BiobaseInfernal 0.5.4.0 → 0.5.4.1

raw patch · 7 files changed

+149/−35 lines, 7 filesdep +PrimitiveArraydep +vectorPVP: major bump suggested

API removals or changes: PVP suggests a major version bump

Dependencies added: PrimitiveArray, vector

API changes (from Hackage documentation)

Files

• Biobase/Infernal/CM.hs +53/−0
• Biobase/Infernal/CM/Export.hs +12/−0
• Biobase/Infernal/CM/Import.hs +34/−0
• Biobase/Infernal/VerboseHit.hs +15/−14
• Biobase/Infernal/VerboseHit/Export.hs +16/−6
• Biobase/Infernal/VerboseHit/Import.hs +8/−7
• BiobaseInfernal.cabal +11/−8

@@ -0,0 +1,53 @@++-- | Infernal CMs.++module Biobase.Infernal.CM where++import Data.Vector as V+import Data.Vector.Unboxed as VU+import Data.ByteString as BS++import Data.PrimitiveArray+import Data.PrimitiveArray.Ix++++-- | 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+-- structures, currently "PrimitiveArray".+--+-- [1] Each "State" of a covariance model has up to 6 transition scores, hence+-- we need s*6 cells for transitions.+--+-- [2] Each "State" of a covariance has up to 16 emission scores, so we have+-- s*16 cells for emissions, with unused cells set to a really high score.+--+-- On top of these basic structures, we then place additional high-level+-- constructs.+--+-- [3] 'paths' are allowed transitions. This can safe a check, if the+-- transition is encoded with a forbidden score.+--+-- [4] 'localBegin' and 'localEnd' are local entry and exit strategies. A+-- '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.+--+-- 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+  , transition :: PrimArray (Int,Int) Double+  , emission :: PrimArray (Int,Int) Double+  , paths :: V.Vector (VU.Vector Double)+  , localBegin :: VU.Vector Double+  , begins :: VU.Vector Int+  , localEnd :: VU.Vector (Double)+  , nodes :: V.Vector (VU.Vector Int)+  }+  deriving (Show)

@@ -0,0 +1,12 @@++-- | Transforms the internal representation of a CM back into a version that+-- can be used by Infernal.+--+-- Note that models are transformed into 'ByteString' as-is, the exporter does+-- not make sure that probabilities add to one, that we write out probabilities+-- instead of scores, and so on.+--+-- TODO some of the notes above will become less problematic once we use+-- newtypes, as a probability-CM will not be accepted by the exporter by then.++module Biobase.Infernal.CM.Export where

@@ -0,0 +1,34 @@++-- | Iteratee-based parsing of Infernal covariance models.++module Biobase.Infernal.CM.Import where++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 Biobase.Infernal.CM++++-- * iteratee stuff++-- | ++eneeCM :: (Monad m) => Enumeratee ByteString [CM] m a+eneeCM = enumLinesBS ><> convStream f where+  f = do+    th <- tryHead+    return undefined+++-- * convenience functions++-- | Read covariance models from file. This parser reads one or more CMs from+-- file.++fromFile :: FilePath -> [CM]+fromFile = undefined

