cobot-io-0.1.5.3: 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        (fastaP, fromFile, toFile)
import Bio.FASTA.Parser (parseOnly)
import Bio.FASTA.Type   (Fasta, FastaItem (..))
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"

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

    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 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 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