Calculate the Hamming difference between two DNA strands.
A mutation is simply a mistake that occurs during the creation or copying of a nucleic acid, in particular DNA. Because nucleic acids are vital to cellular functions, mutations tend to cause a ripple effect throughout the cell. Although mutations are technically mistakes, a very rare mutation may equip the cell with a beneficial attribute. In fact, the macro effects of evolution are attributable by the accumulated result of beneficial microscopic mutations over many generations.
The simplest and most common type of nucleic acid mutation is a point mutation, which replaces one base with another at a single nucleotide.
By counting the number of differences between two homologous DNA strands taken from different genomes with a common ancestor, we get a measure of the minimum number of point mutations that could have occurred on the evolutionary path between the two strands.
This is called the 'Hamming distance'.
It is found by comparing two DNA strands and counting how many of the nucleotides are different from their equivalent in the other string.
GAGCCTACTAACGGGAT
CATCGTAATGACGGCCT
^ ^ ^ ^ ^ ^^
The Hamming distance between these two DNA strands is 7.
The Hamming distance is only defined for sequences of equal length. This means that based on the definition, each language could deal with getting sequences of equal length differently.
Option
is used to indicate a computation that may possibly have no useful result
(for example due to an error or invalid input).
If you are unfamiliar with Option
you may read this tutorial.
Option
is a so-called Monad which covers a "computational aspect", in this case possible absence of a value.
Proper use of Monads can result in very concise yet elegant
and readable code. Improper use can easily result in the contrary.
Watch this video to learn more.
There are a few rules of thumbs for Option
:
- If you don't need it don't use it. Instead of
def add1(x: Int): Option[Int] = Some(x + 1)
better have
def add1(x: Int): Int = x + 1
(there is Option.map
to apply such simple functions,
so you don't have to clutter them with Option
).
2. Don't "unwrap" if you don't really need to.
Often there are built-in functions for your purpose. Indicators of premature
unwrapping are isDefined/isEmpty
or pattern matching. Instead of
val x: Option[Int] = ...
if (x.isDefined) x.get + 1 else 0
// or
x match {
case Some(n) => n + 1
case None => 0
}
better have
x map (_ + 1) getOrElse 0
- Monads can be used inside a for-comprehension FTW.
This is advisable when you want to "compose" several
Option
instances. Instead of
val xo: Option[Int] = ...
val yo: Option[Int] = ...
val zo: Option[Int] = ...
xo.flatMap(x =>
yo.flatMap(y =>
zo.map(z =>
x + y + z)))
better have
for {
x <- xo
y <- yo
z <- zo
} yield x + y + z
The Scala exercises assume an SBT project scheme. The exercise solution source should be placed within the exercise directory/src/main/scala. The exercise unit tests can be found within the exercise directory/src/test/scala.
To run the tests simply run the command sbt test
in the exercise directory.
For more detailed info about the Scala track see the help page.
The Calculating Point Mutations problem at Rosalind http://rosalind.info/problems/hamm/
It's possible to submit an incomplete solution so you can see how others have completed the exercise.