cobot-io-0.1.5.2: test/FASTASpec.hs

{-# LANGUAGE OverloadedStrings #-}

module FASTASpec where

import Bio.FASTA              (fastaP, fromFile, toFile)
import Bio.FASTA.Parser       (parseOnly)
import Bio.FASTA.Type         (Fasta, FastaItem (..))
import Bio.Sequence           (bareSequence)
import Control.Monad.IO.Class (liftIO)
import Data.Text.IO           (readFile)
import Prelude                hiding (readFile, writeFile)
import System.Directory       (removeFile)
import Test.Hspec

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
        badRes `shouldBe` 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