 1: Array indexing

  v=(`ls | egrep '*.fa$|*.fasta$'`)        # Convert into array 
  
  echo ${v[0]}                             # First-index of array
  echo ${v[1]}                             # Second-index of array
  echo ${v[2]}                             # Third-index of array
  echo ${v[3]}                             # Fourth-index of array
  echo ${v[4]}                             # Fifth-index of array
  
  echo ${#v[*]}                            # length of the array; alternatively ${#v[@]} 

• Step 2: Array with for-index-loop

  v=(`ls | egrep '*.fa$|*.fasta$'`)           # Convert into array
  
  for (( i = 0; i < ${#v[*]}; i++ )); do      # length of array is ${#v[*]} or ${#v[@]} 
      echo ${v[$i]}                           # Access each element of the array
  done

• Step 3: Array with for-each-loop

  v=(`ls | egrep '*.fa$|*.fasta$'`)
  
  for i in ${v[*]}; do
      echo $i
  done

   

Note: The step doesn't mean you have to follow one by one.