set $wsep= " "   
  
# Read file 1.   
  
var str data1 ; cat "FILE1" > $data1   
  
# Read lines in file1 one by one.   
  
while ($data1 <> "")   
  
do   
  
    # Get the next line.   
  
    var str line1 ; lex "1" $data1 > $line1   
  
    # $line1 is "1154 10 + AAD6"   
  
    # Get columns 1, 2 and 3 in $line1   
  
    var str col1, col2, col3 ; wex -p "1" $line1 > $col1 ; wex -p "2" $line1 > $col2 ; wex -p "3" $line1 > $col3   
  
    # $col1 is "1154", $col2 is "10", $col3 is "+".   
  
    # Read file 2.   
  
    var str data2 ; cat "FILE2" > $data2   
  
    # Strip off everything up to $col1 (which has 1154) and the newline.   
  
    stex ("^"+col1+"\n^]") $data2 > null # We don't want to see the stripped off portion, thus > null.   
  
    # $data2 now begins with "ATCTCACTCGTAATTCTACATAATTTT...".   
  
    # Strip off everything beginning with the 10th ($col2) chars.   
  
    stex ("["+col2) $data2 > null # Again, we don't want to see the removed portion.   
  
    # $data2 now is "ATCTCACTC".   
  
    # We want to collect the last 8 chars. That means we want to remove the first (10-2) chars.   
  
    # Remember $col2 is "10".   
  
    var int chars ; set $chars = makeint(str($col2))- 8 - 1   
  
    # $chars is now 1.   
  
    # Extract starting at 1st char. This time, print the output to screen.   
  
    stex ("["+makestr(int($chars))) $data2   
  
done

   script sequence.txt

 C:\biterScripting\biterScripting.exe sequence.txt > output.txt