2.8 KiB
Hamming
Calculate the Hamming Distance between two DNA strands.
Your body is made up of cells that contain DNA. Those cells regularly wear out and need replacing, which they achieve by dividing into daughter cells. In fact, the average human body experiences about 10 quadrillion cell divisions in a lifetime!
When cells divide, their DNA replicates too. Sometimes during this process mistakes happen and single pieces of DNA get encoded with the incorrect information. If we compare two strands of DNA and count the differences between them we can see how many mistakes occurred. This is known as the "Hamming Distance".
We read DNA using the letters C,A,G and T. Two strands might look like this:
GAGCCTACTAACGGGAT
CATCGTAATGACGGCCT
^ ^ ^ ^ ^ ^^
They have 7 differences, and therefore the Hamming Distance is 7.
The Hamming Distance is useful for lots of things in science, not just biology, so it's a nice phrase to be familiar with :)
Implementation notes
The Hamming distance is only defined for sequences of equal length, so an attempt to calculate it between sequences of different lengths should not work. The general handling of this situation (e.g., raising an exception vs returning a special value) may differ between languages.
Run the tests with:
bats hamming_test.sh
After the first test(s) pass, continue by commenting out or removing the
[[ $BATS_RUN_SKIPPED == true ]] || skip
annotations prepending other tests.
To run all tests, including the ones with skip annotations, run:
BATS_RUN_SKIPPED=true bats hamming_test.sh
Source
The Calculating Point Mutations problem at Rosalind http://rosalind.info/problems/hamm/
External utilities
Bash is a language to write "scripts" -- programs that can call
external tools, such as
sed,
awk,
date
and even programs written in other programming languages,
like Python.
This track does not restrict the usage of these utilities, and as long
as your solution is portable between systems and does not require
installation of third party applications, feel free to use them to solve
the exercise.
For an extra challenge, if you would like to have a better understanding
of the language, try to re-implement the solution in pure Bash,
without using any external tools. Note that there are some types of
problems that bash cannot solve, such as performing floating point
arithmetic and manipulating dates: for those, you must call out to an
external tool.
Submitting Incomplete Solutions
It's possible to submit an incomplete solution so you can see how others have completed the exercise.