BiobaseInfernal 0.5.3.1 → 0.5.4.0

raw patch · 5 files changed

+40/−26 lines, 5 filesPVP: major bump suggested

API removals or changes: PVP suggests a major version bump

API changes (from Hackage documentation)

Files

• Biobase/Infernal/VerboseHit.hs +11/−8
• Biobase/Infernal/VerboseHit/Export.hs +6/−4
• Biobase/Infernal/VerboseHit/Import.hs +12/−10
• Biobase/Infernal/VerboseHit/Internal.hs +4/−3
• BiobaseInfernal.cabal +7/−1

@@ -1,10 +1,12 @@ {-# LANGUAGE RecordWildCards #-} --- | Provides a datatype for cmsearch verbose output.+-- | Provides a datatype for cmsearch verbose output. The Import/Export system+-- now allows for primitive annotations using "##" as the first two characters.+-- Annotations are only accepted for individual hits.  module Biobase.Infernal.VerboseHit where -import qualified Data.ByteString.Char8 as BS+import Data.ByteString.Char8 as BS import Text.Printf  @@ -14,17 +16,18 @@ 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      :: BS.ByteString  -- ^ the CM for this alignment+  , 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 :: BS.ByteString -- ^ scaffold, chromosome, ... (the name of the sequence, not the sequence data!)-  , vhWuss :: BS.ByteString -- ^ fancy secondary structure annotation using wuss notation-  , vhConsensus :: BS.ByteString -- ^ query consensus (upper: highly, lower: weak/no)-  , vhScoring   :: BS.ByteString -- ^ represents where positive and negative scores come from-  , vhSequence :: BS.ByteString -- ^ the target sequence which aligns to the model+  , 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

@@ -27,7 +27,7 @@ -- TOOD How to append the last line "//" to the finished stream, if at least -- one element was printed? -eneeByteString :: Monad m => Enumeratee [VerboseHit] BS.ByteString m a+eneeByteString :: Monad m => Enumeratee [VerboseHit] ByteString m a eneeByteString = eneeByteStrings ><> mapChunks BS.concat  -- | This transformer keeps a 1-1 relationship between each 'VerboseHit' and@@ -35,17 +35,19 @@ -- individual 'VerboseHit's are to be annotated.  eneeByteStrings :: Monad m => Enumeratee [VerboseHit] [ByteString] m a-eneeByteStrings = unfoldConvStream f (AliGo BS.empty BS.empty '?') where+eneeByteStrings = unfoldConvStream f (AliGo BS.empty BS.empty '?' []) where   f acc = do     h <- I.head     let na = newAcc acc h-    return (fst na , return . BS.unlines $ snd na ++ [showVerboseHit h])+    return ( fst na+           , return . BS.unlines $ snd na ++ P.map (append "## ") (vhAnnotation h)  ++ [showVerboseHit h]+           )  -- | Given the current state "a" and verbose hit "h", determine if any state -- switches have to be emitted.  newAcc a@(AliGo{..}) h@VerboseHit{..}-  | otherwise = ( AliGo vhCM vhScaffold vhStrand, ls )+  | 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 ] ++

@@ -35,25 +35,26 @@ -- accumulator to keep track of the current CM, scaffold and strand.  eneeVerboseHit :: (Functor m, Monad m) => Enumeratee BS.ByteString [VerboseHit] m a-eneeVerboseHit = enumLinesBS ><> I.filter (not . BS.null) ><> unfoldConvStream f (AliGo BS.empty BS.empty '?') where+eneeVerboseHit = enumLinesBS ><> I.filter (not . BS.null) ><> unfoldConvStream f (AliGo BS.empty BS.empty '?' []) where   f acc = do     h' <- tryHead     case h' of       Nothing -> return (acc, [])       (Just h)-        | "CM: "    `BS.isInfixOf` h -> return (acc{aliCM = BS.copy $ BS.drop 4 h}, [])-        | ">"       `BS.isInfixOf` h -> return (acc{aliScaffold = BS.copy $ BS.drop 1 h}, [])-        | "  Plus"  `BS.isInfixOf` h -> return (acc{aliStrand = '+'}, [])-        | "  Minus" `BS.isInfixOf` h -> return (acc{aliStrand = '-'}, [])-        | " Query"  `BS.isInfixOf` h -> do-            x <- qs h (aliCM acc) (aliScaffold acc) (aliStrand acc)-            return (acc,x)+        | "##"      `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+            x <- qs h (aliCM acc) (aliScaffold acc) (aliStrand acc) (aliAnnotation acc)+            return (acc{aliAnnotation = []},x)         | otherwise -> return (acc,[])  -- | Parses one CM query result. -qs :: Monad m => BS.ByteString -> BS.ByteString -> BS.ByteString -> Char -> Iteratee [BS.ByteString] m [VerboseHit]-qs query cm scaf pm = do+qs :: Monad m => ByteString -> ByteString -> ByteString -> Char -> [ByteString] -> Iteratee [ByteString] m [VerboseHit]+qs query cm scaf pm anno = do   let q = fromRight . parseOnly qt $ query   s <- I.head >>= return . fromRight . parseOnly sepg   l <- fourLines $ sel4 q@@ -71,6 +72,7 @@     , vhConsensus = cpy $ l!!1     , vhScoring = cpy $ l!!2     , vhSequence = cpy $ l!!3+    , vhAnnotation = anno     }   where     cpy = BS.copy . BS.concat

@@ -3,15 +3,16 @@  module Biobase.Infernal.VerboseHit.Internal where -import qualified Data.ByteString.Char8 as BS+import Data.ByteString.Char8 as BS    -- | State for import and export functions  data AliGo = AliGo-  { aliCM :: BS.ByteString-  , aliScaffold :: BS.ByteString+  { aliCM :: ByteString+  , aliScaffold :: ByteString   , aliStrand :: Char+  , aliAnnotation :: [ByteString]   } deriving (Show) 

@@ -1,5 +1,5 @@ name:           BiobaseInfernal-version:        0.5.3.1+version:        0.5.4.0 author:         Christian Hoener zu Siederdissen maintainer:     choener@tbi.univie.ac.at homepage:       http://www.tbi.univie.ac.at/~choener/@@ -15,6 +15,12 @@                 Provides import and export facilities for Infernal/Rfam data                 formats. We include Stockholm, CM, verbose Infernal results,                 and tabulated Infernal results. Some small tools are included.+                .+                The VerboseHit format is slightly extended to allow simple+                annotations. This extension should be backward-compatible with+                standard-compliant parsers.+                .+                .                 .                 With the BioHaskell library split, this package is officially                 back! And the package is not feature-complete yet, take the