subroutine problem

Anonymous Monk has asked for the wisdom of the Perl Monks concerning the following question:

Hi monks, My problem is that given a DNA sequence is am trying to find all the pairs in it e.g. ATACG = AT TA AC CG. I have written a sub-routine that handles this fine. I am trying to extend the sub-routine so it calculates the frequency of each pair and sorts the pairs accordingly. However, what I have written makes no change to the output. Please could you try to point out my mistakes?! Any help is massively appreciated.

# snippet

@pairs = get_nn_pairs (@segment1);




sub get_nn_pairs    {


          (@segment1) = @_;
          my $base;
          my $pair;
          my @pairs;
          my $i;
          my $nn_pair;



          #  find and print all nn pairs form the sequence.



          foreach $i (1..$#segment1)      {


               $base = $segment1[$i-1];
               $pair = $segment1[$i];
               @pairs = "$segment1[$i-1]$segment1[$i]\n";


# only seems to know the value of @pairs from inside foreach loop


        # problems start here.

        @pairs = split ('', $nn_pair);

         my %freq;

         foreach  $nn_pair (@pairs)    {

                 {$freq{$_}++}

         }

  my @sorted_array = sort { $freq{$b} <=> $freq{$a} } keys %freq;

         print @sorted_array;

      }

   }
[download]

Comment on subroutine problem Download Code

Replies are listed 'Best First'.
Re: subroutine problem by Paladin (Vicar) on Feb 26, 2003 at 16:46 UTC
The indentation in your code makes it a bit difficult to see what is in your foreach loops and what isn't. In addition to the problems with `@pairs` that jasonk and meetraz pointed out, there are some other things that don't make sense with the code pasted. You declare and assign to `$base` and `$pair` but never use them. In your last `foreach` you have `$nn_pair` as the loop variable, but use `$_` inside the loop. At the top you say `@pairs = get_nn_pairs (@segment1);` but you are printing `@sorted_array` at the end of the sub, not returning the array. You may want to try something like the code below: `sub get_nn_pairs { my @segment1 = @_; my @pairs; # find and print all nn pairs form the sequence. foreach my $i (1 .. $#segment1) { push @pairs, "$segment1[$i-1]$segment1[$i]"; } my %freq; foreach my $nn_pair (@pairs) { $freq{$nn_pair}++; } my @sorted_array = sort { $freq{$b} <=> $freq{$a} } keys %freq; return @sorted_array; } my @ordered_pairs = get_nn_pairs(@input);` [download]	[reply] [d/l] [select]
Re: subroutine problem by jasonk (Parson) on Feb 26, 2003 at 16:28 UTC
You have several problems with your use of the @pairs array, first you are assigning to it using `@pairs = "$segment1[$i-1]$segment1[$i]\n";`, which ensures that the array will never contain more than one entry, you probably want `push(@pairs, $segment1[$i-1].$segment1[$i])` instead. Immediately after that assignment however, you are assigning it again with `@pairs = split('', $nn_pair)`, so the content from the previous assignment is useless because you just overwrote it with whatever was split from $nn_pair (which you never assigned, and thus @pairs is always empty after this line). Perhaps your first assignment to @pairs should have been assigning to $nn_pair instead?. (`use strict;` will help you find these kinds of problems)	[reply] [d/l] [select]
Re: subroutine problem by meetraz (Hermit) on Feb 26, 2003 at 16:28 UTC
What is the value of @segment1 ? And why are you assigning a string to an array in this line: `@pairs = "$segment1[$i-1]$segment1[$i]\n";` You probably mean to do: `$nn_pair = $segment1[$i-1] . $segment1[$i] . "\n";`	[reply] [d/l] [select]