From eb76c608263cf1483b62fa0741b8ab33246597a8 Mon Sep 17 00:00:00 2001 From: Danylo Negrienko Date: Wed, 26 Jun 2024 23:52:34 -0400 Subject: [PATCH] hamming --- elixir/hamming/.exercism/config.json | 33 ++++++++++++ elixir/hamming/.exercism/metadata.json | 1 + elixir/hamming/.formatter.exs | 4 ++ elixir/hamming/.gitignore | 24 +++++++++ elixir/hamming/HELP.md | 75 ++++++++++++++++++++++++++ elixir/hamming/README.md | 57 ++++++++++++++++++++ elixir/hamming/lib/hamming.ex | 15 ++++++ elixir/hamming/mix.exs | 28 ++++++++++ elixir/hamming/test/hamming_test.exs | 41 ++++++++++++++ elixir/hamming/test/test_helper.exs | 2 + 10 files changed, 280 insertions(+) create mode 100644 elixir/hamming/.exercism/config.json create mode 100644 elixir/hamming/.exercism/metadata.json create mode 100644 elixir/hamming/.formatter.exs create mode 100644 elixir/hamming/.gitignore create mode 100644 elixir/hamming/HELP.md create mode 100644 elixir/hamming/README.md create mode 100644 elixir/hamming/lib/hamming.ex create mode 100644 elixir/hamming/mix.exs create mode 100644 elixir/hamming/test/hamming_test.exs create mode 100644 elixir/hamming/test/test_helper.exs diff --git a/elixir/hamming/.exercism/config.json b/elixir/hamming/.exercism/config.json new file mode 100644 index 0000000..841c77e --- /dev/null +++ b/elixir/hamming/.exercism/config.json @@ -0,0 +1,33 @@ +{ + "authors": [ + "Teapane" + ], + "contributors": [ + "angelikatyborska", + "Cohen-Carlisle", + "dalexj", + "devonestes", + "jedschneider", + "lpil", + "neenjaw", + "parkerl", + "percygrunwald", + "sotojuan", + "veelenga", + "waiting-for-dev" + ], + "files": { + "solution": [ + "lib/hamming.ex" + ], + "test": [ + "test/hamming_test.exs" + ], + "example": [ + ".meta/example.ex" + ] + }, + "blurb": "Calculate the Hamming difference between two DNA strands.", + "source": "The Calculating Point Mutations problem at Rosalind", + "source_url": "https://rosalind.info/problems/hamm/" +} diff --git a/elixir/hamming/.exercism/metadata.json b/elixir/hamming/.exercism/metadata.json new file mode 100644 index 0000000..440414b --- /dev/null +++ b/elixir/hamming/.exercism/metadata.json @@ -0,0 +1 @@ +{"track":"elixir","exercise":"hamming","id":"834311640e76451ab99f7b24cbe83404","url":"https://exercism.org/tracks/elixir/exercises/hamming","handle":"negrienko","is_requester":true,"auto_approve":false} \ No newline at end of file diff --git a/elixir/hamming/.formatter.exs b/elixir/hamming/.formatter.exs new file mode 100644 index 0000000..d2cda26 --- /dev/null +++ b/elixir/hamming/.formatter.exs @@ -0,0 +1,4 @@ +# Used by "mix format" +[ + inputs: ["{mix,.formatter}.exs", "{config,lib,test}/**/*.{ex,exs}"] +] diff --git a/elixir/hamming/.gitignore b/elixir/hamming/.gitignore new file mode 100644 index 0000000..8d65fe6 --- /dev/null +++ b/elixir/hamming/.gitignore @@ -0,0 +1,24 @@ +# The directory Mix will write compiled artifacts to. +/_build/ + +# If you run "mix test --cover", coverage assets end up here. +/cover/ + +# The directory Mix downloads your dependencies sources to. +/deps/ + +# Where third-party dependencies like ExDoc output generated docs. +/doc/ + +# Ignore .fetch files in case you like to edit your project deps locally. +/.fetch + +# If the VM crashes, it generates a dump, let's ignore it too. +erl_crash.dump + +# Also ignore archive artifacts (built via "mix archive.build"). +*.ez + +# Ignore package tarball (built via "mix hex.build"). +hamming-*.tar + diff --git a/elixir/hamming/HELP.md b/elixir/hamming/HELP.md new file mode 100644 index 0000000..d6a1939 --- /dev/null +++ b/elixir/hamming/HELP.md @@ -0,0 +1,75 @@ +# Help + +## Running the tests + +From the terminal, change to the base directory of the exercise then execute the tests with: + +```bash +$ mix test +``` + +This will execute the test file found in the `test` subfolder -- a file ending in `_test.exs` + +Documentation: + +* [`mix test` - Elixir's test execution tool](https://hexdocs.pm/mix/Mix.Tasks.Test.html) +* [`ExUnit` - Elixir's unit test library](https://hexdocs.pm/ex_unit/ExUnit.html) + +## Pending tests + +In test suites of practice exercises, all but the first test have been tagged to be skipped. + +Once you get a test passing, you can unskip the next one by commenting out the relevant `@tag :pending` with a `#` symbol. + +For example: + +```elixir +# @tag :pending +test "shouting" do + assert Bob.hey("WATCH OUT!") == "Whoa, chill out!" +end +``` + +If you wish to run all tests at once, you can include all skipped test by using the `--include` flag on the `mix test` command: + +```bash +$ mix test --include pending +``` + +Or, you can enable all the tests by commenting out the `ExUnit.configure` line in the file `test/test_helper.exs`. + +```elixir +# ExUnit.configure(exclude: :pending, trace: true) +``` + +## Useful `mix test` options + +* `test/.exs:LINENUM` - runs only a single test, the test from `.exs` whose definition is on line `LINENUM` +* `--failed` - runs only tests that failed the last time they ran +* `--max-failures` - the suite stops evaluating tests when this number of test failures +is reached +* `--seed 0` - disables