@@ -1,4 +1,5 @@ {-# LANGUAGE RecordWildCards #-}+{-# OPTIONS_GHC -funbox-strict-fields #-}  -- | Provides a datatype for cmsearch verbose output. The Import/Export system -- now allows for primitive annotations using "##" as the first two characters.@@ -14,20 +15,20 @@ -- | Captures a complete alignment  data VerboseHit = VerboseHit-  { vhTarget  :: (Int,Int)  -- ^ part of target sequence (start counting at 1)-  , vhQuery   :: (Int,Int)  -- ^ which part of the CM/stk do we align to-  , vhCM      :: ByteString  -- ^ the CM for this alignment-  , vhStrand  :: Strand     -- ^ should be either '+' or '-'-  , vhScore   :: Double     -- ^ bit score-  , vhEvalue  :: Double     -- ^ number of hits we expect to find with 'score' or higher for 'targetSequence' length-  , vhPvalue  :: Double     -- ^ ?-  , vhGC      :: Int        -- ^ ?-  , vhScaffold :: ByteString -- ^ scaffold, chromosome, ... (the name of the sequence, not the sequence data!)-  , vhWuss :: ByteString -- ^ fancy secondary structure annotation using wuss notation-  , vhConsensus :: ByteString -- ^ query consensus (upper: highly, lower: weak/no)-  , vhScoring   :: ByteString -- ^ represents where positive and negative scores come from-  , vhSequence :: ByteString -- ^ the target sequence which aligns to the model-  , vhAnnotation :: [ByteString] -- ^ any annotations that could be associated (# lines)+  { vhTarget      :: !(Int,Int)     -- ^ part of target sequence (start counting at 1)+  , vhQuery       :: !(Int,Int)     -- ^ which part of the CM/stk do we align to+  , vhCM          :: !ByteString    -- ^ the CM for this alignment+  , vhStrand      :: !Strand        -- ^ should be either '+' or '-'+  , vhScore       :: !Double        -- ^ bit score+  , vhEvalue      :: !Double        -- ^ number of hits we expect to find with 'score' or higher for 'targetSequence' length+  , vhPvalue      :: !Double        -- ^ ?+  , vhGC          :: !Int           -- ^ ?+  , vhScaffold    :: !ByteString    -- ^ scaffold, chromosome, ... (the name of the sequence, not the sequence data!)+  , vhWuss        :: !ByteString    -- ^ fancy secondary structure annotation using wuss notation+  , vhConsensus   :: !ByteString    -- ^ query consensus (upper: highly, lower: weak/no)+  , vhScoring     :: !ByteString    -- ^ represents where positive and negative scores come from+  , vhSequence    :: !ByteString    -- ^ the target sequence which aligns to the model+  , vhAnnotation  :: ![ByteString]  -- ^ any annotations that could be associated (# lines)   } deriving (Show,Read)  type Strand = Char

@@ -1,3 +1,4 @@+{-# LANGUAGE NoMonomorphismRestriction #-} {-# LANGUAGE RankNTypes #-} {-# LANGUAGE RecordWildCards #-} {-# LANGUAGE OverloadedStrings #-}@@ -39,8 +40,9 @@   f acc = do     h <- I.head     let na = newAcc acc h+    p <- I.peek     return ( fst na-           , return . BS.unlines $ snd na ++ P.map (append "## ") (vhAnnotation h)  ++ [showVerboseHit h]+           , return . BS.unlines $ snd na ++ P.map (append "##") (vhAnnotation h)  ++ [showVerboseHit h] ++ maybe ["//"] (const []) p            )  -- | Given the current state "a" and verbose hit "h", determine if any state@@ -48,10 +50,13 @@  newAcc a@(AliGo{..}) h@VerboseHit{..}   | otherwise = ( AliGo vhCM vhScaffold vhStrand [], ls )-  where ls = [ "//" | aliCM /= BS.empty && aliCM /= vhCM ] ++-             [ "CM: " `BS.append` vhCM | aliCM /= vhCM ] ++-             [ ">" `BS.append` vhScaffold `BS.append` "\n" | aliScaffold /= vhScaffold ] ++-             [ str `BS.append` " strand results:\n" | aliStrand /= vhStrand ]+  where ls = [ "//" | aliCM /= BS.empty && bCM ] +++             [ "CM: " `BS.append` vhCM | bCM ] +++             [ ">" `BS.append` vhScaffold `BS.append` "\n" | bCM || bSc] +++             [ str `BS.append` " strand results:\n" | bCM || bSc || bSt ]+        bCM = aliCM /= vhCM+        bSc = aliScaffold /= vhScaffold+        bSt = aliStrand /= vhStrand         str           | vhStrand == '+' = "Plus"           | vhStrand == '-' = "Minus"@@ -83,14 +88,19 @@   {--import Biobase.Infernal.VerboseHit.Import+--import Biobase.Infernal.VerboseHit.Import  test = do   xs <- fromFile "/home/choener/tmp/infernal-1.0.2/tutorial/tmp.res"   i <- enumList [xs] $ joinI $ eneeByteString stream2stream   ys <- run i+  {-   BS.putStrLn ys   print $ BS.length ys   print $ P.length $ BS.lines ys+  -}+  BS.putStrLn $ BS.take 1000 ys   return () -}++

