bioinformatics-toolkit 0.4.0 → 0.4.1

raw patch · 5 files changed

+20/−18 lines, 5 filesdep ~HsHTSLibdep ~conduit

Dependency ranges changed: HsHTSLib, conduit

Files

• bioinformatics-toolkit.cabal +3/−3
• src/Bio/ChIPSeq.hs +1/−1
• src/Bio/Data/Bam.hs +6/−6
• src/Bio/Data/Bed.hs +4/−4
• tests/Tests/Bam.hs +6/−4

@@ -1,5 +1,5 @@ name:                bioinformatics-toolkit-version:             0.4.0+version:             0.4.1 synopsis:            A collection of bioinformatics tools description:         A collection of bioinformatics tools license:             MIT@@ -58,12 +58,12 @@     , bytestring-lexing >=0.5     , case-insensitive     , clustering-    , conduit-combinators+    , conduit >=1.3.0     , containers >=0.5     , data-ordlist     , data-default-class     , double-conversion-    , HsHTSLib+    , HsHTSLib >=1.3.2.3     , http-conduit >=2.1.8     , hexpat     , IntervalMap >=0.5.0.0

@@ -241,7 +241,7 @@             -> Int   -- ^ radius             -> Int   -- ^ cutoff             -> Source m BED-peakCluster peaks r th = mergeBedWith mergeFn peaks' $= filterC g+peakCluster peaks r th = mergeBedWith mergeFn peaks' .| filterC g   where     peaks' = map f peaks     f b = let chr = chrom b

@@ -2,7 +2,7 @@ module Bio.Data.Bam     ( Bam     , HeaderState-    , runBam+    , withBamFile     , readBam     , writeBam     , bamToBed@@ -13,11 +13,11 @@ import           Bio.HTS import           Bio.HTS.Types             (Bam, FileHeader (..)) import           Conduit-import           Control.Monad.State (get, lift)+import           Control.Monad.Reader (ask, lift)  -- | Convert bam record to bed record. Unmapped reads will be discarded. bamToBed :: Conduit Bam HeaderState BED-bamToBed = mapMC bamToBed1 =$= concatC+bamToBed = mapMC bamToBed1 .| concatC {-# INLINE bamToBed #-}  -- | Convert pairedend bam file to bed. the bam file must be sorted by names,@@ -29,9 +29,9 @@         Nothing -> return ()         Just b' -> do             leftover b'-            sortOrd <- getSortOrder <$> lift get+            sortOrd <- getSortOrder <$> lift ask             case sortOrd of-                Queryname -> loopBedPE =$= concatC+                Queryname -> loopBedPE .| concatC                 _ -> error "Bam file must be sorted by NAME."   where     loopBedPE :: Conduit Bam HeaderState (Maybe (BED, BED))@@ -54,7 +54,7 @@  bamToBed1 :: Bam -> HeaderState (Maybe BED) bamToBed1 bam = do-    BamHeader hdr <- lift get+    BamHeader hdr <- lift ask     return $ (\chr -> BED chr start end nm sc strand) <$> getChr hdr bam   where     start = fromIntegral $ position bam

@@ -498,7 +498,7 @@  -- | Non-streaming version. hReadBed' :: (BEDLike b, MonadIO m) => Handle -> m [b]-hReadBed' h = hReadBed h $$ sinkList+hReadBed' h = runConduit $ hReadBed h .| sinkList {-# INLINE hReadBed' #-}  -- | Read records from a bed file in a streaming fashion.@@ -510,7 +510,7 @@  -- | Non-streaming version. readBed' :: (BEDLike b, MonadIO m) => FilePath -> m [b]-readBed' fl = readBed fl $$ sinkList+readBed' fl = runConduit $ readBed fl .| sinkList {-# INLINE readBed' #-}  hWriteBed :: (BEDLike b, MonadIO m) => Handle -> Sink b m ()@@ -522,7 +522,7 @@ {-# INLINE hWriteBed #-}  hWriteBed' :: (BEDLike b, MonadIO m) => Handle -> [b] -> m ()-hWriteBed' handle beds = yieldMany beds $$ hWriteBed handle+hWriteBed' handle beds = runConduit $ yieldMany beds .| hWriteBed handle {-# INLINE hWriteBed' #-}  writeBed :: (BEDLike b, MonadIO m) => FilePath -> Sink b m ()@@ -547,7 +547,7 @@ {-# INLINE fetchSeq #-}  fetchSeq' :: (BioSeq DNA a, MonadIO m) => Genome -> [BED] -> m [Either String (DNA a)]-fetchSeq' g beds = yieldMany beds $= fetchSeq g $$ sinkList+fetchSeq' g beds = runConduit $ yieldMany beds .| fetchSeq g .| sinkList {-# INLINE fetchSeq' #-}  -- | Identify motif binding sites

@@ -24,21 +24,23 @@ bamIOTest = do     goldenVsFile "BAM Read/Write Test" input output io   where-    io = runBam $ readBam input $$ writeBam output+    io = withBamFile input $ \h -> runConduit $ readBam h .| writeBam output     input = "tests/data/example.bam"     output = "tests/data/example_copy.bam"  bamToBedTest :: Assertion bamToBedTest = do     bed <- readBed' "tests/data/example.bed"-    bed' <- runBam $ readBam "tests/data/example.bam" =$= bamToBed $$ sinkList+    bed' <- withBamFile "tests/data/example.bam" $ \h ->+        runConduit $ readBam h .| bamToBed .| sinkList     (bed == bed') @? "bamToBedTest"  sortedBamToBedPETest :: Assertion sortedBamToBedPETest = do     bedpe <- readBedPE "tests/data/pairedend.bedpe"-    bedpe' <- runBam $ readBam "tests/data/pairedend.bam" =$= sortedBamToBedPE =$=-        mapC (\(x,y) -> (convert x, convert y)) $$ sinkList+    bedpe' <- withBamFile "tests/data/pairedend.bam" $ \h -> runConduit $+        readBam h .| sortedBamToBedPE .|+        mapC (\(x,y) -> (convert x, convert y)) .| sinkList     forM_ (zip bedpe bedpe') $ \(b1, b2) -> (b1 == b2 || b1 == swap b2) @? show (b1,b2)   where     readBedPE fl = do