Bioinformatics/Sequence mutation: Difference between revisions

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</pre>

=={{header|Haskell}}==

<lang haskell>import ~~Data~~.~~List~~ (~~group, sort~~)

<lang haskell>import Control.Monad ((>=>))

import Data.List (group, sort)

import Data.List.Split (chunksOf)

import System.Random (Random, randomR, random, newStdGen, randoms, getStdRandom)

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toChar = head . show

fromChar c = read [c]

dropIndex :: Int -> [a] -> [a]

⚫

dropIndex i xs = take (pred i) xs <> drop i xs

insertIndex :: Int -> a -> [a] -> [a]

⚫

insertIndex i e xs = take i xs <> [e] <> drop i xs

swapIndex :: Int -> a -> [a] -> [a]

⚫

swapIndex i a xs = take (pred i) xs <> [a] <> drop i xs

chunkedDNASequence :: DNASequence -> [(Int, [DNABase])]

chunkedDNASequence = zip [50,100..] . chunksOf 50

baseCounts :: DNASequence -> [(DNABase, Int)]

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mutateSequence :: DNASequence -> IO ((Mutation, Int), DNASequence)

mutateSequence xs = ~~randomMutation~~ >>= ~~(`mutate` xs)~~

mutateSequence ds = mutate ds =<< randomMutation

where

⚫

randomMutation = head . randoms <$> newStdGen

mutate :: Mutation -> DNASequence -> IO ((Mutation, Int), DNASequence)

~~mutate~~ m xs = do

mutate xs m = do

i <- randomIndex (length xs)

case m of

Swap -> randomDNA >>= \d -> pure ((Swap, i), swapIndex i d xs)

Insert -> randomDNA >>= \d -> pure ((Insert, i), insertIndex i d xs)

Delete -> pure ((Delete, i), dropIndex i xs)

where

⚫

dropIndex i xs = take (pred i) xs <> drop i xs

randomIndex :: Int -> IO Int

⚫

insertIndex i e xs = take i xs <> [e] <> drop i xs

⚫

randomIndex max = getStdRandom (randomR (1, max))

⚫

swapIndex i a xs = take (pred i) xs <> [a] <> drop i xs

⚫

randomIndex max = getStdRandom (randomR (1, max))

randomDNA :: IO DNABase

randomDNA = head . randoms <$> newStdGen

randomMutation :: IO Mutation

⚫

randomMutation = head . randoms <$> newStdGen

mutations :: Int -> DNASequence -> IO DNASequence

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Total: 201

</pre>

=={{header|J}}==

<lang J>ACGT=: 'ACGT'