diff --git a/hyraxAbif.cabal b/hyraxAbif.cabal --- a/hyraxAbif.cabal +++ b/hyraxAbif.cabal @@ -1,6 +1,6 @@ cabal-version: 2.2 name: hyraxAbif -version: 0.2.4.4 +version: 0.2.4.5 synopsis: Modules for parsing, generating and manipulating AB1 files. homepage: https://github.com/hyraxbio/hyraxAbif/#readme license: BSD-3-Clause OR Apache-2.0 @@ -17,7 +17,7 @@ <> . Any AB1 file conforming to the standard at should be supported. - . + . This library also support generating a minimal ABIF file from a FASTA input sequence. . A basic terminal application that can dump and generate AB1s is included. See @@ -44,13 +44,13 @@ , Examples.ReadAb1 build-depends: base >= 4.9.1.0 && < 5 , verset >= 0.0.1.8 && < 0.0.2.0 - , binary >= 0.8.9 && < 0.9 - , bytestring >= 0.11.3 && < 0.12 + , binary >= 0.8.9 && < 0.10 + , bytestring >= 0.11.3 && < 0.13 , directory >= 1.3.6 && < 1.4 - , filepath >= 1.4.2 && < 1.5 - , hscolour >= 1.24.4 && < 1.25 + , filepath >= 1.4.2 && < 1.6 + , hscolour >= 1.24.4 && < 1.26 , pretty-show >= 1.10 && < 1.11 - , text >= 1.2.5 && < 2.1 + , text >= 1.2.5 && < 2.2 default-language: Haskell2010 @@ -61,10 +61,10 @@ build-depends: base >= 4.9.1.0 && < 5 , hyraxAbif , verset >= 0.0.1.8 && < 0.0.2.0 - , text >= 1.2.5 && < 2.1 - , bytestring >= 0.11.3 && < 0.12 + , text >= 1.2.5 && < 2.2 + , bytestring >= 0.11.3 && < 0.13 , pretty-show >= 1.10 && < 1.11 - , hscolour >= 1.24.4 && < 1.25 + , hscolour >= 1.24.4 && < 1.26 default-language: Haskell2010 test-suite hyraxAbif-test @@ -74,10 +74,10 @@ build-depends: base >= 4.9.1.0 && < 5 , hyraxAbif , verset >= 0.0.1.8 && < 0.0.2.0 - , text >= 1.2.5 && < 2.1 - , bytestring >= 0.11.3 && < 0.12 - , binary >= 0.8.9 && < 0.9 - , hedgehog + , text >= 1.2.5 && < 2.2 + , bytestring >= 0.11.3 && < 0.13 + , binary >= 0.8.9 && < 0.10 + , hedgehog >= 1.2 && < 1.5 other-modules: AbifTests , FastaTests , Generators diff --git a/test/AbifTests.hs b/test/AbifTests.hs --- a/test/AbifTests.hs +++ b/test/AbifTests.hs @@ -32,10 +32,10 @@ nucs === n2 - + -- | Test that an ab1 (write, read, write, read) results in the original data prop_roundtrip :: Property -prop_roundtrip = property $ do +prop_roundtrip = property $ do fdata <- forAll $ genFastaData 2 let fasta = TxtE.encodeUtf8 $ toFastaTxt False fdata @@ -47,8 +47,8 @@ ab1Read2 <- evalEither $ H.getAbif ab1Written2 ab1Read1 === ab1Read2 - - + + -- | Generate an ab1 from a fasta and then confirm that the generated peaks of the -- chromatogram match the original fasta. -- Note that we are only testing the simple/single fasta case (i.e. no mixes) @@ -93,15 +93,17 @@ case reverse $ Lst.sortOn snd [('A', a), ('C', c), ('G', g), ('T', t)] of ((n,_) : _) -> n _ -> '?' - + readDataPeaks :: H.Abif -> Int -> [Int] -> Either Text [Int] readDataPeaks ab1 dirNum peaks = case readShorts <$> getDirEntry ab1 "DATA" dirNum of Left e -> Left e Right vs -> let valsAtPeaks = atMay vs <$> peaks in - maybeToRight "peaks" $ sequenceA valsAtPeaks - + case sequenceA valsAtPeaks of + Nothing -> Left "Could not read peaks" + Just vs' -> Right vs' + getDirEntry :: H.Abif -> Text -> Int -> Either Text BSL.ByteString getDirEntry ab1 dirName dirNum = diff --git a/test/Generators.hs b/test/Generators.hs --- a/test/Generators.hs +++ b/test/Generators.hs @@ -13,21 +13,21 @@ -- | Generate random set of nucleotides, including ambiguous ones nucsGen :: GenT Identity Text -nucsGen = - Gen.text (Range.linear 1 1000) (Gen.element "ACGTMRWSYKVHDBNX") +nucsGen = + Gen.text (Range.linear 1 1000) (Gen.element ("ACGTMRWSYKVHDBNX" :: [Char])) -- | Generate random set of nucleotides, no ambiguous ones nucsNoIupacGen :: (Monad m) => PropertyT m Text -nucsNoIupacGen = - forAll $ Gen.text (Range.linear 1 1000) (Gen.element "ACGT") +nucsNoIupacGen = + forAll $ Gen.text (Range.linear 1 1000) (Gen.element ("ACGT" :: [Char])) - + -- | Generate data to construct a fasta "file" -- List of tuples of (name, lines of reads) -- maxReads controls the max number in the list genFastaData :: Int -> Gen [(Int, [Text])] -genFastaData maxReads = +genFastaData maxReads = Gen.list (Range.linear 1 maxReads) $ (,) <$> Gen.int (Range.linear 1 9999) <*> Gen.list (Range.linear 1 15) nucsGen @@ -36,7 +36,7 @@ toFastaTxt :: Bool -> [(Int, [Text])] -> Text toFastaTxt addSpaces is = Txt.intercalate "\n" $ toRead <$> is - + where toRead (weight, ls) = let sp = if addSpaces then " " else "" in @@ -47,7 +47,7 @@ toFasta :: [(Int, [Text])] -> [F.Fasta] toFasta is = toRead <$> is - + where toRead (weight, ls) = F.Fasta (show weight) $ Txt.concat ls diff --git a/test/Tests.hs b/test/Tests.hs --- a/test/Tests.hs +++ b/test/Tests.hs @@ -2,6 +2,7 @@ import Verset import qualified System.IO as IO +import System.Exit (exitFailure) import qualified AbifTests import qualified FastaTests @@ -11,9 +12,9 @@ IO.hSetBuffering IO.stdout IO.LineBuffering IO.hSetBuffering IO.stderr IO.LineBuffering - results <- sequence [ AbifTests.tests - , FastaTests.tests - ] + results <- sequenceA [ AbifTests.tests + , FastaTests.tests + ] if and results then pass