Bioinformatics/Sequence mutation: Difference between revisions

Line 946:

i <- randomIndex (length xs)

case m of

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

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

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

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

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

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

where

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

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

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

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

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

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

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

randomDNA = head . randoms <$> newStdGen

~~mutations~~ :: Int -> DNASequence -> IO DNASequence

mutate :: Int -> DNASequence -> IO DNASequence

~~mutations~~ 0 s = pure s

mutate 0 s = pure s

~~mutations~~ n s = do

mutate n s = do

(m, ms) <- mutateSequence s

uncurry (printf "%6s @ %d\n") m

~~mutations~~ (pred n) ms

mutate (pred n) ms

main :: IO ()

main = do

~~dnaseq~~ <- newSequence 200

ds <- newSequence 200

putStrLn "\nInitial Sequence:" >> showSequence ~~dnaseq~~

putStrLn "\nInitial Sequence:" >> showSequence ds

putStrLn "\nBase Counts:" >> showBaseCounts ~~dnaseq~~

putStrLn "\nBase Counts:" >> showBaseCounts ds

printf "Total: %d\n\n" $ length ~~dnaseq~~

printf "Total: %d\n\n" $ length ds

ms <- ~~mutations~~ 10 ~~dnaseq~~

ms <- mutate 10 ds

putStrLn "\nMutated Sequence:" >> showSequence ms

putStrLn "\nBase Counts:" >> showBaseCounts ms