It seems like you’re using the ** operator wrong. You should use Ruby’s
Math.exp instead (which is the direct equivalent to Perl’s exp).
-Matthias
Thank you Mat
i have changed that. here is the full script in ruby:
Pn = 0.25 #probabilty of any nuclotide
match = 10
mismatch = -10
expected_score = match * 0.25 + mismatch * 0.75
if match <=0 or expected_score >= 0
puts “illegal scores”
quit
end
#calculate lambda
#initial estimates
lambda = 1
high = 2
low = 0
while (high - low > 0.001) do
#calculate the sum of all normalized scores
sum = Pn * Pn * Math.exp(lambda * match) * 4 + Pn * Pn *
Math.exp(lambda * mismatch) * 12
#refine guess at lambda
if sum > 1
high = lambda
lambda = (lambda + low)/2
else
low = lambda
lambda = (lambda+high)/2
end
end
#compute target frequencies and H
target_id = Pn * Pn * Math.exp(lambda * match) * 4
h = lambda * match * target_id + lambda * mismatch * (1 - target_id)
puts “expected_score #{expected_score}\n”
puts “lambda: #{lambda} nats, #{lambda/Math.log(2)} bits”
puts “H: #{h} nats , #{h/Math.log(2)} bits”
puts “%ID: #{target_id * 100}”
and the original perl script is here:
#!/usr/bin/perl -w use strict;
use constant Pn => 0.25; # probability of any nucleotide
die “usage: $0 \n” unless @ARGV == 2;
my ($match, $mismatch) = @ARGV;
my $expected_score = $match * 0.25 + $mismatch * 0.75;
die “illegal scores\n” if $match <= 0 or $expected_score >= 0;
calculate lambda
my ($lambda, $high, $low) = (1, 2, 0); # initial estimates
while ($high - $low > 0.001) { # precision
# calculate the sum of all normalized scores
my $sum = Pn * Pn * exp($lambda * $match) * 4
+ Pn * Pn * exp($lambda * $mismatch) * 12;
# refine guess at lambda
if ($sum > 1) {
$high = $lambda;
$lambda = ($lambda + $low)/2;
}
else {
$low = $lambda;
$lambda = ($lambda + $high)/2;
}
}
compute target frequency and H
my $targetID = Pn * Pn * exp($lambda * $match) * 4;
my $H = $lambda * $match * $targetID
+ $lambda * $mismatch * (1 -$targetID);
output
print “expscore: $expected_score\n”;
print “lambda: $lambda nats (”, $lambda/log(2), " bits)\n";
print “H: $H nats (”, $H/log(2), " bits)\n";
print "%ID: ", $targetID * 100, “\n”;
The ruby version seems to get into an infinite loop. while the perl
version executes nicely and with the expected results.