hyraxAbif 0.2.3.5 → 0.2.3.7
raw patch · 9 files changed
+183/−22 lines, 9 filesdep ~pretty-showPVP: major bump suggested
API removals or changes: PVP suggests a major version bump
Dependency ranges changed: pretty-show
API changes (from Hackage documentation)
- Examples.ReadAb1: addComment :: IO ()
+ Examples.ReadAb1: readAbif :: IO ()
+ Hyrax.Abif.Generate: complementNucleotides :: Text -> Text
Files
- README.md +8/−0
- hyraxAbif.cabal +2/−2
- src/Examples/ReadAb1.hs +2/−2
- src/Hyrax/Abif.hs +6/−0
- src/Hyrax/Abif/Fasta.hs +2/−0
- src/Hyrax/Abif/Generate.hs +98/−11
- src/Hyrax/Abif/Read.hs +33/−5
- src/Hyrax/Abif/Write.hs +18/−2
- test/AbifTests.hs +14/−0
README.md view
@@ -138,6 +138,14 @@ *Note that the reads do not need to be the same length.* ++### Reverse reads++A weighted FASTA can represent a reverse read. To do this add a `R` suffix to the weight.+The data you enter should be entered as if it was a forward read. This data will be complemented+and reversed before writing to the ABIF++ --- #### Example FASTA - single file
hyraxAbif.cabal view
@@ -1,6 +1,6 @@ cabal-version: 2.0 name: hyraxAbif-version: 0.2.3.5+version: 0.2.3.7 synopsis: Modules for parsing, generating and manipulating AB1 files. homepage: https://github.com/hyraxbio/hyraxAbif/#readme license: BSD3@@ -60,7 +60,7 @@ , protolude >= 0.2.2 && < 0.2.3 , text >= 1.2.3.0 && < 1.2.4.0 , bytestring >= 0.10.8.2 && < 0.10.9.0- , pretty-show >= 1.6.16 && < 1.7.0+ , pretty-show >= 1.6.16 && < 1.9.0 , hscolour >= 1.24.4 && < 1.25.0 default-language: Haskell2010
src/Examples/ReadAb1.hs view
@@ -17,8 +17,8 @@ import qualified Hyrax.Abif.Read as H -- | Read and print a ABIF file-addComment :: IO ()-addComment = do+readAbif :: IO ()+readAbif = do abif' <- H.readAbif "example.ab1" case abif' of
src/Hyrax/Abif.hs view
@@ -18,6 +18,7 @@ * <http://www6.appliedbiosystems.com/support/software_community/ABIF_File_Format.pdf The ABIF spec> -}+{-! SECTION< abif_module !-} module Hyrax.Abif ( Abif (..) , Header (..)@@ -29,8 +30,10 @@ import Protolude import qualified Data.ByteString.Lazy as BSL+{-! SECTION> abif_module !-} +{-! SECTION< abif_type !-} -- | A single ABIF data Abif = Abif { aHeader :: !Header , aRootDir :: !Directory@@ -59,8 +62,10 @@ , dData :: !BSL.ByteString -- ^ The entry's data , dDataDebug :: ![Text] -- ^ Optinal debug data, populated by 'Hyrax.Abif.Read.getDebug' when a ABIF is parsed } deriving (Show, Eq)+{-! SECTION> abif_type !-} +{-! SECTION< abif_elemType !-} -- | Type of the elements in a directory entry. See the spec for details on each type if required. data ElemType = ElemUnknown | ElemCustom@@ -122,3 +127,4 @@ describeElemType 384 = (ElemCompressedDataUnsupported, "Compressed Data (*unsupported*)") describeElemType 1023 = (ElemRoot, "root") describeElemType v = if v >= 1024 then (ElemCustom, "custom") else (ElemUnknown, "unknown")+{-! SECTION> abif_elemType !-}
src/Hyrax/Abif/Fasta.hs view
@@ -19,6 +19,7 @@ import Protolude import qualified Data.Text as Txt +{-! SECTION< fasta !-} -- | FASTA data data Fasta = Fasta { fastaName :: !Text -- ^ Name , fastaRead :: !Text -- ^ Data@@ -48,3 +49,4 @@ Left "Expecting read" go [] (Just name) read acc = Right $ Fasta (Txt.strip name) read : acc+{-! SECTION> fasta !-}
src/Hyrax/Abif/Generate.hs view
@@ -66,6 +66,20 @@ <<docs/eg_multi_mix.png>> ++== Reverse reads++A weighted FASTA can represent a reverse read. To do this add a `R` suffix to the weight.+The data you enter should be entered as if it was a forward read. This data will be complemented+and reversed before writing to the ABIF++E.g.++@+> 1R+ACAG+@+ See README.md for additional details and examples -} module Hyrax.Abif.Generate@@ -74,6 +88,7 @@ , readWeightedFasta , iupac , unIupac+ , complementNucleotides ) where import Protolude@@ -112,6 +127,7 @@ traverse_ (\(name, ab1) -> BS.writeFile (dest </> Txt.unpack name <> ".ab1") $ BSL.toStrict ab1) ab1s +{-! SECTION< gen_generateAb1_fn !-} -- | Create the 'ByteString' data for an AB1 given the data from a weighted FASTA (see 'readWeightedFasta') generateAb1 :: (Text, [(Double, Text)]) -> BSL.ByteString generateAb1 (fName, sourceFasta) = @@ -120,14 +136,17 @@ valsPerBase = trValsPerBase tr generatedFastaLen = (Txt.length $ trFasta tr) +{-! SECTION< gen_generateAb1_peak !-} -- The point that is the peak of the trace, i.e. mid point of trace for a single base midPeek = valsPerBase `div` 2 -- Get the peak locations for all bases peakLocations = take generatedFastaLen [midPeek, valsPerBase + midPeek..]+{-! SECTION> gen_generateAb1_peak !-} -- Sample name (from the FASTA name) sampleName = fst . Txt.breakOn "_" $ fName +{-! SECTION< gen_generateAb1_abif !-} -- Create the ABIF directories dirs = [ mkData 9 $ trData09G tr -- G , mkData 10 $ trData10A tr -- A@@ -149,33 +168,48 @@ , aRootDir = mkRoot , aDirs = dirs }+{-! SECTION> gen_generateAb1_abif !-} in -- Generate the data B.runPut (putAbif abif)+{-! SECTION> gen_generateAb1_fn !-} +{-! SECTION< gen_generateTraceData !-}+{-! SECTION< gen_generateTraceData_type !-} -- | Generate the traces for the AB1 from the parsed weighted FASTA generateTraceData :: [(Double, Text)] -> TraceData generateTraceData weighted =+{-! SECTION> gen_generateTraceData_type !-} let+{-! SECTION< gen_generateTraceData_weighted !-} weightedNucs' = (\(w, ns) -> (w,) . unIupac <$> Txt.unpack ns) <$> weighted weightedNucs = Lst.transpose weightedNucs'+{-! SECTION> gen_generateTraceData_weighted !-} - -- Values for a base that was present. This defines the shape of the chromatogram curve, and defines the number of values per base+{-! SECTION< gen_generateTraceData_curve !-}+ -- Values for a base that was present. This defines the shape of the chromatogram curve,+ -- and defines the number of values per base curve = [0, 0, 128, 512, 1024, 1024, 512, 128, 0, 0] valsPerBase = length curve+{-! SECTION> gen_generateTraceData_curve !-} +{-! SECTION< gen_generateTraceData_traces !-} -- Create the G, A, T and C traces data09G = concat $ getWeightedTrace curve 'G' <$> weightedNucs data10A = concat $ getWeightedTrace curve 'A' <$> weightedNucs data11T = concat $ getWeightedTrace curve 'T' <$> weightedNucs data12C = concat $ getWeightedTrace curve 'C' <$> weightedNucs+{-! SECTION> gen_generateTraceData_traces !-} +{-! SECTION< gen_generateTraceData_fasta !-} -- Create fasta sequence for the trace fastaSeq = concat <$> (snd <<$>> weightedNucs) fasta = Txt.pack $ iupac fastaSeq+{-! SECTION> gen_generateTraceData_fasta !-} in +{-! SECTION< gen_generateTraceData_ret !-} TraceData { trData09G = data09G , trData10A = data10A , trData11T = data11T@@ -183,8 +217,10 @@ , trFasta = fasta , trValsPerBase = valsPerBase }+{-! SECTION> gen_generateTraceData_ret !-} where+{-! SECTION< gen_generateTraceData_getWeightedTrace !-} getWeightedTrace :: [Int] -> Char -> [(Double, [Char])] -> [Int16] getWeightedTrace curve nuc ws = let@@ -194,10 +230,13 @@ wave = floor . (score *) . fromIntegral <$> curve in wave+{-! SECTION> gen_generateTraceData_getWeightedTrace !