packages feed

flower 0.7 → 0.7.2

raw patch · 5 files changed

+30/−74 lines, 5 filesdep ~bio

Dependency ranges changed: bio

Files

flower.cabal view
@@ -1,5 +1,5 @@ Name:           flower-Version:        0.7+Version:        0.7.2 License:        GPL Cabal-Version:  >= 1.6 Author:         Ketil Malde@@ -8,20 +8,21 @@ Category:       Bioinformatics Synopsis:       Analyze 454 flowgrams  (.SFF files) Description:    flower - FLOWgram ExtractoR tools+		.+		This is now obsolete, please install the biosff library +		(which includes the 'flower' exectuable) instead.                 .                 The flower executable reads files in SFF-format and produces various output,                  including sequences with quality, or flowgram data in tabular format.  By default,                 it outputs a textual representation of the data in the SFF-file, much like                 'sffinfo' from Roche does.                 .-                The fselect executable extracts reads from SFF-files, generating a new-                SFF-file with a subset of the reads based on various criteria.-                .-                Sometimes SFF files will appear to be corrupted, with all-zero blocks in the-                file. The frecover program ignores these and tries to resync with the file after an -                invalid region.  This was likely a one-time bug in the 454 software, so this program-                is probably not so useful any more.-+                The flowselect executable extracts reads from SFF-files, generating a new+                SFF-file with a subset of the reads based on various quality criteria.+		.+		The flowt program removes (artificial) duplicates from SFF files.  It's currently a work+		in progress, but included if you'd like to play with it.  It's faster than other approaches +		(e.g. CD-HIT), and ought to be more sensitive and specific, but this needs to be proven. HomePage:       http://biohaskell.org/Applications/Flower -- Source-Repository: http//malde.org/~ketil/biohaskell/flower Build-Type:     Simple@@ -44,18 +45,6 @@     Build-Depends:  bio >= 0.4.9, random, base >= 3 && < 5     Extensions:     ExistentialQuantification -Executable     frecover-    Main-Is:        FRecover.hs-    Hs-Source-Dirs: src-    Build-Depends:  bio >= 0.4.9, base >= 3 && < 5-    Ghc-Options:    -Wall--Executable     frename-    Main-Is:        FRename.hs-    Hs-Source-Dirs: src-    Build-Depends:  bio >= 0.4.9, base >= 3 && < 5, bytestring >= 0.9.1-    Ghc-Options:    -Wall- Executable     flowt     Main-Is:        Flowt.hs     Hs-Source-Dirs: src@@ -63,5 +52,5 @@       Ghc-Options:     -Wall -fno-warn-unused-do-bind     else       Ghc-Options:     -Wall-    Build-Depends:  bio >= 0.4.9, base >= 3 && < 5, cmdargs >= 0.5, containers, bytestring >= 0.9.1+    Build-Depends:  bio > 0.4.9, base >= 3 && < 5, cmdargs >= 0.5, containers, bytestring >= 0.9.1     Extensions:     DeriveDataTypeable
− src/FRecover.hs 
@@ -1,9 +0,0 @@--module Main where-import Bio.Sequence.SFF-import System.Environment (getArgs)--main :: IO ()-main = mapM_ recoverFile =<< getArgs-  where recoverFile f = writeSFF (f++"_recovered") =<< recoverSFF f-
− src/FRename.hs 
@@ -1,30 +0,0 @@--{-|-  Rename reads in .SFF files to avoid name clashes.-  Apparently, reads with the same name crashes Newbler, and is-  in any case a bad idea.  This ensures uniqueness by appending a serial number to each read name in a set of files.--}--module Main where--import Bio.Sequence.SFF-import System.Environment (getArgs)-import qualified Data.ByteString.Char8 as B--main :: IO ()-main = do-  fs <- getArgs-  if null fs then putStrLn "Usage: frename file1.sff [file2.sff ...]"-    else renameSFFs fs-         -renameSFFs :: [FilePath] -> IO ()-renameSFFs = go 0 -  where go _ [] = return ()-        go current (f:fs) = do-          (SFF h rs) <- readSFF f-          writeSFF ("r_"++f) (SFF h $ renameFrom current rs)-          go (current+num_reads h) fs-        renameFrom i rs = zipWith update [i..] rs-          where update j r = let h = read_header r-                                 rn = B.concat [read_name h, B.pack "_", B.pack (show j)]-                             in r { read_header = h { name_length = fromIntegral $ B.length rn, read_name = rn }}
