manipulating hashes

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

Hi all, I have some code that I can't get working. The code essentially sorts through an array and counts the occurrences of a particular pattern. The frequency of occurrences of each pattern are then inputted into a hash with the pattern as its key. Here is the code:

The arrays contain data similar to this:
@truncated_sequences = qw(JFADLKGJLFLGJGAFDJ DSJLJFLDJSLF...E.T.C);
@triamino_combo = qw(AAA AAB AAC AAD.......e.t.c);

foreach $prot_string (@truncated_sequences) {
    foreach $tri_seq (@triamino_combo) {
        while ($prot_string =~ /$tri_seq/g) {
            $tri_freq{$tri_seq}++;
            }
    }
}
[download]

This works fine and gets it right, but I also want the patterns that do not occur to be entered into the hash with a value of 0. I've tried to add the following code but it seems to mess up the counts of the matched patterns:

foreach $prot_string (@truncated_sequences) {
    foreach $tri_seq (@triamino_combo) {
        if ($prot_string =~ /$tri_seq/g) {
            $tri_freq{$tri_seq}++;
            }
        else {
            $tri_freq{$tri_seq} = "0";
            }
    }
}
[download]

Any help would be appreciated, thanks

Comment on manipulating hashes Select or Download Code

Replies are listed 'Best First'.
Re: manipulating hashes by thelenm (Vicar) on Nov 19, 2002 at 19:14 UTC
The counts get messed up because you changed the while loop to an if statement... to get 0 for the unseen combinations, just assign 0 before the while loop, like this: `foreach $prot_string (@truncated_sequences) { foreach $tri_seq (@triamino_combo) { $tri_freq{$tri_seq} = 0; while ($prot_string =~ /$tri_seq/g) { $tri_freq{$tri_seq}++; } } }` [download] -- Mike `-- just,my${.02}`	[reply] [d/l]
Re: Re: manipulating hashes by insensate (Hermit) on Nov 19, 2002 at 19:23 UTC
Then you're starting back at 0 for each $prot_string... I'm not sure that's what you want...You can also use `index()` `foreach $prot_string (@truncated_sequences) { foreach $tri_seq (@triamino_combo) { $i=-1; while(($i=index($prot_string,$tri_seq,$i)) > -1){ $tri_freq{$tri_seq}++; $i+=3; } $tri_freq{$tri_seq}='0' unless defined $tri_freq{$tri_seq}; } }` [download]	[reply] [d/l] [select]
Re: manipulating hashes by Thelonius (Priest) on Nov 19, 2002 at 19:31 UTC
`The arrays contain data similar to this: @truncated_sequences = qw(JFADLKGJLFLGJGAFDJ DSJLJFLDJSLF...E.T.C); @triamino_combo = qw(AAA AAB AAC AAD.......e.t.c); $tri_freq{$_} = 0 for @triamino_combo; # <==== NOTE foreach $prot_string (@truncated_sequences) { foreach $tri_seq (@triamino_combo) { while ($prot_string =~ /$tri_seq/g) { $tri_freq{$tri_seq}++; } } }` [download]	[reply] [d/l]
Re: manipulating hashes by John M. Dlugosz (Monsignor) on Nov 19, 2002 at 19:26 UTC
And you don't have to use a string "0", you can use numeric 0.	[reply]