Biobase.Turner.Import

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

Documentation

fromDir :: FilePath -> Prefix -> Suffix -> IO Turner2004

Given a directory, fill in the Turner2004 data structure

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

Conduit stuff

values :: ByteString -> [Energy]

extract values. . - values are extracted as > 100k

parseTabulated :: Monad m => Sink ByteString m [(ByteString, Energy)]

Iteratee to parse tabulated loops (hairpins).

blockFromFile :: FilePath -> IO [Energy]

Convenience function

parseBlocks :: Monad m => Conduit ByteString m [Energy]

Transform input stream into list of list of doubles

parseMiscLoop :: Monad m => Sink ByteString m [[Double]]

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.

readD :: ByteString -> Double

Parses stupidly encoded values like .6 and -.0.

miscFromFile :: FilePath -> IO [[Double]]

tabFromFile :: FilePath -> IO [(Primary, Energy)]

allEq :: Eq a => [a] -> Bool

type Prefix = FilePath

type Suffix = FilePath