@@ -41,12 +41,12 @@     case h' of       Nothing -> return (acc, [])       (Just h)-        | "##"      `isPrefixOf` h -> return (acc{aliAnnotation = aliAnnotation acc ++ [BS.drop 2 h]},[])-        | "CM: "    `isInfixOf`  h -> return (acc{aliCM = BS.copy $ BS.drop 4 h, aliAnnotation = []}, [])-        | ">"       `isInfixOf`  h -> return (acc{aliScaffold = BS.copy $ BS.drop 1 h, aliAnnotation = []}, [])-        | "  Plus"  `isInfixOf`  h -> return (acc{aliStrand = '+', aliAnnotation = []}, [])-        | "  Minus" `isInfixOf`  h -> return (acc{aliStrand = '-', aliAnnotation = []}, [])-        | " Query"  `isInfixOf`  h -> do+        | "##"   `isPrefixOf` h -> return (acc{aliAnnotation = aliAnnotation acc ++ [BS.drop 2 h]},[])+        | "CM: " `isPrefixOf` h -> return (acc{aliCM = BS.copy $ BS.drop 4 h, aliAnnotation = []}, [])+        | ">"    `isPrefixOf` h -> return (acc{aliScaffold = BS.copy $ BS.drop 1 h, aliAnnotation = []}, [])+        | "Plus strand results"  `isInfixOf` h -> return (acc{aliStrand = '+', aliAnnotation = []}, [])+        | "Minus strand results" `isInfixOf` h -> return (acc{aliStrand = '-', aliAnnotation = []}, [])+        | " Query" `isInfixOf` h -> do             x <- qs h (aliCM acc) (aliScaffold acc) (aliStrand acc) (aliAnnotation acc)             return (acc{aliAnnotation = []},x)         | otherwise -> return (acc,[])@@ -130,9 +130,10 @@  -- How to use this enumeratee. +{- test = do   i <- enumFile 8192 "test.vh" $ joinI $ eneeVerboseHit stream2list   xs <- run i   P.mapM_ (\x -> print x >> P.putStrLn "\n\n\n") xs   print $ P.length xs-+-}

@@ -1,5 +1,5 @@ name:           BiobaseInfernal-version:        0.5.4.0+version:        0.5.4.1 author:         Christian Hoener zu Siederdissen maintainer:     choener@tbi.univie.ac.at homepage:       http://www.tbi.univie.ac.at/~choener/@@ -22,13 +22,11 @@                 .                 .                 .-                With the BioHaskell library split, this package is officially-                back! And the package is not feature-complete yet, take the-                above as a will-include-soon list.+                Changes in 0.5.4.1                 .-                The taxonomy importer makes use of Iteratee.zip, hence the-                switch from Enumerator. (See the Biohaskell wiki pages for-                discussion on Iteratee/Enumerator).+                * fix-up for VH export+                .+                * half-baked CM type (not useful yet)  extra-source-files: @@ -42,12 +40,17 @@     either-unwrap,     iteratee,     transformers,-    tuple+    tuple,+    vector,+    PrimitiveArray    exposed-modules:     Biobase.Infernal     Biobase.Infernal.Clan     Biobase.Infernal.Clan.Import+    Biobase.Infernal.CM+    Biobase.Infernal.CM.Export+    Biobase.Infernal.CM.Import     Biobase.Infernal.TabularHit     Biobase.Infernal.TabularHit.Import     Biobase.Infernal.Taxonomy