cobot-io-0.1.5.4: test/FASTASpec.hs

{-# LANGUAGE OverloadedStrings #-}

module FASTASpec where

import           Control.Monad.IO.Class (liftIO)
import           Data.Bifunctor         (first)
import qualified Data.Text              as T
import           Data.Text.IO           (readFile)
import           Prelude                hiding (readFile, writeFile)
import           System.Directory       (removeFile)
import           Test.Hspec

import Bio.FASTA        (ParsableFastaToken, fastaP, fromFile, toFile)
import Bio.FASTA.Parser (parseOnly)
import Bio.FASTA.Type   (Fasta, FastaItem (..), ModItem (..), Modification (..))
import Bio.Sequence     (bareSequence)

correctFasta1 :: Fasta Char
correctFasta1 = [ FastaItem "3HMX:A|PDBID|CHAIN|SEQUENCE" (bareSequence "IWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEDGITWTLDQSSEVLGSGKTLTIQVKEFGDAGQYTCHKGGEVLSHSLL")
                , FastaItem "7HMX:A|PDBID|CHAIN|SEQUENCE" (bareSequence "EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEVLGSGKTLTIQVKEFGDAGQYTCHKGGEVLSHSLL")
                , FastaItem "With_spaces" (bareSequence "MDFFDLDIEIKQERLPAECSLNSPLNYSLSAQLTDRMTPRTENVRRQRERMDFFDLDIEIKQERLPAECSLNSPLNYSLSAQLTDRMTPRTENVRRQRERMDFFDLDIEIKQERLPAECSLNSPLNYSLSAQLTDRMTPRTENVRRQRER")
                , FastaItem "Empty_ha_ha_ha" (bareSequence "")
                ]

badFasta2 :: Either String (Fasta Char)
badFasta2 = Left "input.fasta:2:5:\n  |\n2 | ACGT....TCG\r\n  |     ^^\nunexpected \"..\"\nexpecting end of input, end of line, or letter\n"


correctFasta3 :: Fasta Char
correctFasta3 = [ FastaItem "N-His-E4Orf6-7-R2(115)" (bareSequence "TGATGGTGATGGTGATGcatGTGGTAAACTCGACTTTCACTTTTCTCTATCACTGATAGGGAGTGGTAAACTCGACTTTCACTTTTCTCTATCACTGATAGGGAaacagtcagcc")
                ]

badFasta4 :: Either String (Fasta Char)
badFasta4 = Left "input.fasta:5:8:\n  |\n5 | HindIII-BFP_F                \r\n  |        ^^\nunexpected \"-B\"\nexpecting end of input, end of line, or letter\n"

correctFasta5 :: Fasta Char
correctFasta5 = [FastaItem "qCHO49 F" (bareSequence "TGGAGAGATGGCTCGAGGTTqCHORTGGTTGCTGGGAATTGAACTC")]

badFasta6 :: Either String (Fasta Char)
badFasta6 = Left "input.fasta:22:1:\n   |\n22 | sPA-LoxP-NheI_R           \r\n   | ^\nunexpected 's'\nexpecting '>' or end of input\n"

badFasta7 :: Either String (Fasta Char)
badFasta7 = Left "input.fasta:2:1:\n  |\n2 | 5\8217-CTTCAAGAGAGAGACCTGCGT-3\8217\r\n  | ^\nunexpected '5'\nexpecting '>', end of input, end of line, or sequence\n"

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
      parseFile "test/FASTA/order1.fasta" correctFasta1
      parseBadFile "test/FASTA/order2.fasta" badFasta2
      parseFile "test/FASTA/order3.fasta" correctFasta3
      parseBadFile "test/FASTA/order4.fasta" badFasta4
      parseFile  "test/FASTA/order5.fasta" correctFasta5
      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 :: (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 :: (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)
        let badRes = parseOnly fastaP res
        noSpaces badRes `shouldBe` noSpaces cf

writeFile :: FilePath -> Fasta Char -> Spec
writeFile path cf =
    it "correctly write fasta into file" $ do
        toFile cf path
        fasta <- fromFile path
        removeFile path
        fasta `shouldBe` cf

-- | megaparsec >= 9.3 added more spaces to error messages, so that our old ones do not match.
noSpaces :: Either String a -> Either String a
noSpaces = first $ T.unpack . T.replace " " "" . T.pack