BiobaseInfernal 0.6.0.1 → 0.6.2.0

raw patch · 5 files changed

+241/−14 lines, 5 filesPVP: major bump suggested

API removals or changes: PVP suggests a major version bump

API changes (from Hackage documentation)

Files

• Biobase/Infernal/Align.hs +36/−0
• Biobase/Infernal/Align/Import.hs +69/−0
• Biobase/Infernal/CM.hs +20/−6
• Biobase/Infernal/CM/Import.hs +103/−6
• BiobaseInfernal.cabal +13/−2

@@ -0,0 +1,36 @@++-- | "cmalign" provides two interesting results, bit scores of sequences+-- aligned to the model and the alignments themselves.++module Biobase.Infernal.Align where++import Data.ByteString.Char8 (ByteString)++import Biobase.Infernal.Types++++-- | cmalign results, includes sequence scores if available.+--+-- TODO stockholmAlignment, should be "biostockholm" (will be set after some+-- fun iteratee tests). For now, the 'ByteString' holds everything needed to+-- parse using biostockholm.++data Align = Align+  { modelIdentification :: ModelIdentification+  , sequenceScores      :: [SequenceScore]+  , stockholmAlignment  :: ByteString+  }++-- | Individual sequence scores.+--+-- TODO avgProbability should use Probability newtype++data SequenceScore = SequenceScore+  { sequenceName      :: !(ModelAccession,ModelIdentification,EmblAccession)  -- ^ sequence name, typically RFxxxxxx;RfamID;embl-accession+  , sLength           :: !Int       -- ^ aligned sequence length+  , totalBitScore     :: !BitScore  -- ^ total alignment bitscore+  , structureBitScore :: !BitScore  -- ^ structural score part+  , avgProbability    :: !Double    -- ^+  }+

@@ -0,0 +1,69 @@+{-# LANGUAGE OverloadedStrings #-}++-- | Parses "cmalign" results.+--+-- NOTE have not tested if this works with multiple results in a file, but+-- could ;-)++module Biobase.Infernal.Align.Import where++import Data.Iteratee as I+import Data.Iteratee.Char as I+import Data.Iteratee.IO as I+import Data.Iteratee.ZLib as IZ+import Data.ByteString.Char8 as BS+import Prelude as P++import Biobase.Infernal.Align+import Biobase.Infernal.Types++++-- | Transforms bytestring to list of 'Align' data.++eneeAlign :: (Monad m) => Enumeratee ByteString [Align] m a+eneeAlign = enumLinesBS ><> convStream go where+  go = do+    -- lets start with some comment lines+    cs <- I.takeWhile (("#" ==) . BS.take 1)+    -- there should be score lines now+    ss <- I.takeWhile (\s -> "# STOCKHOLM 1.0" /= s && (not $ BS.null s))+    -- Stockholm lines+    xs <- I.takeWhile (/="//")+    x <- I.head+    return [Align+      { modelIdentification = ModelIdentification ""+      , sequenceScores = P.map mkScore ss+      , stockholmAlignment = BS.unlines $ xs++[x]+      }]++-- | Creates the required sequence score.++mkScore s = SequenceScore+  { sequenceName = undefined $ ws!!0+  , sLength = read . BS.unpack $ ws!!1+  , totalBitScore = BitScore . read . BS.unpack $ ws!!2+  , structureBitScore = BitScore . read . BS.unpack $ ws!!3+  , avgProbability = read . BS.unpack $ ws!!4+  } where ws = BS.words s++-- | Convenience function creating all maps.++fromFileZip :: FilePath -> IO [Align]+fromFileZip fp = run =<< ( enumFile 8192 fp+                         . joinI+                         . enumInflate GZipOrZlib defaultDecompressParams+                         . joinI+                         . eneeAlign+                         $ stream2stream+                         )++-- | Convenience function creating all maps.++fromFile :: FilePath -> IO [Align]+fromFile fp = run =<< ( enumFile 8192 fp+                      . joinI+                      . eneeAlign+                      $ stream2stream+                      )+