randomization so the tests in a single file will always be ran +in the same order they were defined in + +## Submitting your solution + +You can submit your solution using the `exercism submit lib/hamming.ex` command. +This command will upload your solution to the Exercism website and print the solution page's URL. + +It's possible to submit an incomplete solution which allows you to: + +- See how others have completed the exercise +- Request help from a mentor + +## Need to get help? + +If you'd like help solving the exercise, check the following pages: + +- The [Elixir track's documentation](https://exercism.org/docs/tracks/elixir) +- The [Elixir track's programming category on the forum](https://forum.exercism.org/c/programming/elixir) +- [Exercism's programming category on the forum](https://forum.exercism.org/c/programming/5) +- The [Frequently Asked Questions](https://exercism.org/docs/using/faqs) + +Should those resources not suffice, you could submit your (incomplete) solution to request mentoring. + +If you're stuck on something, it may help to look at some of the [available resources](https://exercism.org/docs/tracks/elixir/resources) out there where answers might be found. \ No newline at end of file diff --git a/elixir/hamming/README.md b/elixir/hamming/README.md new file mode 100644 index 0000000..bf3c386 --- /dev/null +++ b/elixir/hamming/README.md @@ -0,0 +1,57 @@ +# Hamming + +Welcome to Hamming on Exercism's Elixir Track. +If you need help running the tests or submitting your code, check out `HELP.md`. + +## Instructions + +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. + +## Source + +### Created by + +- @Teapane + +### Contributed to by + +- @angelikatyborska +- @Cohen-Carlisle +- @dalexj +- @devonestes +- @jedschneider +- @lpil +- @neenjaw +- @parkerl +- @percygrunwald +- @sotojuan +- @veelenga +- @waiting-for-dev + +### Based on + +The Calculating Point Mutations problem at Rosalind - https://rosalind.info/problems/hamm/ \ No newline at end of file diff --git a/elixir/hamming/lib/hamming.ex b/elixir/hamming/lib/hamming.ex new file mode 100644 index 0000000..c004423 --- /dev/null +++ b/elixir/hamming/lib/hamming.ex @@ -0,0 +1,15 @@ +defmodule Hamming do + @doc """ + Returns number of differences between two strands of DNA, known as the Hamming Distance. + + ## Examples + + iex> Hamming.hamming_distance(~c"AAGTCATA", ~c"TAGCGATC") + {:ok, 4} + """ + @spec hamming_distance([char], [char]) :: {:ok, non_neg_integer} | {:error, String.t()} + def hamming_distance(strand1, strand2) when length(strand1) != length(strand2), do: {:error, "strands must be of equal length"} + def hamming_distance(strand1, strand2) do + {:ok, Enum.count(Enum.zip(strand1, strand2), fn {s1, s2} -> s1 != s2 end)} + end +end diff --git a/elixir/hamming/mix.exs b/elixir/hamming/mix.exs new file mode 100644 index 0000000..d225285 --- /dev/null +++ b/elixir/hamming/mix.exs @@ -0,0 +1,28 @@ +defmodule Hamming.MixProject do + use Mix.Project + + def project do + [ + app: :hamming, + version: "0.1.0", + # elixir: "~> 1.8", + start_permanent: Mix.env() == :prod, + deps: deps() + ] + end + + # Run "mix help compile.app" to learn about applications. + def application do + [ + extra_applications: [:logger] + ] + end + + # Run "mix help deps" to learn about dependencies. + defp deps do + [ + # {:dep_from_hexpm, "~> 0.3.0"}, + # {:dep_from_git, git: "https://github.com/elixir-lang/my_dep.git", tag: "0.1.0"} + ] + end +end diff --git a/elixir/hamming/test/hamming_test.exs b/elixir/hamming/test/hamming_test.exs new file mode 100644 index 0000000..03317fe --- /dev/null +++ b/elixir/hamming/test/hamming_test.exs @@ -0,0 +1,41 @@ +defmodule HammingTest do + use ExUnit.Case + + test "empty strands" do + assert Hamming.hamming_distance(~c"", ~c"") == {:ok, 0} + end + + test "single letter identical strands" do + assert Hamming.hamming_distance(~c"A", ~c"A") == {:ok, 0} + end + + test "single letter different strands" do + assert Hamming.hamming_distance(~c"G", ~c"T") == {:ok, 1} + end + + test "long identical strands" do + assert Hamming.hamming_distance(~c"GGACTGAAATCTG", ~c"GGACTGAAATCTG") == {:ok, 0} + end + + test "long different strands" do + assert Hamming.hamming_distance(~c"GGACGGATTCTG", ~c"AGGACGGATTCT") == {:ok, 9} + end + + test "disallow first strand longer" do + assert {:error, "strands must be of equal length"} = + Hamming.hamming_distance(~c"AATG", ~c"AAA") + end + + test "disallow second strand longer" do + assert {:error, "strands must be of equal length"} = + Hamming.hamming_distance(~c"ATA", ~c"AGTG") + end + + test "disallow empty first strand" do + assert {:error, "strands must be of equal length"} = Hamming.hamming_distance(~c"", ~c"G") + end + + test "disallow empty second strand" do + assert {:error, "strands must be of equal length"} = Hamming.hamming_distance(~c"G", ~c"") + end +end diff --git a/elixir/hamming/test/test_helper.exs b/elixir/hamming/test/test_helper.exs new file mode 100644 index 0000000..35fc5bf --- /dev/null +++ b/elixir/hamming/test/test_helper.exs @@ -0,0 +1,2 @@ +ExUnit.start() +ExUnit.configure(exclude: :pending, trace: true)