Gene-CluEDO-0.0.0.2: Hox gene clustering

Safe HaskellNone
LanguageHaskell2010

BioInf.GeneCluEDO

Description

Run all steps of the GeneCluEDO algorithms in order.

This will produce the following:

  1. run the minimal distance algorithm, give the minimal distance score and return all co-optimal paths
  2. run the end-probability algorithm and return the probability that each node is the begin/end of a chain
  3. run the edge probability algorithm and give the probability for each from :-> to edge
  4. 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

runGeneCluEDO Source #

Arguments

:: FillWeight 
-> FillStyle 
-> Double

Temperature for probability-related parts of the algorithms. Lower temperatures favor a single path.

-> FilePath

The input score matrix

-> String

In the current directory, create output files with this name prefix

-> IO () 

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 
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 

data FillStyle :: * #

Instances

Eq FillStyle 
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