biosff 0.2 → 0.3.1

raw patch · 4 files changed

+24/−11 lines, 4 filesPVP ok

version bump matches the API change (PVP)

API changes (from Hackage documentation)

Files

• biosff.cabal +3/−3
• src/Bio/Sequence/SFF.hs +7/−5
• src/Flower/Main.hs +10/−2
• src/Flower/Options.hs +4/−1

@@ -1,5 +1,5 @@ Name:                biosff-Version:             0.2+Version:             0.3.1 Synopsis:            Library and executables for working with SFF files Description:         The library contains the functionality for reading and writing 		     SFF files (sequencing data from 454 and Ion Torrent).  It duplicates@@ -23,8 +23,8 @@   Tag:      0.2  Library-  Exposed-modules: Bio.Sequence.SFF-  Other-modules:   Bio.Sequence.SFF_name, Bio.Sequence.SFF_filters+  Exposed-modules: Bio.Sequence.SFF, Bio.Sequence.SFF_filters+  Other-modules:   Bio.Sequence.SFF_name   Build-depends:   base >= 3 && < 5, biocore >= 0.1, binary, bytestring, array   Hs-Source-Dirs:  src   Ghc-Options:     -Wall

@@ -189,11 +189,13 @@ -- | Write 'ReadBlock's to a file handle. writeReads :: Handle -> Int -> [ReadBlock] -> IO Int32 writeReads _ _ [] = return 0-writeReads h i (r:rs) = do-  LBC.hPut h $ encode (RBI i r)-  c <- writeReads h i rs-  return $! (c+1)-+writeReads h i xs = go 0 xs+  where go c (r:rs) = do+          LBC.hPut h $ encode (RBI i r)+          let c' = c+1+          c' `seq` go c' rs+        go c [] = return c+         data RBI = RBI Int ReadBlock  -- | Wrapper for ReadBlocks since they need additional information

@@ -20,7 +20,8 @@ import qualified Data.ByteString.Lazy as L1  import Data.Array.Unboxed-import Data.Array.ST+import Data.Array.Unsafe -- unsafeFreeze is deprecated in D.A.ST+import Data.Array.ST hiding (unsafeFreeze) import Control.Monad.ST import Control.Monad.State @@ -52,7 +53,7 @@       on (O.fastq o)     (\h -> mapM_ (L1.hPut h . L1.concat . map toFastQ . tr . rs) =<< inp)       on (O.summarize o) (\h -> mapM_ (L1.hPut h . summarize . tr . rs) =<< inp)  -- should we trim?       on (O.filters o)   (\h -> mapM_ (L1.hPut h . sum_filters . rs) =<< inp)-      on (O.histogram o) (\h -> mapM_ (\(SFF c r) -> hPutStrLn h . showHist 9999 ["A","C","G","T"] . histogram (B.unpack $ flow c) . map flowgram . tr $ r) =<< inp)+      on (O.histogram o) (\h -> mapM_ (\(SFF c r) -> hPutStrLn h . (case O.plot o of Just str -> showPlot str 1000; Nothing -> showHist 9999)  ["A","C","G","T"] . histogram (B.unpack $ flow c) . map flowgram . tr $ r) =<< inp)       on (O.histpos o)   (\h -> mapM_ (\(SFF _ r) -> hPutStrLn h . showHist 549 [] . histpos 549 . tr $ r) =<< inp)       on (O.flowgram o)  (\h -> mapM_ (\(SFF c r) -> L1.hPut h . L1.fromChunks . intersperse (B.pack "\n") . concatMap (showread c) $ r) =<< inp) @@ -239,6 +240,13 @@   g' <- unsafeFreeze g   t' <- unsafeFreeze t   return [a',c',g',t']++-- ouput a histogram in gnuplot format+showPlot :: String -> Int -> [String] -> [Hist] -> String+showPlot cmds mx hd hs = "set style data lines\nset logscale y\nset xlabel 'Flow value'\nset ylabel 'Count'\nset xtic 1\n\n"++cmds+  ++"\n\nplot "+  ++ concat (intersperse "," [" '-' ti "++show c | c <- hd]) ++ "\n"+  ++ unlines [ unlines [showFFloat (Just 2) (fromIntegral sc/100::Double) ""++"\t"++show (h!sc) | sc <- [0..fromIntegral mx]] ++ "e\n" | h <- hs]  showHist :: Int -> [String] -> [Hist] -> String showHist mx hd hs = (if not (null hd) then concat (intersperse "\t" ("Score":hd)) ++ "\n" else "") ++

@@ -4,11 +4,12 @@  import System.Console.CmdArgs import Control.Monad (when)-import Data.Maybe (isJust)+import Data.Maybe (isJust, isNothing)  data Opts = Opts              { trimKey :: Bool             , trim    :: Bool+            , plot    :: Maybe String             , summarize :: Maybe FilePath             , filters :: Maybe FilePath             , info    :: Maybe FilePath@@ -38,6 +39,7 @@   , flowgram = def  &= help "Output flowgram information in tabular form" &= typFile &= name "F" &= optdef   , histogram = def &= help "Output histogram of flow values by nucleotide" &= typFile &= name "h" &= optdef   , histpos   = def &= help "Output histogram of flow values by flow cycle" &= typFile &= name "H" &= optdef+  , plot      = Nothing &= help "Output gnuplot script for visualization" &= opt ""   , text      = def &= help "Output SFF information as text (default)"    &= typFile &= name "T" &= optdef   , inputs  = def &= args &= typFile   } @@ -50,5 +52,6 @@   -- print o   let outs = filter isJust $ map ($o) [summarize,filters,info,fasta,fqual,fastq,flowgram,histogram,histpos,text]   when ((length $ filter (==Just "-") $ outs) > 1) $ error "If you specify more than one output format, you need to specify output files"+  when (isJust (plot o) && isNothing (histogram o)) $ error "Gnuplot output only supported for histograms"   let o' = if null outs then o { text = Just "-" } else o   return o'