Use of uninitialized value

[madM]

Hi people! If i run this code i get this error:"Use of uninitialized value in division (/) at aprende2.pl line 64." does anybody knows how to solve it?

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]);
        }
    }
            for (my $i=0; $i<20; $i++){
                $mutrate += $frequency[0][$i]*(1-$PAM1[$i][$i]);
            }
            
    
    
    
    print " iteration: $iter, k: $k, MutationRate:$mutrate\n";
    
}

[farang]

I get those warnings (with use warnings in effect). The problem comes from this loop.

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;
        }
    }
}

When a matrix element equals zero, that value of @lnPAM1 remains undefined, and that undefined value is being used at line 64.

            $lnPAM1[$i][$j]= ($lnPAM1[$i][$j]) /($mutrate*100);

For instance, $lnPAM1[0][17] and $lnPAM1[0][18] are undef. To avoid the warnings, you'll need to either assign some value to all of them or exclude matrix elements which are undef from executing line 64.

[frozenwithjoy]

Assuming line 64 is $lnPAM1[$i][$j]= ($lnPAM1[$i][$j]) /($mutrate*100);, you could try troubleshooting with something like this on the line before:

say "$lnPAM1[$i][$j]:$i:$j";

When I do this I see something like this snippet:

-3.91202300542815:3:7
-3.50655789731998:3:8
:3:9
:3:10
:3:11
:3:12
:3:13
:3:14
:3:15
:3:16
:3:17
:3:18
:3:19
-4.60517018598809:4:0
:4:1
:4:2
:4:3

Taking a look at where the matrix is built, it seems that the problem stems from your use of next in:

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;
        }
    }
}

By using next, you don't use all 20 iterations of i or j when building the matrix, but you do later on. You could look to see the dimensions of the matrix before iterating through its dimensions.

[BillKSmith]

Is there a reason you cannot use BrowserUK's suggestion from your previous post? If you can assume that the zero is just the roundoff of a small number, replace the zero with a any small number before you take the log. If you believe that the zero is exact and that its log has no meaning, use my suggestion. Store HUGE_VAL as the value of the log. It will fail if you try to use it, but you will know for sure where it came from.

[5mi11er]

I downloaded and ran it just fine. Perhaps you didn't post the version of code that you thought you did?

-Scott

[madM]

Thats strange... Im still getting the same error.. are you using warning and strict?