# What is happening here

**URL:** <https://www.ruby-forum.com/t/what-is-happening-here/165034>\
**Category:** Ruby\
**Created:** [April 8, 2009, 2:01pm UTC](https://www.ruby-forum.com/t/what-is-happening-here/165034 "2009-04-08T14:01:38Z")\
**Posts on this page:** 7\
**Page:** 1

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**Author:** ![georgeuoa](https://www.ruby-forum.com/letter_avatar_proxy/v4/letter/g/7ab992/32.png) [@georgeuoa](https://www.ruby-forum.com/u/georgeuoa)\
**Post date:** [April 8, 2009, 2:01pm UTC](https://www.ruby-forum.com/t/what-is-happening-here/165034/1 "2009-04-08T14:01:38Z")

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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?

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<div class="post-metadata">

**Author:** ![georgeuoa](https://www.ruby-forum.com/letter_avatar_proxy/v4/letter/g/7ab992/32.png) [@georgeuoa](https://www.ruby-forum.com/u/georgeuoa)\
**Post date:** [April 8, 2009, 2:32pm UTC](https://www.ruby-forum.com/t/what-is-happening-here/165034/2 "2009-04-08T14:32:26Z")

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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

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<div class="post-metadata">

**Author:** ![georgeuoa](https://www.ruby-forum.com/letter_avatar_proxy/v4/letter/g/7ab992/32.png) [@georgeuoa](https://www.ruby-forum.com/u/georgeuoa)\
**Post date:** [April 8, 2009, 2:57pm UTC](https://www.ruby-forum.com/t/what-is-happening-here/165034/3 "2009-04-08T14:57:17Z")

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> 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.

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<div class="post-metadata">

**Author:** ![georgeuoa](https://www.ruby-forum.com/letter_avatar_proxy/v4/letter/g/7ab992/32.png) [@georgeuoa](https://www.ruby-forum.com/u/georgeuoa)\
**Post date:** [April 8, 2009, 3:32pm UTC](https://www.ruby-forum.com/t/what-is-happening-here/165034/4 "2009-04-08T15:32:50Z")

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Quoting George G. [removed\_email\_address@domain.invalid](mailto:removed_email_address@domain.invalid):

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

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

WBR, Peter Z.

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<div class="post-metadata">

**Author:** ![georgeuoa](https://www.ruby-forum.com/letter_avatar_proxy/v4/letter/g/7ab992/32.png) [@georgeuoa](https://www.ruby-forum.com/u/georgeuoa)\
**Post date:** [April 9, 2009, 9:27am UTC](https://www.ruby-forum.com/t/what-is-happening-here/165034/5 "2009-04-09T09:27:41Z")

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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.:

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<div class="post-metadata">

**Author:** ![georgeuoa](https://www.ruby-forum.com/letter_avatar_proxy/v4/letter/g/7ab992/32.png) [@georgeuoa](https://www.ruby-forum.com/u/georgeuoa)\
**Post date:** [April 9, 2009, 10:33am UTC](https://www.ruby-forum.com/t/what-is-happening-here/165034/6 "2009-04-09T10:33:44Z")

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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

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<div class="post-metadata">

**Author:** ![georgeuoa](https://www.ruby-forum.com/letter_avatar_proxy/v4/letter/g/7ab992/32.png) [@georgeuoa](https://www.ruby-forum.com/u/georgeuoa)\
**Post date:** [April 8, 2009, 3:25pm UTC](https://www.ruby-forum.com/t/what-is-happening-here/165034/7 "2009-04-08T15:25:48Z")

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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.: