# Count the occurence of nucleobases in DNA string

Inspired by this meta question I decided to take a look at Rosalind. Their first challenge seemed easy enough:

An example of a length 21 DNA string (whose alphabet contains the symbols 'A', 'C', 'G', and 'T') is "ATGCTTCAGAAAGGTCTTACG."

Given: A DNA string s of length at most 1000 nt.

Return: Four integers (separated by spaces) counting the respective number of times that the symbols 'A', 'C', 'G', and 'T' occur in s.

Sample Dataset

AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC


Sample Output

20 12 17 21


Since I'm still on my quest to learn both regex and Ruby, I decided to go that route:

def countACGT(str)
list = [0,0,0,0]
str.scan(/A|C|G|T/) do |sub|
if sub == "A"
list[0] += 1
end
if sub == "C"
list[1] += 1
end
if sub == "G"
list[2] += 1
end
if sub == "T"
list[3] += 1
end
end
return list
end


I'm not a big fan of long if chains. Luckily, Ruby has a case statement as well:

def countACGT(str)
list = [0,0,0,0]
str.scan(/A|C|G|T/) do |sub|
puts case sub
when "A"
list[0] += 1
when "C"
list[1] += 1
when "G"
list[2] += 1
when "T"
list[3] += 1
end
end
return list
end


Both can be invoked like:

p countACGT("TCCCACTTCAGGGTCAGGGAGCTCCAAACTCTCTTTCTAGAGATGACAATCGAGAGTGAGATAAGGTGGATAGCAATCGTTATGGGATGTAAGCGCCAAGCGTTCGGGTAGCCCACGTTGCGGGCTAATCGCTAGGCTAGAACCTCTAAGCTGTACTTCTGTCAAAACGGAAAGAATCATACCGCACACCAACACTCGATGTAATGTAAGGATATCCTGTGCAGATGAGGTGCTTGGTACGCTAGATACTAGTATTACTAACACACAACATTACCGCCCAAGCGTGTCAGCCACGGACCAGATGACTCTTGCCGATTGAATACCTATCATCCTTACGGTCCGGAATCAGTATATCGCGTGCACAGTTACAGTGGTTAACTTGAGCTAGAGCAAGATAATGTGCGATCTGCGCACTCGGTGGGCTTGGATCACCCTACTTCCAATTGCCCGCGTATGATAGTTCCACCACTCACAAGTCTGTCATAGTGATTATCAAGAGTAGGCGTAGTGGGCACCCAAGAAATTAATGAATCTCACAGTCGAGTGTATCTTCGGCCATATCCCTACGGCAAATGGTCGCTCAGCTTGTCTCCGAGAGTTCGTTGGTTCAGAACCTCCGAAGGGTTGGGTGATTGTTGCGGCGCGCATGCGAGCTATGGTGGCTGTGTGTGGAGGTATTATCAGGGGAAATTTATTCCGAGTACTTGCTTGACTGCTCTTTTGTAAGCCGTTTGGGGTGCGTCCTCTGTATAGTCGTCGCCGCGAAGCCGATTCCCTCTAATCAAACACGCCAGAGGATCACTGGTCTTCTTCAAATTCCTGTATACCTCTGGCTAAATGACCCGACGGTACGAGCGTTTACTTCGAAGTG")


Yes, the dataset I had to solve was that long.

However, my interpreter suddenly feels the need to print the updated list[x] every time a new value gets assigned. This leads to a significant decrease in performance.

It almost looks like case is not the preferred way of doing this, but that's not intuitive.

I'm mainly looking for a definitive answer on which version I should stick with (and why) and general maintainability improvements. I'm perfectly aware regex may not be the optimal solution here, but I'd like to stick with it anyway.

Your code is fine and readable from a C/Java perspective. I don't think it's particularly Ruby-ic to use return statements. Just put list at the end on its own.

### Why your case is slow

You have this extra puts here:

str.scan(/A|C|G|T/) do |sub|
puts case sub
^^^^
when "A"
...


You may want to get rid of that :) That's why you interpreter prints the list every time. You told it to...

### Functionally better

But functionally, we can do way better. Ruby's enumerables have a group_by method:

def countACGT(str)
str.chars.group_by(&:chr)
end


That'll give you a hash from each key (nucleotide base) to the values in the collection (a list of each occurence of each nucleotide base). All you have to do then is map it to just give you the size:

def countACGT(str)
str.chars.group_by(&:chr).map { |k, v| [k, v.size] }
end


That'll give you, for your example, the list:

[["T", 228], ["C", 209], ["A", 214], ["G", 220]]


If you want to get it in ACGT order like your original, you can just sort it and map off the key:

def countACGT(str)
str.chars.group_by(&:chr).sort.map{|k, v| v.size}
end

• I'm feeling quite stupid about putting the puts before the case. Thanks for catching that and the rest of the advice!
– Mast
Dec 31, 2015 at 14:27

I've make small research on your question. My first idea was:

def countACGT(str)
str.chars.sort.join.scan(/A+|C+|G+|T+/).map(&:length)
end


Then I've write few another methods (Benchmark used to asses their performance). Also include method proposed by Barry.

require 'benchmark'

REP_NUM = 10_000 # number of tests runs.
PATTERN = "..." # here is string from your example.

def countACGT(str)
list = [0,0,0,0]
str.scan(/A|C|G|T/) do |sub|
# code of original method
return list
end

def countACGT_with_object(str)
str.chars.each.with_object(Hash.new(0)) do |letter, hash|
hash[letter] += 1
end.sort.map(&:last)
end

def countACGT_scan(str)
str.chars.sort.join.scan(/A+|C+|G+|T+/).map(&:length)
end

def countACGT_pack(str)
str.unpack("c*").sort.pack("c*").scan(/A+|C+|G+|T+/).map(&:length)
end

def countACGT_group_by(str)
str.chars.group_by(&:chr).sort.map{|k, v| v.size}
end

def count_unpack_group_by(str)
str.unpack("c*").group_by{|i| i}.values.sort.map(&:size)
end

Benchmark.bm do |x|
x.report('countACGT') { REP_NUM.times { countACGT(PATTERN) } }
x.report('countACGT_with_object') { REP_NUM.times { countACGT_with_object(PATTERN) } }
x.report('countACGT_scan') { REP_NUM.times { countACGT_scan(PATTERN) } }
x.report('countACGT_pack') { REP_NUM.times { countACGT_pack(PATTERN) } }
x.report('countACGT_group_by') { REP_NUM.times { countACGT_group_by(PATTERN) } }
x.report('count_unpack_group_by') { REP_NUM.times { count_unpack_group_by(PATTERN) } }
end


Results:

Method                  user    system  total   real
countACGT               8.76    0.00    8.76    8.777035
countACGT_with_object   4.73    0.00    4.73    4.745783
countACGT_scan          4.56    0.00    4.56    4.563267
countACGT_pack          3.37    0.00    3.37    3.380988
countACGT_group_by      4.93    0.00    4.93    4.941314
count_unpack_group_by   2.67    0.01    2.68    2.706674


Last method is the fastest (for now). It uses unpack and there is no additional method call in group_by block.

• Welcome to Code Review! Your post looks useful. But is it a review of the code in the question? Not really... Could you please kindly adjust your answer in a way so that looks more like a review of the code in the question? Thanks! Dec 31, 2015 at 15:26
• At some point you're right. I've not posted first part of my answer (with actual review) because Barry is few minutes ahead of me. I don't like when answers repeating each other(but with other words). And thanks to Mast, because of his question I've found some interesting use-cases of unpack/pack. Dec 31, 2015 at 16:23
• @janos, I think you're applying the rules too literally. This is fantastic post, and his rewrite of the OP is very helpful. The "review" is implicit. Sometimes over-explanation with words -- when the code speaks -- makes a post worse. Jan 2, 2016 at 2:17