gact (empty) → 0.1

raw patch · 3 files changed

+65/−0 lines, 3 filesdep +basedep +biopsldep +bytestringsetup-changed

Dependencies added: base, biopsl, bytestring, cmdargs, hashable, unordered-containers

Files

• Setup.hs +2/−0
• gact.cabal +14/−0
• src/GACT.hs +49/−0

@@ -0,0 +1,2 @@+import Distribution.Simple+main = defaultMain

@@ -0,0 +1,14 @@+Name: gact+Version:       0.1+License:       GPL+Cabal-Version: >= 1.6+Build-Type:    Simple+Category:      Bioinformatics+Author:        Ketil Malde+Maintainer:    Ketil Malde <ketil@malde.org>+Synopsis:      General Alignment Clustering Tool++Executable gact+    Hs-Source-Dirs:  src+    Main-Is:         GACT.hs+    Build-Depends:   base >= 4 && < 5, biopsl >= 0.2, cmdargs, hashable, unordered-containers, bytestring

@@ -0,0 +1,49 @@+{-# Language PackageImports #-}++module Main where++import "biopsl" Bio.Alignment.PSL+-- import Bio.Sequence (SeqData)+import qualified Data.HashSet as S+import Data.List (partition,foldl',sortBy)+import qualified Data.ByteString.Lazy.Char8 as B+import Data.Hashable++import Options++main :: IO ()+main = do+  opts <- getArgs+  pss <- mapM readPSL $ files opts+  mapM_ (if long_output opts then print_cluster else print_list) . cluster_sl qname tname . concat $ pss++print_list :: (S.HashSet B.ByteString, [PSL]) -> IO ()+print_list (s,_) = B.putStrLn . B.unwords . S.toList $ s++print_cluster :: (S.HashSet B.ByteString, [PSL]) -> IO ()+print_cluster (s,b) = do +  B.putStrLn . B.unwords . S.toList $ s+  B.putStrLn $ unparsePSL $ sortOn tname $ sortOn tstarts $ b++sortOn :: Ord a1 => (a -> a1) -> [a] -> [a]+sortOn f = sortBy (\x y -> compare (f x) (f y))++cluster_sl  :: (Hashable a, Ord a) => (b->a) -> (b->a) -> [b] -> [(S.HashSet a,[b])]+cluster_sl f1 f2 = foldl' csl []+    where csl cs b = +              -- can be short circuited for more performance+              let (acs,tmp)   = partition (S.member (f1 b) . fst) cs+                  (bcs,rest)  = partition (S.member (f2 b) . fst) tmp+              in case (acs,bcs) of +                   ([(ao,as)],[(bo,bs)]) -> (S.union ao bo,b:as++bs):rest+                   ([(ao,as)],[])        -> (S.insert (f2 b) ao, b:as):rest+                   ([],[(bo,bs)])        -> (S.insert (f1 b) bo, b:bs):rest+                   ([],[])               -> (S.fromList [f1 b,f2 b],[b]):rest+                   _                     -> error "Grave mistake"++select :: (t -> Bool) -> [t] -> ([t],[t])+select p = go []+  where go acc (x:xs) | p x = ([x],acc++xs)+                      | otherwise = go (x:acc) xs+        go acc [] = ([],acc)+