cobot-io-0.1.3.9: test/FastaParserSpec.hs

{-# LANGUAGE OverloadedStrings #-}

module FastaParserSpec where

import           Bio.FASTA.Parser     (fastaP)
import           Bio.FASTA.Type       (Fasta, FastaItem (..))
import           Bio.Sequence         (bareSequence)
import           Data.Attoparsec.Text (endOfInput, parseOnly)
import           Data.Text            (Text)
import qualified Data.Text            as T
import           Test.Hspec

fastaParserSpec :: Spec
fastaParserSpec = describe "Fasta format parser." $ do
    emptyFasta
    onlyName
    oneSequence
    twoSequences
    sequenceWithDigit
    sequenceWithWrongName
    sequenceWithSpacesInName
    sequenceWithSeveralEndOfLine
    sequenceWithSeveralEndOfLineInSequence
    sequenceWithTabsInName
    sequenceWithTabsInSequence
    toughParserTests

emptyFasta :: Spec
emptyFasta = describe "emptyFasta" $ do
    it "correctly parses empty fasta" $ do
        let res = parseOnly fastaP ""
        res `shouldBe` Right []

onlyName :: Spec
onlyName = describe "onlyName" $ do
    it "correctly parses fasta without sequence" $ do
        let res = parseOnly fastaP ">3HMX:A|PDBID|CHAIN|SEQUENCE"
        res `shouldBe` Right [FastaItem "3HMX:A|PDBID|CHAIN|SEQUENCE" (bareSequence "")]

oneSequence :: Spec
oneSequence = describe "oneSequence" $ do
    it "correctly parses one correct sequence" $ do
        let res = parseOnly fastaP ">3HMX:A|PDBID|CHAIN|SEQUENCE\nIWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEDGITWTLDQSSE\nVLGSGKTLTIQVKEFGDAGQYTCHKGGEVLSHSLL\n"
        res `shouldBe` Right [FastaItem "3HMX:A|PDBID|CHAIN|SEQUENCE" (bareSequence "IWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEDGITWTLDQSSEVLGSGKTLTIQVKEFGDAGQYTCHKGGEVLSHSLL")]

twoSequences :: Spec
twoSequences = describe "twoSequences" $ do
    it "correctly parses two correct sequences" $ do
        let res = parseOnly fastaP ">3HMX:A|PDBID|CHAIN|SEQUENCE\nIWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEDGITWTLDQSSE\nVLGSGKTLTIQVKEFGDAGQYTCHKGGEVLSHSLL\n>7HMX:A|PDBID|CHAIN|SEQUENCE\nEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE\nVLGSGKTLTIQVKEFGDAGQYTCHKGGEVLSHSLL"
        res `shouldBe` Right [FastaItem "3HMX:A|PDBID|CHAIN|SEQUENCE" (bareSequence "IWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEDGITWTLDQSSEVLGSGKTLTIQVKEFGDAGQYTCHKGGEVLSHSLL"), FastaItem "7HMX:A|PDBID|CHAIN|SEQUENCE" (bareSequence "EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEVLGSGKTLTIQVKEFGDAGQYTCHKGGEVLSHSLL")]

sequenceWithDigit :: Spec
sequenceWithDigit = describe "sequenceWithDigit" $ do
    it "correctly parses incorrect sequence with digit" $ do
        let res = parseOnly fastaP ">123\nIWELKKDVYVVELDWYPDAPGEMVVLTCDTPEE4GITWTLDQSSE"
        res `shouldBe` Right [FastaItem "123" (bareSequence "")]

sequenceWithWrongName :: Spec
sequenceWithWrongName = describe "sequenceWithWrongName" $ do
    it "correctly parses incorrect sequence with wrong name" $ do
        let res = parseOnly fastaP "123\nIWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEGITWTLDQSSE"
        res `shouldBe` Right []

sequenceWithSpacesInName :: Spec
sequenceWithSpacesInName = describe "sequenceWithSpacesInName" $ do
    it "correctly parses sequence with spaces in name" $ do
        let res = parseOnly fastaP ">  this is my sequence   \nIWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEGITWTLDQSSE"
        res `shouldBe` Right [FastaItem "this is my sequence" (bareSequence "IWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEGITWTLDQSSE")]

