version 0.1.5.4 Fix Fasta parser with modification (#74)

Author: maksbotan

ChangeLog.md

@@ -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.
 

package.yaml

@@ -1,5 +1,5 @@
 name:                cobot-io
-version:             0.1.5.3
+version:             0.1.5.4
 github:              "biocad/cobot-io"
 license:             BSD3
 category:            Bio

src/Bio/FASTA.hs

@@ -28,7 +28,7 @@ import Bio.FASTA.Writer (WritableFastaToken (..), fastaToText)
 
 -- | 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.

src/Bio/FASTA/Parser.hs

@@ -36,8 +36,14 @@ type Parser = Parsec Void Text
 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

test/FASTA/order10.fasta

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

test/FASTA/order9.fasta

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

test/FASTASpec.hs

@@ -10,9 +10,9 @@ import           Prelude                hiding (readFile, writeFile)
 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 @@ badFasta7 = Left "input.fasta:2:1:\n  |\n2 | 5\8217-CTTCAAGAGAGAGACCTGCGT-3\8217
 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 @@ fastaSpec = describe "Fasta files parser" $ do
       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)