BiobaseInfernal 0.5.3.0 → 0.5.3.1

raw patch · 2 files changed

+31/−7 lines, 2 filesPVP ok

version bump matches the API change (PVP)

API changes (from Hackage documentation)

Files

• Biobase/Infernal/VerboseHit/Import.hs +30/−6
• BiobaseInfernal.cabal +1/−1

@@ -12,6 +12,7 @@   ) where  import Control.Applicative+import Control.Monad as M import Data.Attoparsec as A import Data.Attoparsec.Char8 as A8 import Data.Attoparsec.Iteratee as EAP@@ -84,16 +85,38 @@  -- | Parses multiple four-line elements. -fourLines to = do+fourLinesOld to = do   I.dropWhile BS.null   ls <- joinI $ I.take 4 stream2stream   let ws = BS.length . BS.takeWhile isSpace . P.head $ ls   let cs = BS.length . BS.dropWhile isSpace . P.head $ ls   let xs = P.map (BS.take cs . BS.drop ws) ls-  if (to == (read . BS.unpack . P.last . BS.words . P.last $ ls))+  if (P.length ls /= 4) ||+     ("-" == (P.last . BS.words . P.last $ ls)) ||+     (to == (read . BS.unpack . P.last . BS.words . P.last $ ls))   then return . P.map (:[]) $ xs   else fourLines to >>= return . (P.zipWith (:) xs) +fourLines to = do+  I.dropWhile BS.null+  mp <- I.peek+  case mp of+    Nothing -> return $ P.replicate 4 []+    Just p+      | "//" `isInfixOf` p+      || "CM" `isInfixOf` p+      || "Query" `isInfixOf` p+      || ">" `isPrefixOf` p+      || "strand" `isInfixOf` p+      || "#" `isPrefixOf` p+      -> return $ P.replicate 4 []+      | otherwise+      -> do ls <- joinI $ I.take 4 stream2stream+            let ws = BS.length . BS.takeWhile isSpace . P.head $ ls+            let cs = BS.length . BS.dropWhile isSpace . P.head $ ls+            let xs = P.map (BS.take cs . BS.drop ws) ls+            fourLines to >>= return . (P.zipWith (:) xs)+ -- | Convenience function: read all results into a single list.  fromFile :: FilePath -> IO [VerboseHit]@@ -101,12 +124,13 @@   i <- enumFile 8192 fp . joinI $ eneeVerboseHit stream2list   run i -{- How to use this enumeratee.  +-- How to use this enumeratee.+ test = do-  i <- enumFile 8192 "/home/choener/tmp/infernal-1.0.2/tutorial/tmp.res" $ joinI $ eneeVerboseHit stream2list+  i <- enumFile 8192 "test.vh" $ joinI $ eneeVerboseHit stream2list   xs <- run i-  print xs+  P.mapM_ (\x -> print x >> P.putStrLn "\n\n\n") xs   print $ P.length xs--}+

@@ -1,5 +1,5 @@ name:           BiobaseInfernal-version:        0.5.3.0+version:        0.5.3.1 author:         Christian Hoener zu Siederdissen maintainer:     choener@tbi.univie.ac.at homepage:       http://www.tbi.univie.ac.at/~choener/