-}+{-! SECTION> gen_generateTraceData !-} --- | Read a weighted FASTA file. See the module comments for the expected format.--- See the module documentation for details on the format of the weighted FASTA +-- | Read a weighted FASTA file. See the module documentation for details on the format of the weighted FASTA +-- Reads with a weight followed by an `R` are reverse reads, and the AB1 generated will contain the complemeted+-- sequence. -- -- e.g. weighted FASTA --@@ -214,14 +253,15 @@ -- The result data has the type -- -- @--- ('Text', [('Double', 'Text')])--- ^ ^ ^--- | | |--- file name -------------+ | +---- read --- | --- +---- weight+-- [('Double', 'Text')]+-- ^ ^+-- | |+-- | +---- read +-- | +-- +---- weight -- @ --+{-! SECTION< gen_readWeightedFasta !-} readWeightedFasta :: ByteString -> Either Text [(Double, Text)] readWeightedFasta fastaData = case parseFasta $ TxtE.decodeUtf8 fastaData of@@ -236,14 +276,36 @@ Right r -> Right r readWeighted :: Fasta -> Either Text (Double, Text)- readWeighted (Fasta hdr dta) =+ readWeighted (Fasta hdr' dta) =+ let (processNucs, hdr) =+ -- If there is a 'R' suffix, then generate a reverse sequence+ -- Which means complement each nucleotide and then reverse the string+ if Txt.isSuffixOf "R" hdr'+ then (Txt.reverse . complementNucleotides, Txt.strip . Txt.dropEnd 1 $ hdr')+ else (identity, hdr')+ in+ case (readMaybe . Txt.unpack $ hdr :: Maybe Double) of- Just weight -> Right (min 1 . max 0 $ weight, Txt.strip dta)+ Just weight -> Right (min 1 . max 0 $ weight, processNucs $ Txt.strip dta) Nothing -> Left $ "Invalid header reading, expecting numeric weight, got: " <> hdr+{-! SECTION> gen_readWeightedFasta !-} +{-! SECTION< gen_readWeightedFastas !-} -- | Read all FASTA files in a directory+--+-- The result data has the type+-- +-- @+-- [ ('Text', [('Double', 'Text')]) ]+-- ^ ^ ^+-- | | |+-- file name -------------+ | +---- read +-- | +-- +---- weight+-- @+-- readWeightedFastas :: FilePath -> IO (Either Text [(Text, [(Double, Text)])]) readWeightedFastas source = do files <- filter (Txt.isSuffixOf ".fasta" . Txt.pack) <$> getFiles source@@ -253,6 +315,7 @@ case sequenceA $ readWeightedFasta <$> contents of Left e -> pure . Left $ e Right rs -> pure . Right $ zip names rs+{-! SECTION> gen_readWeightedFastas !-} -- | Find all files in a directory@@ -262,8 +325,11 @@ filterM Dir.doesFileExist entries +{-! SECTION< gen_unIupac_fn !-} -- | Convert a IUPAC ambiguity code to the set of nucleotides it represents+{-! SECTION< gen_unIupac_type !-} unIupac :: Char -> [Char]+{-! SECTION> gen_unIupac_type !-} unIupac c = case c of 'T' -> "T"@@ -286,6 +352,7 @@ 'X' -> "GATC" _ -> ""+{-! SECTION> gen_unIupac_fn !-} -- | Given a set of nucleotides get the IUPAC ambiguity code@@ -318,3 +385,23 @@ (False, True, True, True ) -> 'B' (True, True, True, True ) -> 'N' _ -> '_'+++{-! SECTION< gen_complement !-}+-- | Return the complement of a nucelotide string+complementNucleotides :: Text -> Text+complementNucleotides ns =+ let+ un = unIupac <$> Txt.unpack ns+ comp = complementNuc <<$>> un+ iu = iupac comp+ in+ Txt.pack iu++ where+ complementNuc 'A' = 'T'+ complementNuc 'G' = 'C'+ complementNuc 'T' = 'A'+ complementNuc 'C' = 'G'+ complementNuc x = x+{-! SECTION> gen_complement !-}
src/Hyrax/Abif/Read.hs view
