Perl Exercise #2

Read a DNA sequence from a text file
Calculate the %GC content

If you add the line Use strict to your program, it will require you to initialize all variables with "My" names. That is too much hassle for this exercise, so we will not bother with that unless you want to.

Write the output to the screen and to a file use append so that the file will grow as you run this program on additional sequences

HINTS:

• Read the whole file into an array in one step rather than line by line
  

   @DNA = <FILE>; 
  

• Use the join function to combine all the lines in the array into a single string
  

   $DNA = join('', @DNA);
  

  
  
• Use the substr function in a loop to grab one letter at a time from the string
  

   $base = substr($DNA, $count, 1); 
  

  
  
  
• Use the eq function to test if the letter is A C T or G - or not one of those!
  
  
• What about upper and lower case letters?
  
  
• Keep a ruunning total for each base - then at the end, divide ($G+$C)*100 by ($G+$C+$A+$T)
  
  

What about non-DNA characters in the file?
- carriage returns and blank spaces
- N's or X's or unexpected letters

Your program would be much more useful if it asked for a filename of the DNA sequence to be entered from the keyboard, rather than requiring you to edit the Perl code each time you want to run it on a new sequence.

If you try to read a file from a name that is typed in at the keyboard, what if there is no such file?