Safe Haskell | None |
---|
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 :: Energy
- values :: ByteString -> [Energy]
- parseTabulated :: Monad m => Sink ByteString m [(ByteString, Energy)]
- blockFromFile :: FilePath -> IO [Energy]
- parseBlocks :: Monad m => Conduit ByteString m [Energy]
- parseMiscLoop :: Monad m => Sink ByteString m [[Double]]
- readD :: ByteString -> Double
- miscFromFile :: FilePath -> IO [[Double]]
- tabFromFile :: FilePath -> IO [(Primary, Energy)]
- 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
Conduit stuff
values :: ByteString -> [Energy]Source
extract values. . - values are extracted as > 100k
parseTabulated :: Monad m => Sink ByteString m [(ByteString, Energy)]Source
Iteratee to parse tabulated loops (hairpins).
blockFromFile :: FilePath -> IO [Energy]Source
Convenience function
parseBlocks :: Monad m => Conduit ByteString m [Energy]Source
Transform input stream into list of list of doubles
parseMiscLoop :: Monad m => Sink ByteString m [[Double]]Source
Parses the miscloop table
NOTE 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