FastaSpec.hs

{- |
Module      :  ELynx.Import.Sequence.FastaSpec
Copyright   :  (c) Dominik Schrempf 2020
License     :  GPL-3.0-or-later

Maintainer  :  dominik.schrempf@gmail.com
Stability   :  unstable
Portability :  portable

Creation date: Fri Jan 18 09:54:38 2019.

-}

module ELynx.Import.Sequence.FastaSpec
  ( spec
  )
where

import           Data.Either
import           Test.Hspec

import           ELynx.Data.Alphabet.Alphabet
import qualified ELynx.Data.Sequence.Alignment as M
import           ELynx.Import.Sequence.Fasta
import           ELynx.Tools

fastaNucleotideFN :: FilePath
fastaNucleotideFN = "data/Nucleotide.fasta"

fastaNucleotideIUPACFN :: FilePath
fastaNucleotideIUPACFN = "data/NucleotideIUPAC.fasta"

fastaErroneousFN :: FilePath
fastaErroneousFN = "data/Erroneous.fasta"

fastaAminoAcidFN :: FilePath
fastaAminoAcidFN = "data/AminoAcid.fasta"

spec :: Spec
spec = describe "fastaFileAlignment" $ do
  it "parses a fasta file with nucleotide sequences with equal length" $ do
    a <-
      either error id
      .   M.fromSequences
      <$> parseFileWith (fasta DNA) fastaNucleotideFN
    M.nSequences a `shouldBe` 3
    M.length a `shouldBe` 40

  it "parses a fasta file with nucleotide IUPAC sequences with equal length"
    $ do
        a <-
          either error id
          .   M.fromSequences
          <$> parseFileWith (fasta DNAI) fastaNucleotideIUPACFN
        M.nSequences a `shouldBe` 3
        M.length a `shouldBe` 40

  it "should not parse erroneous files" $ do
    ea <- runParserOnFile (fasta DNAI) fastaErroneousFN
    ea `shouldSatisfy` isLeft

  it "parses a fasta file with amino acid sequences with equal length" $ do
    a <-
      either error id
      .   M.fromSequences
      <$> parseFileWith (fasta Protein) fastaAminoAcidFN
    M.nSequences a `shouldBe` 2
    M.length a `shouldBe` 237

  it "should not parse erroneous files" $ do
    a <- runParserOnFile (fasta ProteinI) fastaErroneousFN
    a `shouldSatisfy` isLeft