Write a Perl script that uses cross validation to determine an appropriate 
gap open and extension penalty for Needleman-Wunsch with affine gaps. 
Start with the NW cv script that we wrote in class. Use the 
alignment_accuracy.pl script posted on the class website 
for computing alignment accuracy and your own affine gap program from assignment
1 for the alignment. To test your script use the training.txt and testing.txt 
files also on the course website. Use match cost of +5 and mismatch cost of -4. 

Select the best gap open from the set 

@go = (-16, -14, -12, -10, -8, -6, -4, -2);

and the best gap extension from the set

@ge = (-2, -1, -.5, -.1);

On the training.txt file best gap combination and accuracy are
-16, -2, and 0.462052519750455. Without affine the best gap and accuracy 
are -16 and 0.441601885024902.

## Assignment details ##

Submit your Perl script by copying it into the directory
/afs/cad/courses/bnfo/f18/bnfo/601/001/<ucid>.
For example if your ucid is abc12 then copy your Perl script into
/afs/cad/courses/bnfo/f18/bnfo/601/001/abs12.
         
Make sure your affine alignment script and the alignment accuracy scripts
are also there.

Submit a hardcopy in class on Oct 10th 2016.