Safe Haskell	None
Language	Haskell2010

BioInf.MutationOrder

Description

Run all steps of the HoxCluster algorithms in order.

This will produce the following:

run the minimal distance algorithm, give the minimal distance score and return all co-optimal paths
run the end-probability algorithm and return the probability that each node is the begin/end of a chain
run the edge probability algorithm and give the probability for each from :-> to edge
with the edge probabilities, run the maximal probability path algorithm, return that probability and all co-optimal paths

TODO -Pretty should yield a structure to be given to the eps or svg generator. This allows more flexibility. Does diagrams offer serialization?

TODO All this should be wrapped and available as a function. not just providing output files.

Synopsis

Documentation

runMutationOrder :: Bool -> FillWeight -> FillStyle -> ScaleFunction -> ScaleFunction -> Int -> Int -> Maybe FilePath -> [Char] -> FilePath -> t -> Bool -> [FilePath] -> IO () Source #

posScaled :: Double -> Double -> ScaleFunction -> ScaleFunction Source #

basepairDistanceMFE :: ScaleFunction Source #

Basepair distance

basepairDistanceCentroid :: ScaleFunction Source #

mfeDelta :: ScaleFunction Source #

Scale function for normal mfe delta energies

centroidDelta :: ScaleFunction Source #

Scale function for normal centroid delta energies

squaredPositive :: ScaleFunction -> ScaleFunction Source #

Square positive "contributions", making bad moves more unlikely

scaleTemperature :: Double -> ScaleFunction -> ScaleFunction Source #

Scale by temperature (for probability stuff)

scaleByFunction :: (t3 -> t2) -> (t1 -> t -> t3) -> t1 -> t -> t2 Source #

stupidReader :: FilePath -> IO ByteString Source #

Basepair distance

Stupid fasta reader

withDumpFile Source #

Arguments

:: Handle
-> FilePath	The path we store the serialized and compressed dump in
-> ByteString	ancestral / origin sequence
-> ByteString	destination sequence
-> Landscape	the element which is to be serialized in the dump, or which would be the data in the dump
-> IO Landscape	the data we put in, but maybe taken from the dump file

withDumpFile is like idIO :: a -> IO a in that it returns the data we give to the function. However, in case the dump file exists, we read it and return its contents, instead of recalculating. If it does not exist, we dump the data in addition to returning it. This forces the Landscape.

data FillWeight :: * #

Fill weight for our grid. If the fill weight is logarithmic, then the line length is 1 / (1 + log value) otherwise it is value.

Constructors

FWlog
FWlinear
FWfill

Instances

Eq FillWeight
Methods (==) :: FillWeight -> FillWeight -> Bool # (/=) :: FillWeight -> FillWeight -> Bool #
Data FillWeight
Methods gfoldl :: (forall d b. Data d => c (d -> b) -> d -> c b) -> (forall g. g -> c g) -> FillWeight -> c FillWeight # gunfold :: (forall b r. Data b => c (b -> r) -> c r) -> (forall r. r -> c r) -> Constr -> c FillWeight # toConstr :: FillWeight -> Constr # dataTypeOf :: FillWeight -> DataType # dataCast1 :: Typeable (* -> ) t => (forall d. Data d => c (t d)) -> Maybe (c FillWeight) # dataCast2 :: Typeable ( -> * -> *) t => (forall d e. (Data d, Data e) => c (t d e)) -> Maybe (c FillWeight) # gmapT :: (forall b. Data b => b -> b) -> FillWeight -> FillWeight # gmapQl :: (r -> r' -> r) -> r -> (forall d. Data d => d -> r') -> FillWeight -> r # gmapQr :: (r' -> r -> r) -> r -> (forall d. Data d => d -> r') -> FillWeight -> r # gmapQ :: (forall d. Data d => d -> u) -> FillWeight -> [u] # gmapQi :: Int -> (forall d. Data d => d -> u) -> FillWeight -> u # gmapM :: Monad m => (forall d. Data d => d -> m d) -> FillWeight -> m FillWeight # gmapMp :: MonadPlus m => (forall d. Data d => d -> m d) -> FillWeight -> m FillWeight # gmapMo :: MonadPlus m => (forall d. Data d => d -> m d) -> FillWeight -> m FillWeight #
Show FillWeight
Methods showsPrec :: Int -> FillWeight -> ShowS # show :: FillWeight -> String # showList :: [FillWeight] -> ShowS #

data FillStyle :: * #

Constructors

FSopacityLog
FSopacityLinear
FSfull

Instances

Eq FillStyle
Methods (==) :: FillStyle -> FillStyle -> Bool # (/=) :: FillStyle -> FillStyle -> Bool #
Data FillStyle
Methods gfoldl :: (forall d b. Data d => c (d -> b) -> d -> c b) -> (forall g. g -> c g) -> FillStyle -> c FillStyle # gunfold :: (forall b r. Data b => c (b -> r) -> c r) -> (forall r. r -> c r) -> Constr -> c FillStyle # toConstr :: FillStyle -> Constr # dataTypeOf :: FillStyle -> DataType # dataCast1 :: Typeable (* -> ) t => (forall d. Data d => c (t d)) -> Maybe (c FillStyle) # dataCast2 :: Typeable ( -> * -> *) t => (forall d e. (Data d, Data e) => c (t d e)) -> Maybe (c FillStyle) # gmapT :: (forall b. Data b => b -> b) -> FillStyle -> FillStyle # gmapQl :: (r -> r' -> r) -> r -> (forall d. Data d => d -> r') -> FillStyle -> r # gmapQr :: (r' -> r -> r) -> r -> (forall d. Data d => d -> r') -> FillStyle -> r # gmapQ :: (forall d. Data d => d -> u) -> FillStyle -> [u] # gmapQi :: Int -> (forall d. Data d => d -> u) -> FillStyle -> u # gmapM :: Monad m => (forall d. Data d => d -> m d) -> FillStyle -> m FillStyle # gmapMp :: MonadPlus m => (forall d. Data d => d -> m d) -> FillStyle -> m FillStyle # gmapMo :: MonadPlus m => (forall d. Data d => d -> m d) -> FillStyle -> m FillStyle #
Show FillStyle
Methods showsPrec :: Int -> FillStyle -> ShowS # show :: FillStyle -> String # showList :: [FillStyle] -> ShowS #

type ScaleFunction = RNA -> RNA -> Double Source #

Given the RNA we come from and the RNA we mutate into, derive the gain or loss by a scaling function.