BiobaseTrainingData 0.1.1.0 → 0.1.2.0

raw patch · 3 files changed

+24/−4 lines, 3 filesPVP ok

version bump matches the API change (PVP)

API changes (from Hackage documentation)

Files

• Biobase/TrainingData/Manip.hs +19/−0
• BiobaseTrainingData.cabal +1/−1
• MkTrainingData.hs +4/−3

@@ -2,6 +2,9 @@  module Biobase.TrainingData.Manip where +import Data.List (sort,sortBy)+import Data.Ord (comparing)+ import Biobase.Secondary.PseudoKnots  import Biobase.TrainingData@@ -17,3 +20,19 @@ removePK rpk td@TrainingData{..}   | not rpk   = td   | otherwise = td{secondary = removeByCounting secondary}++-- | Remove triplets from training data. "rmTs" will check each extPair and+-- remove it, if it is the worst in a triplet. If not, the pair is rotated to+-- the last position and we continue. In the non-triplet case, we simply remove+-- the pair from consideration and put it into the output (x:).++fRemoveTriplets False td = td+fRemoveTriplets True td@TrainingData{..} = td{secondary = sort $ rmTs secondary} where+  rmTs [] = []+  rmTs (x:xs)+    | ys <- triplets x xs+    , not $ null ys = if worst x ys then rmTs xs else rmTs xs++[x]+    | otherwise = x : rmTs xs+    where+      triplets ((i,j),_) zs = filter (\((k,l),_) -> i==k || i==l || j==k || j==l) zs+      worst z zs = last (sortBy (comparing snd) $ z : zs) == z

@@ -1,5 +1,5 @@ name:           BiobaseTrainingData-version:        0.1.1.0+version:        0.1.2.0 author:         Christian Hoener zu Siederdissen maintainer:     choener@tbi.univie.ac.at homepage:       http://www.tbi.univie.ac.at/~choener/

@@ -30,6 +30,7 @@     , fromdir   :: FilePath     , errorFile :: Maybe FilePath     , relativePairs :: Maybe Double+    , removeTriplets :: Bool     }   -- | RNAstrand reads from one file   | RNAstrand@@ -45,6 +46,7 @@   , fromdir   = "./"  &= args   , errorFile = def   &= help "put TrainingData which falls through the filter in this file (default: disabled)"   , relativePairs = def &= help "Keep only TrainingData with that fraction of basepairs."+  , removeTriplets = False &= help "remove triplets pairs (tries to remove non-canonical part first) (default: disabled)"   }  rnastrand = RNAstrand@@ -63,16 +65,15 @@   let (ys :: [TDmanip]) = id           . map (fErrorCheck)                 -- basic error-checking           . map (fMinRelPairs relativePairs)  -- filtering out trainingdata with too few pairs+          . map (fmap $ fRemoveTriplets removeTriplets)  -- removes triplet pairs (parts of)           . map (fmap (removePK removepk))    -- remove pseudoknots from trainingdata           . map (fmap (mkTrainingData . removeBIF . F.linearizeFR3D)) -- basic conversions           . map Right           $ xs   let (ls,rs) = partition isLeft ys+  mapM_ (print . fromRight) rs   when (isJust errorFile) $ do     writeFile (fromJust errorFile) . unlines . map (show . fromLeft) $ ls-  mapM_ (print . fromRight) rs-  return ()-  -- mapM_ print $ map (removePK removepk . mkTrainingData . removeBIF . F.linearizeFR3D) xs  -- | RNAstrand importer