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 <match> <mismatch>\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.