Safe Haskell | Safe-Infered |
---|
Turner file parser. Returns a Turner2004 data structure. Requires an annoying amount of boilerplate.
How is stack
data stored:
AX UY -> ((A,U),(Y,X))
How iloop1x1
is stored:
X A G U C -> ((A,U),(C,G),X,Y) Y
Now iloop1x2
is stored:
X A G U C -> ((A,U),(C,G),X,C,Y), single (X) first, then 5' to 3' YC
iloop2x2
is stored:
XY A G U C -> ((A,U),(C,G),X,Y,y,x), X-->Y then x<--y xy
TODO not sure if dangle3/dangle5 are correctly split or if they should switch
- fromDir :: FilePath -> Prefix -> Suffix -> IO Turner2004
- minPP :: :. (:. (:. (:. Z Nuc) Nuc) Nuc) Nuc
- maxPP :: :. (:. (:. (:. Z Nuc) Nuc) Nuc) Nuc
- minP :: :. (:. Z Nuc) Nuc
- maxP :: :. (:. Z Nuc) Nuc
- minPB :: :. (:. (:. Z Nuc) Nuc) Nuc
- maxPB :: :. (:. (:. Z Nuc) Nuc) Nuc
- minPBB :: :. (:. (:. (:. Z Nuc) Nuc) Nuc) Nuc
- maxPBB :: :. (:. (:. (:. Z Nuc) Nuc) Nuc) Nuc
- minPPBB :: :. (:. (:. (:. (:. (:. Z Nuc) Nuc) Nuc) Nuc) Nuc) Nuc
- maxPPBB :: :. (:. (:. (:. (:. (:. Z Nuc) Nuc) Nuc) Nuc) Nuc) Nuc
- minPPBBB :: :. (:. (:. (:. (:. (:. (:. Z Nuc) Nuc) Nuc) Nuc) Nuc) Nuc) Nuc
- maxPPBBB :: :. (:. (:. (:. (:. (:. (:. Z Nuc) Nuc) Nuc) Nuc) Nuc) Nuc) Nuc
- minPPBBBB :: :. (:. (:. (:. (:. (:. (:. (:. Z Nuc) Nuc) Nuc) Nuc) Nuc) Nuc) Nuc) Nuc
- maxPPBBBB :: :. (:. (:. (:. (:. (:. (:. (:. Z Nuc) Nuc) Nuc) Nuc) Nuc) Nuc) Nuc) Nuc
- d1_30 :: (Enum a, Num a) => [:. Z a]
- keysPP :: [:. (:. (:. (:. Z Nuc) Nuc) Nuc) Nuc]
- keysPB :: [:. (:. (:. Z Nuc) Nuc) Nuc]
- keysPBB :: [:. (:. (:. (:. Z Nuc) Nuc) Nuc) Nuc]
- keysPPBB :: [:. (:. (:. (:. (:. (:. Z Nuc) Nuc) Nuc) Nuc) Nuc) Nuc]
- keysPPBBB :: [:. (:. (:. (:. (:. (:. (:. Z Nuc) Nuc) Nuc) Nuc) Nuc) Nuc) Nuc]
- keysPPBBBBrna :: [:. (:. (:. (:. (:. (:. (:. (:. Z Nuc) Nuc) Nuc) Nuc) Nuc) Nuc) Nuc) Nuc]
- keysPPBBBBdna :: [:. (:. (:. (:. (:. (:. (:. (:. Z Nuc) Nuc) Nuc) Nuc) Nuc) Nuc) Nuc) Nuc]
- plist11 :: [(Nuc, Nuc)]
- plist22rna :: [(Nuc, Nuc)]
- plist22dna :: [(Nuc, Nuc)]
- infE :: Double
- eneeBlocks :: (Functor m, Monad m) => Enumeratee ByteString [[Double]] m a
- values :: ByteString -> [Double]
- iTabulated :: (Functor m, Monad m) => Iteratee ByteString m [(ByteString, Double)]
- blockFromFile :: FilePath -> IO [Double]
- iMiscLoop :: (Functor m, Monad m) => Iteratee ByteString m [[Double]]
- readD :: ByteString -> Double
- miscFromFile :: FilePath -> IO [[Double]]
- tabFromFile :: FilePath -> IO [(ByteString, Double)]
- allEq :: Eq a => [a] -> Bool
- type Prefix = FilePath
- type Suffix = FilePath
Documentation
fromDir :: FilePath -> Prefix -> Suffix -> IO Turner2004Source
Given a directory, fill in the Turner2004
data structure
plist22rna :: [(Nuc, Nuc)]Source
plist22dna :: [(Nuc, Nuc)]Source
Iteratee stuff
eneeBlocks :: (Functor m, Monad m) => Enumeratee ByteString [[Double]] m aSource
Transform input stream into list of list of doubles
values :: ByteString -> [Double]Source
extract values. . - values are extracted as > 100k
iTabulated :: (Functor m, Monad m) => Iteratee ByteString m [(ByteString, Double)]Source
Iteratee to parse tabulated loops (hairpins).
blockFromFile :: FilePath -> IO [Double]Source
Convenience function
iMiscLoop :: (Functor m, Monad m) => Iteratee ByteString m [[Double]]Source
Parses the miscloop table
NOTO extra brownie points for miscloop.dat for providing data in a form that does not conform to normal number encoding.
miscFromFile :: FilePath -> IO [[Double]]Source
tabFromFile :: FilePath -> IO [(ByteString, Double)]Source