@@ -3,15 +3,18 @@  module Biobase.Infernal.CM where +import Data.ByteString as BS+import Data.Map as M import Data.Vector as V import Data.Vector.Unboxed as VU-import Data.ByteString as BS  import Data.PrimitiveArray import Data.PrimitiveArray.Ix +import Biobase.Infernal.Types  + -- | A datatype representing Infernal covariance models. This is a new -- representation that is incompatible with the one once found in "Biobase". -- The most important difference is that lookups are mapped onto efficient data@@ -33,15 +36,17 @@ -- 'localBegin' is a transition score to certain states, all such transitions -- are in 'begins'. A 'localEnd' is a transition score to a local end state. --+-- NOTE that trustedCutoff > gathering > noiseCutoff+-- -- TODO as with other projects, we should not use Double's but "Score" and -- "Probability" newtypes.  data CM = CM-  { name :: ByteString-  , accession :: Int-  , ga :: Double-  , tc :: Double-  , nc :: Double+  { name          :: ModelIdentification  -- ^ name of model as in "tRNA"+  , accession     :: ModelAccession       -- ^ RFxxxxx identification+  , trustedCutoff :: BitScore -- ^ lowest score of true member+  , gathering     :: BitScore -- ^ all scores at or above 'gathering' score are in the "full" alignment+  , noiseCutoff   :: Maybe BitScore -- ^ highest score NOT included as member   , transition :: PrimArray (Int,Int) Double   , emission :: PrimArray (Int,Int) Double   , paths :: V.Vector (VU.Vector Double)@@ -51,3 +56,12 @@   , nodes :: V.Vector (VU.Vector Int)   }   deriving (Show)++-- | Map of model names to individual CMs.++type ID2CM = M.Map ModelIdentification CM++-- | Map of model accession numbers to individual CMs.++type AC2CM = M.Map ModelAccession CM+