src/Flowt.hs view
@@ -29,8 +29,10 @@ splitRes (Then x rs) = let (ys,e) = splitRes rs in (x:ys,e) splitRes (EndWith e) = ([],e) +-- trim :: ReadBlock -> ReadBlock+-- trim = id -- trimFromTo 4 10000 <- this trims to last base called position! (use trimKey?) trim :: ReadBlock -> ReadBlock-trim = id -- trimFromTo 4 10000 <- this trims to last base called position! (use trimKey?)+trim rb = let rh = read_header rb in trimFromTo (clip_qual_left rh) (clip_qual_right rh) rb  data Options = O { thresh :: Double                  , fplen  :: Int@@ -79,9 +81,9 @@ gensum :: String -> IntMap [ReadBlock] -> IO () gensum f ds = write $ unlines $ map showcluster $ M.assocs ds   where write = if f == "-" then putStrLn else writeFile f-        showcluster (k,v) = let a = averageflow v +        showcluster (k,v) = let a = map fromIntegral $ flowgram $ trim $ head v -- averageflow v                              in printf "%16x" k++":\t" ++ show (length v) ++ unwords (map (BC.unpack . read_name . read_header) v) ++ "\n" ++ -                               unlines [let fs = flowgram (trim x) in printf "%6.1f " (dist a $ map fromIntegral fs) ++ concatMap (printf "%3d ") fs | x <- v]+                               unlines [let fs = flowgram (trim x) in printf "%8.1f " (dist a $ map fromIntegral fs) ++ concatMap (printf "%3d ") fs | x <- v]          filter_unique :: Options -> FingerPrints -> [ReadBlock] -> ResultList filter_unique opts dups = go M.empty @@ -101,12 +103,6 @@       go _ dup [] = dup   return $ go S.empty S.empty $ map (fingerprint $ fplen opts) rs -{--mkbf sff = do -  SFF _ rs <- readSFF sff-  return $ snd $ mkFilters 1000000 $ map fingerprint rs--}- -- | Calculating a fingerprint - basically just a hash of the first 20 elements of the flow_index.  On 64 bits, it is  --   possible to use more, this is a sensitivity/specificity tradeoff. fingerprint :: Int -> ReadBlock -> Int@@ -129,9 +125,14 @@ matches :: ReadBlock -> ReadBlock -> Double matches old new = let f = map fromIntegral . flowgram . trim in dist (f old) (f new) +-- Flowgram distance, not including zeroes at end of flowgram dist :: [Double] -> [Double] -> Double-dist = (.) sum . zipWith (\x y -> (6*(x-y)/(x+y+4))^(2::Int))-+dist as bs = go (reverse as) (reverse bs)+  where go (x:xs) (y:ys) = +          if x==0 || y==0 then go xs ys +          else sum $ zipWith (\i j  -> (6*(i-j)/(i+j+4))^(2::Int)) (x:xs) (y:ys)+        go _ _ = 0+         averageflow :: [ReadBlock] -> [Double] averageflow = go . map (map fromIntegral . flowgram . trim)   where go [] = []
src/Print.hs view
@@ -18,7 +18,7 @@            else putInt' y     where putInt' x =  case x `divMod` 1000 of              (0,r) -> fromByteString (ints!r)-             (a,r) -> putInt a `append` putInt3 r+             (a,r) -> putInt a `append` putInt3_0 r  -- zero padded ints @@ -30,10 +30,15 @@ putInt3 x | x<1000 = fromByteString (int3s!x)           | otherwise = fromByteString (pack "xxx") -ints, int2s, int3s :: Array Int ByteString+putInt3_0 :: Int -> Builder+putInt3_0 x | x<1000 = fromByteString (int3s0!x)+            | otherwise = fromByteString (pack "xxx")++ints, int2s, int3s, int3s0 :: Array Int ByteString ints  = listArray (0,999) [pack (show i) | i <- [0..999::Int]] int2s = listArray (0,99) (map (pack . ('0':) . show) [0..9::Int]++[pack (show i) | i <- [10..99::Int]]) int3s = listArray (0,999) (map (pack . (' ':) . (' ':) . show) [0..9::Int] ++ map (pack . (' ':) . show ) [10..99::Int] ++ map (pack . show) [100..999::Int])+int3s0 = listArray (0,999) (map (pack . ('0':) . ('0':) . show) [0..9::Int] ++ map (pack . ('0':) . show ) [10..99::Int] ++ map (pack . show) [100..999::Int])  putDate :: Int -> Int -> Int -> Builder putDate y m d = mconcat [putInt y, dash, putInt2 m, dash, putInt2 d]