The first reason is because this loop is never entered:

while( $mutrate - 0.01 > $DBL_EPSILON ){
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So the ends without ever executing your print statement.

The reason the loop is never entered is because this condition: $mutrate - 0.01 > $DBL_EPSILON is always false.

You are setting $DBL_EPSILON to $e = 1:

my $DBL_EPSILON = $e =1; $e /= 2 while $e /2 +1 > 1;
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Which means that unless $mutrate is greater than 1.1 when you reach the loop; you're never going to enter the loop and thus never going to print anything.

I can only guess what value you actually wanted to set $DBL_EPSILON to, so I won't try.

Also, this: if ($matrix[$i][$j] =~ /[^0.00]/){ isn't doing what you want it to either.

Hi! Thanks.. i made some corrections now and the loop is getting started but i dont get the results i expect. Iīm actually trying to translate this Darwin code: Any suggestions? Thanks a lot again!

PAM1 := MutationMatrix:
lnPAM1 := ln(MutationMatrix):
k := 1:
RateMutation := sum(Freq[i] * (1 - PAM1[i,i]), i= 1..20):
iter := 0:

# The following loop goes until the difference reach the computer's
# precision.
while abs(RateMutation - 0.01) > DBL_EPSILON do
    iter := iter + 1;
    k:= k * RateMutation * 100:
    lnPAM1 := lnPAM1 / (RateMutation * 100):
    PAM1 := exp(lnPAM1):
    RateMutation := sum(Freq[i] * (1 - PAM1[i,i]), i= 1..20);
    printf('After %d iteration(s), k=%f, RateMutation=%f
', iter, k, RateMutation);
od:
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And the outcome i expect is this:

After 1 iteration(s), k=44.530219, RateMutation=0.014324
After 2 iteration(s), k=63.785069, RateMutation=0.010027
After 3 iteration(s), k=63.959878, RateMutation=0.010000
After 4 iteration(s), k=63.960985, RateMutation=0.010000
After 5 iteration(s), k=63.960992, RateMutation=0.010000
After 6 iteration(s), k=63.960992, RateMutation=0.010000
After 7 iteration(s), k=63.960992, RateMutation=0.010000
After 8 iteration(s), k=63.960992, RateMutation=0.010000
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my @matrix =(
[0.54, 0.03, 0.03, 0.03, 0.08, 0.04, 0.05, 0.05, 0.02, 0.02, 0.03, 0.0
+4, 0.03, 0.01, 0.06, 0.11, 0.06, 0.01, 0.01,0.06],
[0.02, 0.57, 0.03, 0.01, 0.02, 0.06, 0.03, 0.01, 0.04, 0.01, 0.01, 0.1
+1, 0.02, 0.01, 0.01, 0.02, 0.02, 0.01, 0.01, 0.01],
[0.01, 0.02, 0.48, 0.06, 0.01, 0.03, 0.03, 0.03, 0.05, 0.01, 0.01, 0.0
+3, 0.01, 0.00, 0.01, 0.04, 0.03, 0.00, 0.02, 0.01],
[0.02, 0.01, 0.09, 0.57, 0.01, 0.04, 0.11, 0.02, 0.03, 0.00, 0.00, 0.0
+3, 0.01, 0.00, 0.02, 0.04, 0.02, 0.00, 0.01, 0.00],
[0.01, 0.00, 0.00, 0.00, 0.57, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.0
+0, 0.00, 0.01, 0.00, 0.01, 0.01, 0.01, 0.01, 0.01],
[0.02, 0.04, 0.03, 0.02, 0.01, 0.42, 0.05, 0.01, 0.04, 0.01, 0.01, 0.0
+5, 0.02, 0.00, 0.01, 0.02, 0.02, 0.01, 0.01, 0.01],
[0.04, 0.04, 0.05, 0.13, 0.01, 0.11, 0.52, 0.02, 0.03, 0.01, 0.01, 0.0
+7, 0.01, 0.00, 0.02, 0.04, 0.04, 0.01, 0.01, 0.01],
[0.05, 0.02, 0.05, 0.03, 0.02, 0.02, 0.02, 0.77, 0.02, 0.00, 0.00, 0.0
+2, 0.01, 0.00, 0.01, 0.04, 0.01, 0.01, 0.00, 0.01],
[0.01, 0.01, 0.02, 0.01, 0.01, 0.02, 0.01, 0.00, 0.54, 0.00, 0.00, 0.0
+1, 0.01, 0.02, 0.01, 0.01, 0.01, 0.02, 0.04, 0.00],
[0.02, 0.01, 0.01, 0.00, 0.03, 0.01, 0.01, 0.00, 0.01, 0.50, 0.10, 0.0
+1, 0.09, 0.04, 0.01, 0.01, 0.03, 0.02, 0.01, 0.18],
[0.03, 0.02, 0.01, 0.01, 0.03, 0.03, 0.01, 0.00, 0.02, 0.13, 0.60, 0.0
+2, 0.19, 0.09, 0.02, 0.02, 0.02, 0.02, 0.03, 0.08],
[0.03, 0.14, 0.06, 0.03, 0.01, 0.09, 0.06, 0.02, 0.05, 0.01, 0.01, 0.5
+0, 0.02, 0.01, 0.02, 0.04, 0.03, 0.01, 0.01, 0.01],
[0.01, 0.01, 0.00, 0.00, 0.01, 0.02, 0.00, 0.00, 0.01, 0.03, 0.05, 0.0
+1, 0.42, 0.02, 0.00, 0.01, 0.01, 0.01, 0.01, 0.02],
[0.01, 0.01, 0.00, 0.00, 0.02, 0.01, 0.00, 0.00, 0.03, 0.02, 0.04, 0.0
+0, 0.04, 0.61, 0.00, 0.01, 0.01, 0.07, 0.14, 0.01],
[0.03, 0.01, 0.01, 0.01, 0.00, 0.01, 0.01, 0.01, 0.02, 0.00, 0.01, 0.0
+1, 0.01, 0.00, 0.72, 0.03, 0.01, 0.00, 0.00, 0.01],
[0.07, 0.03, 0.06, 0.04, 0.05, 0.04, 0.03, 0.03, 0.02, 0.01, 0.01, 0.0
+4, 0.02, 0.01, 0.04, 0.43, 0.09, 0.02, 0.01, 0.01],
[0.04, 0.02, 0.04, 0.02, 0.04, 0.03, 0.03, 0.01, 0.02, 0.02, 0.02, 0.0
+3, 0.03, 0.01, 0.02, 0.09, 0.52, 0.01, 0.01, 0.04],
[0.00, 0.00, 0.00, 0.00, 0.01, 0.00, 0.00, 0.00, 0.01, 0.00, 0.00, 0.0
+0, 0.00, 0.02, 0.00, 0.00, 0.00, 0.71, 0.02, 0.00],
[0.00, 0.01, 0.01, 0.00, 0.01, 0.01, 0.00, 0.00, 0.05, 0.01, 0.01, 0.0
+1, 0.01, 0.10, 0.00, 0.01, 0.01, 0.06, 0.61, 0.01],
[0.05, 0.01, 0.01, 0.01, 0.07, 0.02, 0.02, 0.01, 0.01, 0.20, 0.07, 0.0
+1, 0.06, 0.03, 0.01, 0.02, 0.06, 0.02, 0.02, 0.51]);