@@ -1,34 +1,131 @@+{-# LANGUAGE BangPatterns #-}+{-# LANGUAGE NoMonomorphismRestriction #-}+{-# LANGUAGE OverloadedStrings #-}  -- | Iteratee-based parsing of Infernal covariance models.+--+-- TODO does not create working CMs yet. Only partial key/value parsing is+-- implemented.  module Biobase.Infernal.CM.Import where +import Control.Arrow+import Control.Monad (unless)+import Data.ByteString.Char8 as BS import Data.Iteratee as I import Data.Iteratee.Char as I import Data.Iteratee.IO as I import Data.Iteratee.Iteratee as I import Data.Iteratee.ListLike as I-import Data.ByteString as BS+import Data.Iteratee.ZLib as IZ+import Data.Map as M+import Prelude as P+import Control.Monad.IO.Class (liftIO, MonadIO) +import Data.PrimitiveArray+import Data.PrimitiveArray.Ix+ import Biobase.Infernal.CM+import Biobase.Infernal.Types    -- * iteratee stuff --- | +-- | iteratee-based parsing of human-readable CMs.  eneeCM :: (Monad m) => Enumeratee ByteString [CM] m a eneeCM = enumLinesBS ><> convStream f where   f = do-    th <- tryHead-    return undefined+    -- initial (mostly key/value) data+    hs' <- I.takeWhile (/="MODEL:")+    let hs = M.fromList . P.map (second (BS.dropWhile (==' ')) . BS.break (==' ')) $ hs'+    -- model begins+    mb <- I.tryHead+    unless (mb == Just "MODEL:") . error $ "model error: " ++ show (hs,mb,"head")+    -- nodes+    ns <- iterNodes+    -- model ends+    me <- I.tryHead+    unless (me == Just "//") . error $ "model error: " ++ show (hs,me,"tail")+    return . (:[]) $ CM+      { name = ModelIdentification $ hs M.! "NAME"+      , accession = ModelAccession . bsRead . BS.drop 2 $ hs M.! "ACCESSION"+      , gathering = BitScore . bsRead $ hs M.! "GA"+      , trustedCutoff = BitScore . bsRead $ hs M.! "TC"+      , noiseCutoff = let x = hs M.! "NC" in if x == "undefined" then Nothing else Just . BitScore . bsRead $ x+      , transition = error "not implemented yet"+      , emission = error "not implemented yet"+      , paths = error "not implemented yet"+      , localBegin = error "not implemented yet"+      , begins = error "not implemented yet"+      , localEnd = error "not implemented yet"+      , nodes = error "not implemented yet"+      } where bsRead = read . BS.unpack +iterNodes :: (Monad m) => Iteratee [ByteString] m [Node]+iterNodes = do+  hdr' <- I.head+  let (ishdr,(hdr,nidx)) = isNodeHeader hdr'+  unless ishdr $ error $ show hdr'+  xs <- I.takeWhile (fst . isState)+  pk <- I.peek+  let n = Node+            { nodeHeader = hdr+            , nodeIndex = nidx+            }+  case pk of+    Just "//" -> return []+    Just x+      | (True,_) <- isNodeHeader x -> do+          ns <- iterNodes+          return $ n:ns+    e -> error $ show e +data Node = Node+  { nodeHeader :: ByteString+  , nodeIndex :: Int+  }++isNodeHeader :: ByteString -> (Bool,(ByteString,Int))+isNodeHeader xs = (isnh,(hdr,nidx)) where+  isnh = BS.elem '[' xs && BS.elem ']' xs+  [hdr,nidx'] = BS.words . BS.init . BS.takeWhile (/=']') . BS.drop 1 . BS.dropWhile (/='[') $ xs+  nidx = read . BS.unpack $ nidx'++isState :: ByteString -> (Bool,ByteString)+isState xs'+  | P.null xs = (False,"")+  | P.head xs `P.elem` [ "[", "//" ] = (False,"")+  | P.head xs `P.elem` [ "S", "IL", "IR", "MATR", "MR", "D", "MP", "ML", "B", "E" ] = (True,"")+  | otherwise = error $ show xs+  where+    xs = BS.words xs'+ -- * convenience functions  -- | Read covariance models from file. This parser reads one or more CMs from -- file. -fromFile :: FilePath -> [CM]-fromFile = undefined+fromFile :: FilePath -> IO (ID2CM, AC2CM)+fromFile fp = run =<< ( enumFile 8192 fp+                      . joinI+                      . eneeCM+                      $ I.zip (mkMap name) (mkMap accession)+                      )++-- | Read covariance models from a compressed file.++fromFileZip :: FilePath -> IO (ID2CM, AC2CM)+fromFileZip fp = run =<< ( enumFile 8192 fp+                         . joinI+                         . enumInflate GZipOrZlib defaultDecompressParams+                         . joinI+                         . eneeCM+                         $ I.zip (mkMap name) (mkMap accession)+                         )++-- | map creation helper++mkMap f = I.foldl' (\ !m x -> M.insert (f x) x m) M.empty+

@@ -1,5 +1,5 @@ name:           BiobaseInfernal-version:        0.6.0.1+version:        0.6.2.0 author:         Christian Hoener zu Siederdissen maintainer:     choener@tbi.univie.ac.at homepage:       http://www.tbi.univie.ac.at/~choener/@@ -26,6 +26,15 @@                 .                 .                 .+                Changes in 0.6.2.0+                .+                * added CM parsing (implementation and interface subject to+                  change)+                .+                Changes in 0.6.1.0+                .+                * added cmalign results parser+                .                 Changes in 0.6.0.1                 .                 * haddock should finish now@@ -44,9 +53,9 @@ library   build-depends:     base >3 && <5,-    biocore,     attoparsec,     attoparsec-iteratee,+    biocore,     bytestring,     containers,     either-unwrap,@@ -59,6 +68,8 @@    exposed-modules:     Biobase.Infernal+    Biobase.Infernal.Align+    Biobase.Infernal.Align.Import     Biobase.Infernal.Clan     Biobase.Infernal.Clan.Import     Biobase.Infernal.CM