cobot-io 0.1.5.3 → 0.1.5.4

raw patch · 7 files changed

+43/−9 lines, 7 filesPVP: major bump suggested

API removals or changes: PVP suggests a major version bump

API changes (from Hackage documentation)

Files

• ChangeLog.md +3/−0
• cobot-io.cabal +6/−3
• src/Bio/FASTA.hs +1/−1
• src/Bio/FASTA/Parser.hs +7/−1
• test/FASTA/order10.fasta +2/−0
• test/FASTA/order9.fasta +8/−0
• test/FASTASpec.hs +16/−4

@@ -2,6 +2,9 @@  ## [Unreleased] +## [0.1.5.4] - 2024-05-16+- Fix Fasta parser for unknown modifications on the end of the line.+ ## [0.1.5.3] - 2023-12-08 - Update tests and dependencies. 

@@ -5,7 +5,7 @@ -- see: https://github.com/sol/hpack  name:           cobot-io-version:        0.1.5.3+version:        0.1.5.4 synopsis:       Biological data file formats and IO description:    Please see the README on GitHub at <https://github.com/biocad/cobot-io#readme> category:       Bio@@ -22,8 +22,9 @@  || ==9.0.2  || ==9.2.8  || ==9.4.8- || ==9.6.3- || ==9.8.1+ || ==9.6.5+ || ==9.8.2+ || ==9.10.1  extra-source-files:     README.md@@ -35,6 +36,7 @@     test/GB/pIntA-TRBV.gb     test/FASTA/correct.fasta     test/FASTA/order1.fasta+    test/FASTA/order10.fasta     test/FASTA/order2.fasta     test/FASTA/order3.fasta     test/FASTA/order4.fasta@@ -42,6 +44,7 @@     test/FASTA/order6.fasta     test/FASTA/order7.fasta     test/FASTA/order8.fasta+    test/FASTA/order9.fasta     test/MAE/Capri.mae     test/MAE/docking_1.mae     test/MAE/docking_1_2.mae

@@ -28,7 +28,7 @@  -- | Reads 'FastaSequence' from given file. ---fromFile :: (MonadFail m, MonadIO m) => FilePath -> m (Fasta Char)+fromFile :: (MonadFail m, MonadIO m, ParsableFastaToken a) => FilePath -> m (Fasta a) fromFile f = liftIO (readFile f) >>= either (fail . errorBundlePretty) pure . parse fastaP (takeBaseName f)  -- | Writes 'FastaSequence' to file.

@@ -36,8 +36,14 @@ parseOnly :: Parsec Void Text a -> Text -> Either String a parseOnly p s = first errorBundlePretty $ parse p "input.fasta" s +-- Using 'hspace1' instead of just 'space1' because our 'fastaLine' parser+-- expects each line to end with line-ending or end of file. But if 'sc' consumes end-of-line,+-- 'lexeme' in 'unknownP' also will and 'fastaLine' will not know that line has ended and will+-- expect more symbols.+--+-- 'hspace1' consumes only "horizontal" space, leaving line-ending for 'fastaLine'. sc :: Parser ()-sc = L.space space1 empty empty+sc = L.space hspace1 empty empty  lexeme :: Parser a -> Parser a lexeme = L.lexeme sc

@@ -0,0 +1,2 @@+>mol1+[FAM]ACGT[UNK][

@@ -0,0 +1,8 @@+>mol1+[FAM]ACGT[UNK]++>mol2+[HEX]ACCGT++>mol3+[HEX]ACGTCA[UNK]

@@ -10,9 +10,9 @@ import           System.Directory       (removeFile) import           Test.Hspec -import Bio.FASTA        (fastaP, fromFile, toFile)+import Bio.FASTA        (ParsableFastaToken, fastaP, fromFile, toFile) import Bio.FASTA.Parser (parseOnly)-import Bio.FASTA.Type   (Fasta, FastaItem (..))+import Bio.FASTA.Type   (Fasta, FastaItem (..), ModItem (..), Modification (..)) import Bio.Sequence     (bareSequence)  correctFasta1 :: Fasta Char@@ -45,6 +45,16 @@ badFasta8 :: Either String (Fasta Char) badFasta8 = Left "input.fasta:21:5:\n   |\n21 | CMV + enhMCK + prcTnT-2\r\n   |     ^^\nunexpected \"+ \"\nexpecting end of input, end of line, or letter\n" +correctFasta9 :: Fasta ModItem+correctFasta9 =+  [ FastaItem "mol1" $ bareSequence [Mod (Unknown "[FAM]"),Letter 'A',Letter 'C',Letter 'G',Letter 'T',Mod (Unknown "[UNK]")]+  , FastaItem "mol2" $ bareSequence [Mod (Unknown "[HEX]"),Letter 'A',Letter 'C',Letter 'C',Letter 'G',Letter 'T']+  , FastaItem "mol3" $ bareSequence [Mod (Unknown "[HEX]"),Letter 'A',Letter 'C',Letter 'G',Letter 'T',Letter 'C',Letter 'A',Mod (Unknown "[UNK]")]+  ]++badFasta10 :: Either String (Fasta ModItem)+badFasta10 = Left "input.fasta:2:16:\n|\n2|[FAM]ACGT[UNK][\n|^\nunexpectednewline\nexpectingmodificationname\n"+ fastaSpec :: Spec fastaSpec = describe "Fasta files parser" $ do     describe "fromFile" $ do@@ -56,19 +66,21 @@       parseBadFile "test/FASTA/order6.fasta" badFasta6       parseBadFile "test/FASTA/order7.fasta" badFasta7       parseBadFile "test/FASTA/order8.fasta" badFasta8+      parseFile "test/FASTA/order9.fasta" correctFasta9+      parseBadFile "test/FASTA/order10.fasta" badFasta10      describe "toFile" $ do       writeFile "test/FASTA/input.fasta" correctFasta5       writeFile "test/FASTA/input.fasta" correctFasta1       writeFile "test/FASTA/input.fasta" correctFasta3 -parseFile :: FilePath -> Fasta Char -> Spec+parseFile :: (Show a, Eq a, ParsableFastaToken a) => FilePath -> Fasta a -> Spec parseFile path cf =     it ("correctly parses good fasta from file " <> path) $ do         fasta <- fromFile path         fasta `shouldBe` cf -parseBadFile :: FilePath -> Either String (Fasta Char) -> Spec+parseBadFile :: (Show a, Eq a, ParsableFastaToken a) => FilePath -> Either String (Fasta a) -> Spec parseBadFile path cf =     it ("correctly parses bad fasta from file " <> path) $ do         res <- liftIO (readFile path)