@@ -47,11 +47,14 @@ import Hyrax.Abif +{-! SECTION< read_readAbif !-} -- | Read and parse an AB1 file readAbif :: FilePath -> IO (Either Text Abif) readAbif path = getAbif <$> BSL.readFile path+{-! SECTION> read_readAbif !-} +{-! SECTION< read_getAbif !-} -- | Parse an AB1 from a 'ByteString' getAbif :: BSL.ByteString -> Either Text Abif getAbif bs = do@@ -63,23 +66,31 @@ ds <- case B.runGetOrFail (getDirectories bs [] $ dElemNum rootDir) dirBytes of Right (_, _, x) -> pure x- Left (_, _, e) -> Left ("Error reading " <> show (dElemNum rootDir) <> " directories (at " <> show (dDataOffset rootDir) <> "): " <> Txt.pack e)+ Left (_, _, e) -> Left ("Error reading "+ <> show (dElemNum rootDir)+ <> " directories (at " <> show (dDataOffset rootDir) <> "): "+ <> Txt.pack e+ ) pure $ Abif header rootDir ds+{-! SECTION> read_getAbif !-} +{-! SECTION< read_clear !-} -- | Removes all data from the ABIF's directories clearAbif :: Abif -> Abif clearAbif a = a { aRootDir = clear $ aRootDir a- , aDirs = clear <$> aDirs a- }+ , aDirs = clear <$> aDirs a+ } -- | Removes all data from a directory entry. This will probably only be useful when trying to show an ABIF value clear :: Directory -> Directory clear d = d { dData = "" }+{-! SECTION> read_clear !-} +{-! SECTION< read_getDebug !-} -- | Populate the directory entry with debug data (into 'dDataDebug'). -- This is done for selected types only, e.g. for strings so that printing the structure will display -- readable/meaningfull info@@ -99,6 +110,7 @@ if dDataSize d <= 4 then d { dDataDebug = [TxtE.decodeUtf8 . BSL.toStrict . BSL.take (fromIntegral $ dDataSize d - 1) $ dData d] } else d { dDataDebug = [B.runGet (lbl . getCString $ dDataSize d) bsAtOffset] }+{-! SECTION> read_getDebug !-} y -> -- For non-array entries@@ -175,6 +187,7 @@ pure (c:cs) +{-! SECTION< read_getStrings !-} -- | Parse a 'ElemPString' getPString :: B.Get Text getPString = do@@ -186,23 +199,29 @@ getCString :: Int -> B.Get Text getCString sz = TxtE.decodeUtf8 <$> B.getByteString (sz - 1)+{-! SECTION> read_getStrings !-} +{-! SECTION< read_getHeader !-} -- | Parse the ABIF 'Header' getHeader :: B.Get Header getHeader = Header <$> (TxtE.decodeUtf8 <$> B.getByteString 4) <*> (fromIntegral <$> B.getInt16be)+{-! SECTION> read_getHeader !-} +{-! SECTION< read_getRoot !-} -- | Parse the root ('Header' and 'Directory') getRoot :: BSL.ByteString -> B.Get (Header, Directory) getRoot bs = do h <- getHeader rd <- getDirectory bs pure (h, rd)+{-! SECTION> read_getRoot !-} +{-! SECTION< read_getDirectory !-} -- | Parse a single 'Directory' entry and read its data getDirectory :: BSL.ByteString -> B.Get Directory getDirectory bs = do@@ -221,7 +240,14 @@ then pure $ BSL.take (fromIntegral dataSize) offsetDataBytes else case B.runGetOrFail (B.getLazyByteString $ fromIntegral dataSize) $ BSL.drop (fromIntegral dataOffset) bs of Right (_, _, x) -> pure x- Left (_, _, e) -> fail $ "error reading data (" <> show dataSize <> " bytes starting at " <> show dataOffset <> ") for directory entry '" <> Txt.unpack tagName <> "': " <> e+ Left (_, _, e) -> fail $ "error reading data ("+ <> show dataSize+ <> " bytes starting at "+ <> show dataOffset+ <> ") for directory entry '"+ <> Txt.unpack tagName+ <> "': "+ <> e let (elemType, elemCode) = describeElemType typeCode pure Directory { dTagName = tagName @@ -236,8 +262,10 @@ , dData = dataBytes , dDataDebug = [] } +{-! SECTION> read_getDirectory !-} +{-! SECTION< read_getDirectories !-} -- | Parse all the directoy entries getDirectories :: BSL.ByteString -> [Directory] -> Int -> B.Get [Directory] getDirectories _ acc 0 = pure acc@@ -246,4 +274,4 @@ B.skip 4 -- Skip the reserved field getDirectories bs (acc <> [d]) (more - 1) -+{-! SECTION> read_getDirectories !-}