my @frequency = ([0.08477395, 0.05103334, 0.03837665, 0.05740129, 0.01
+256165, 0.03471746,
0.06883297, 0.07907659, 0.02077239, 0.06813598, 0.08906677, 0.06501537
+,
0.02318017, 0.03823936, 0.04036729, 0.05668318, 0.05721648, 0.00871765
+,
0.02785317, 0.07797831]);

my $mutrate=0;
my $matrix2={};
my $e;
$e=1;$e/=2 while $e/2+1>1;

my @PAM1= @matrix;

my @lnPAM1=();
LINE: for (my $i=0; $i<20; $i++){
    for (my $j=0; $j<20; $j++){
        if ($matrix[$i][$j] > 0){
            $lnPAM1[$i][$j] = log $matrix[$i][$j];
        }else{ next LINE;
        }
    }
}


for (my $i=0; $i<20; $i++){
    $mutrate += $frequency[0][$i]*(1-$matrix[$i][$i]);
}

my $k=1;
my $iter = 0;

while (($mutrate-0.01) > $e){
    $iter++;
    $k= $k * $mutrate * 100;
    for (my $i=0; $i<20; $i++){
        for (my $j=0; $j<20; $j++){
            $lnPAM1[$i][$j] = $lnPAM1[$i][$j]/($mutrate * 100);
            $PAM1[$i][$j]=exp($lnPAM1[$i][$j]);
            $mutrate += $frequency[0][$i]*(1-$PAM1[$i][$i]);
            
        }
    }
    
    print " iteration: $iter, k: $k, MutationRate:$mutrate\n";
    
}
[download]

Where does Freq[] come from in the Darwin code?

---

With the rise and rise of 'Social' network sites: 'Computers are making people easier to use everyday'

Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.

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In the absence of evidence, opinion is indistinguishable from prejudice.

G'day madM,

In this sort of situation, you need to print out critical values at appropriate points in your code to see why things are, or are not, happening.

The only place you'll output anything (except, perhaps, for error messages) is in the print statement in the second while loop. If you're not printing anything, that suggests the while loop is not being entered. As $DBL_EPSILON is set to 1 and never changes, the while loop will only be entered if ($mutrate > 1.01).

Modifying your code to check that with:

...
print "\$mutrate = $mutrate\n";
while ($mutrate-0.01 > $DBL_EPSILON){
...
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I get this output:

$ pm_1048891_test.pl
$mutrate = 0.4451357658
[download]

That explains your current issue and, hopefully, adds a debugging aid to your toolbox.