# What is happening here

i have some perl code

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;
}
}

trying to rewrite this in ruby
while (high - low > 0.001)
#calculate the sum of all normalized scores
sum = Pn * Pn **(lambda * match) * 4 + Pn * Pn **(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

Is this the right way?

i seem to get different results when i execute the ruby version.
any ideas?

George G. wrote:

sum = Pn * Pn **(lambda * match) * 4 + Pn * Pn **(lambda * mismatch) *
12

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

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.

Quoting George G. [email protected]:

``````}
else {
\$low = \$lambda;
\$lambda = (\$lambda + \$high)/2;
}
``````

}

Pn * exp(\$lambda * \$match) is Pn * (Math::E ** (lambda + match)), not
Pn ** (lambda + match).

WBR, Peter Z.

define lambda, high and low as floats, lambda = 1.0, high=2.0, low = 0.0

Am Mittwoch, den 08.04.2009, 07:57 -0500 schrieb George G.:

Fritz Heinrichmeyer wrote:

define lambda, high and low as floats, lambda = 1.0, high=2.0, low = 0.0

Thank you so much everyone for your responses, it works nicely now!

GG

in ruby lambda, high and low are integers and divide by two is also
integer arithmetic. Perl uses float for scalars by default.

Am Mittwoch, den 08.04.2009, 07:57 -0500 schrieb George G.:

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