sequenceWithSeveralEndOfLine :: Spec
sequenceWithSeveralEndOfLine = describe "sequenceWithSeveralEndOfLine" $ do
    it "correctly parses sequence with several \n after name" $ do
        let res = parseOnly fastaP ">this is my sequence\n\n\nIWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEGITWTLDQSSE"
        res `shouldBe` Right [FastaItem "this is my sequence" (bareSequence "IWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEGITWTLDQSSE")]

sequenceWithSeveralEndOfLineInSequence :: Spec
sequenceWithSeveralEndOfLineInSequence = describe "sequenceWithSeveralEndOfLineInSequence" $ do
    it "correctly parses sequence with several \n between sequence parts" $ do
        let res = parseOnly fastaP ">this is my sequence\nIWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEGITWTLDQSSE\n\n\nYYYYYYYYYYYYYYYYYYYYYYYY"
        res `shouldBe` Right [FastaItem "this is my sequence" (bareSequence "IWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEGITWTLDQSSEYYYYYYYYYYYYYYYYYYYYYYYY")]

sequenceWithTabsInName :: Spec
sequenceWithTabsInName = describe "sequenceWithTabsInName" $ do
    it "correctly parses sequence with tabs in name" $ do
        let res = parseOnly fastaP ">\tthis\tis\tmy\tsequence\t\t\nIWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEGITWTLDQSSE"
        res `shouldBe` Right [FastaItem "this\tis\tmy\tsequence" (bareSequence "IWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEGITWTLDQSSE")]

sequenceWithTabsInSequence :: Spec
sequenceWithTabsInSequence = describe "sequenceWithTabsInSequence" $ do
    it "correctly parses sequence with tabs between sequence parts" $ do
        let res = parseOnly fastaP ">this is my sequence\nIWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEGITWTLDQSSE\t\t\nYYYYYYYYYYYYYYYYYYYYYYYY\t\n"
        res `shouldBe` Right [FastaItem "this is my sequence" (bareSequence "IWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEGITWTLDQSSEYYYYYYYYYYYYYYYYYYYYYYYY")]

toughParserTests :: Spec
toughParserTests = describe "various parser tests" $ do
    it "correctly parses empty lines" $ checkParser correctTest1 (Right correctAnswer)
    it "correctly parses empty lines with spaces" $ checkParser correctTest2 (Right correctAnswer)
    it "correctly parses empty lines with tabs" $ checkParser correctTest3 (Right correctAnswer)
    it "correctly fails to parse a name without >" $ checkParser incorrectTest1 (Left "endOfInput")
    it "correctly fails to parse a new sequence at the same line" $ checkParser incorrectTest2 (Left "endOfInput")

correctTest1 :: Text
correctTest1 = T.unlines
  [ ">test1"
  , "ABCDEF"
  , "GHIJKL"
  , ""
  , ">test2"
  , "ABCDEF"
  ]

correctTest2 :: Text
correctTest2 = T.unlines
  [ ">test1"
  , "ABCDEF"
  , "GHIJKL"
  , " "
  , ">test2"
  , "ABCDEF"
  ]

correctTest3 :: Text
correctTest3 = T.unlines
  [ ">test1"
  , "ABCDEF"
  , "GHIJKL"
  , "\t"
  , ">test2"
  , "ABCDEF"
  ]

incorrectTest1 :: Text
incorrectTest1 = T.unlines
  [ "test1"
  , "ABCDEF"
  , "GHIJKL"
  , ">test2"
  , "ABCDEF"
  ]

incorrectTest2 :: Text
incorrectTest2 = T.unlines
  [ ">test1"
  , "ABCDEF"
  , "GHIJKL >test2"
  , "ABCDEF"
  ]

correctAnswer :: Fasta Char
correctAnswer = [FastaItem "test1" (bareSequence "ABCDEFGHIJKL"), FastaItem "test2" (bareSequence "ABCDEF")]

checkParser :: Text -> Either String (Fasta Char) -> Expectation
checkParser source expectation = parseOnly (fastaP <* endOfInput) source `shouldBe` expectation