Two-Dimensional Arrays.

The numbers on the edges are the indexes of the array.  (Just as Henry Ford allowed his Model T customers any color of car they wanted, as long as it was black, so Perl gives us a single choice for the start of an array: 0.)

We call out an item from the array by using two numbers in brackets: the row number, then the column number. If our array is called @sequences, then in the top row, $sequences[0][0] is "A", $sequences[0][1] is also "A", $sequence[0][6] is "G", and so forth.  Moving away from the top row, $sequences[8][12] is "A", and $sequences[9][6] if "G".

As with a one-dimensional array, one of the most straightforward things we can do is to print out the contents of an array. Here's a start:

for (my $row= 0; $row < @sequences; $row = $row+1) {
    print the contents of the row
}

for (my $row= 0; $row < @sequences; $row = $row+1) {
    for (some number of $columns) {
        print $sequences[$row][$column];
    }
}

for (my $row= 0; $row < @sequences; $row = $row+1) {
    for (my $column = 0; $column < $sequence_length; $column = $column+1) {
        print $sequences[$row][$column];
    }
}

If $sequence_length is not too big, we can add the "\n" at the end of each row:

for (my $row= 0; $row < @sequences; $row = $row+1) {
    for (my $column = 0; $column < $sequence_length; $column = $column+1) {
        print $sequences[$row][$column];
    }
   print "\n";
}

SQ6. In consensus.pl, why does the calculate_consensus_sequence routine have $column in the outside for loop, and $row on the inside for loop, the opposite of the printing routine?

   for (my $column = 0; $column < $sequence_length; $column = $column+1) {
      for (my $row = 0; $row < @sequences; $row = $row+1) {
      ...
         }
      }

SQ7. Write a subroutine that will print out part of the scoring matrix. It should look something like this:

sub print_score {        
# prints out scoring matrix
# It's called by print_score(a,b,c,d)
# where a is assigned to $first_target
#       b is assigned to $last_target
#       c is assigned to $first_query
#       d is assigned to $last_query
# The table produced should look something like what's shown below
# (you don't have to print labels, just the numbers)

                #                 Query
                #        1st                     last
                # T  1st score score score  ...  score
                # a      score score score  ...  score
                # r      score score score  ...  score
                # g      score score score  ...  score
                # e       ...   ...   ...   ...   ...
                # t last score score score  ...  score

my ($first_target,$last_target,$first_query,$last_query) = @_;
   foreach $t (  CONTINUE THIS LINE
      foreach $q (  CONTINUE THIS LINE
         print  CONTINUE THIS LINE
      }
      print  CONTINUE THIS LINE
   }
}

• Not every item in the scoring table is defined. You can check this with if (defined(...)), replacing the ... with the item in the scoring matrix you want to test.
• You'll probably want the numbers to line up.  One way to do that is by using the printf command instead of print.  If you say

printf "%6d", $n;

you'll print the number $n in a column six spaces wide.
• Don't forget that you need to call the subroutine before it does anything. You call it with a statement like:
 
print_score ( PUT FOUR NUMBERS OR VARIABLES HERE, SEPARATED BY COMMAS );

sub print_score {        
my ($first_target,$last_target,$first_query,$last_query) = @_;
   foreach $t (  CONTINUE THIS LINE
      foreach $q (  CONTINUE THIS LINE
         if (defined( PUT SOMETHING HERE )) {

            printf "%6d",   CONTINUE THIS LINE
         }

      }
      print  CONTINUE THIS LINE
   }
}