src/Hyrax/Abif/Write.hs view
@@ -44,10 +44,13 @@ import Hyrax.Abif +{-! SECTION< write_base !-} -- | Used to specify the base order for the FWO directry entry, see 'mkBaseOrder' data Base = BaseA | BaseC | BaseG | BaseT+{-! SECTION> write_base !-} +{-! SECTION< write_create !-} -- | Write an 'Abif' to a 'ByteString' createAbifBytes :: Abif -> BSL.ByteString createAbifBytes ab1 =@@ -59,19 +62,21 @@ writeAbif destPath ab1 = do let b = createAbifBytes ab1 BS.writeFile destPath $ BSL.toStrict b+{-! SECTION> write_create !-} +{-! SECTION< write_putAbif !-} -- | Create the 'Abif' using "Data.Binary" putAbif :: Abif -> B.Put putAbif (Abif header root dirs) = do- -- Data starts at offset 128- let startDataOffset = 128 -- Total data size let dataSize = foldl' (\acc i -> if i > 4 then acc + i else acc) 0 $ dDataSize <$> dirs -- Write the header putHeader header + -- Data starts at offset 128+ let startDataOffset = 128 -- Write the root directory entry putDirectory (startDataOffset + dataSize) $ root { dDataSize = 28 * length dirs , dElemNum = length dirs@@ -91,8 +96,10 @@ pure $ if dDataSize dir > 4 then offset + dDataSize dir else offset+{-! SECTION> write_putAbif !-} +{-! SECTION< write_strings !-} -- | Write 'Text' putTextStr :: Text -> B.Put putTextStr t = B.putByteString $ TxtE.encodeUtf8 t@@ -103,15 +110,19 @@ putPStr t = do B.putInt8 . fromIntegral $ Txt.length t B.putByteString $ TxtE.encodeUtf8 t+{-! SECTION> write_strings !-} +{-! SECTION< write_putHeader !-} -- | Write a 'Header' putHeader :: Header -> B.Put putHeader h = do putTextStr $ hName h B.putInt16be . fromIntegral $ hVersion h+{-! SECTION> write_putHeader !-} +{-! SECTION< write_putDirectory !-} -- | Write a 'Directory' putDirectory :: Int -> Directory -> B.Put putDirectory dirOffset d = do@@ -129,6 +140,7 @@ else B.putLazyByteString . BSL.take 4 $ dData d <> "\0\0\0\0" B.putInt32be 0 -- reserved / datahandle+{-! SECTION> write_putDirectory !-} -- | Create a 'Header'@@ -192,6 +204,7 @@ , dDataSize = fromIntegral (BSL.length sampleName) } +{-! SECTION< write_mk !-} -- | Create a base order (FWO_) 'Directory' entry data mkBaseOrder :: Base -> Base -> Base -> Base -> Directory mkBaseOrder w x y z =@@ -229,6 +242,7 @@ , dData = B.runPut $ B.putInt16be lane , dDataDebug = [] }+{-! SECTION> write_mk !-} -- | Create a called bases (PBAS) 'Directory' entry and data@@ -328,7 +342,9 @@ , dElemNum = length ds } +{-! SECTION< write_addDirectory !-} -- | Add a directory to an 'Abif' addDirectory :: Abif -> Directory -> Abif addDirectory abif dir = abif { aDirs = aDirs abif <> [dir] }+{-! SECTION> write_addDirectory !-}
test/AbifTests.hs view
@@ -20,6 +20,19 @@ import qualified Hyrax.Abif.Generate as H import Generators ++-- | Test that complementing nucleotides is reversible+prop_complementNucs :: Property+prop_complementNucs = property $ do+ nucs' <- forAll $ nucsGen+ let nucs = Txt.replace "X" "N" nucs'++ let n1 = H.complementNucleotides nucs+ let n2 = Txt.replace "X" "N" $ H.complementNucleotides n1++ nucs === n2++ -- | Test that an ab1 (write, read, write, read) results in the original data prop_roundtrip :: Property prop_roundtrip = property $ do @@ -112,6 +125,7 @@ c <- getFn cs <- readArray getFn pure (c:cs)+ tests :: IO Bool