ClustalParser-1.2.3: test-suite/ClustalParserSpec.hs

module ClustalParserSpec (spec) where

import Bio.ClustalParser 
import Test.Hspec
import Test.Hspec.QuickCheck
import Text.Parsec.Error
import Text.Parsec.Pos
import Text.ParserCombinators.Parsec.Error
import qualified Data.Text as T

spec :: Spec
spec = do
  describe "Clustal W Parser" $ do
    context "Parsing RNAalifold input" $ do
      it "Returns ClustalAlignment type" $ do
        (parseClustalAlignment clustalExample) `shouldBe` (Right clustalResult)
    context "Parsing invalid input" $ do
      it "Returns ParseError" $ do
        (parseClustalAlignment "invalid input") `shouldBe` Left clustalParseError
  describe "Structural Clustal Parser" $ do
    context "Parsing Structural Clustal input" $ do
      it "Returns StructuralClustalAlignment type" $ do
        (parseStructuralClustalAlignment structuralClustalExample) `shouldBe` Right structuralClustalResult
    context "Parsing invalid input" $ do
      it "Returns ParseError" $ do
        (parseStructuralClustalAlignment "invalid input") `shouldBe` Left structuralClustalParseError
  describe "Structural Clustal Parser 2" $ do
    context "Parsing Structural Clustal input 2" $ do
      it "Returns StructuralClustalAlignment type" $ do
        (parseStructuralClustalAlignment structuralClustalExample2) `shouldBe` Right structuralClustalResult2
    context "Parsing invalid input" $ do
      it "Returns ParseError" $ do
        (parseStructuralClustalAlignment "invalid input") `shouldBe` Left structuralClustalParseError
                                                       
 
clustalParseError :: ParseError
clustalParseError = (addErrorMessage (Expect "\"CLUSTAL\"") (newErrorMessage clustalErrorMessage clustalErrorSourcePosition))

clustalErrorMessage :: Message
clustalErrorMessage = SysUnExpect "\"i\""

clustalErrorSourcePosition :: SourcePos
clustalErrorSourcePosition = newPos "genParserClustalAlignment" 1 1

clustalExample :: String
clustalExample = "CLUSTAL 2.1 multiple sequence alignment\n\n\nNC_0123:123-540 AATATATATTTTTTTTTTTTTTTTTTTTTTAAAAAAAAAAAAAAAAAAAAAAATTTTTTT\nNC_0223:123-540 AATATATATTTTTTTTTTTTTTTTTTTTTTAAAAAAAAAAAAAAAAAAAAAAATTTTTTT\nNC_0323:123-540 AATATATATTTTTTTTTTTTTTTTTTTTTTAAAAAAAAAAAAAAAAAAAAAAATTTTTTT\n                ************************************************************\nNC_0123:123-540 TTTTTTTTTTTTTT----------------------------------------------\nNC_0223:123-540 TTTTTTTTTTTTTTAATATATATTTTTTTTTTTTTTTTTTTTTTAAAAAAAAAAAAAAAA\nNC_0323:123-540 TTTTTTTTTTTTTTAATATATATTTTTTTTTTTTTTTTTTTTTTAAAAAAAAAAAAAAAA\n                **************                                              \n\nNC_0123:123-540 ----------------------------\nNC_0223:123-540 AAAAAAATTTTTTTTTTTTTTTTTTTTT\nNC_0323:123-540 AAAAAAATTTTTTTTTTTTTTTTTTTTT\n                *                           \n"

clustalResult :: ClustalAlignment
clustalResult = ClustalAlignment [ClustalAlignmentEntry (T.pack "NC_0123:123-540") (T.pack "AATATATATTTTTTTTTTTTTTTTTTTTTTAAAAAAAAAAAAAAAAAAAAAAATTTTTTTTTTTTTTTTTTTTT--------------------------------------------------------------------------"),ClustalAlignmentEntry (T.pack "NC_0223:123-540") (T.pack "AATATATATTTTTTTTTTTTTTTTTTTTTTAAAAAAAAAAAAAAAAAAAAAAATTTTTTTTTTTTTTTTTTTTTAATATATATTTTTTTTTTTTTTTTTTTTTTAAAAAAAAAAAAAAAAAAAAAAATTTTTTTTTTTTTTTTTTTTT"),ClustalAlignmentEntry (T.pack "NC_0323:123-540") (T.pack "AATATATATTTTTTTTTTTTTTTTTTTTTTAAAAAAAAAAAAAAAAAAAAAAATTTTTTTTTTTTTTTTTTTTTAATATATATTTTTTTTTTTTTTTTTTTTTTAAAAAAAAAAAAAAAAAAAAAAATTTTTTTTTTTTTTTTTTTTT")] (T.pack "**************************************************************************                                              *                           ")

structuralClustalParseError :: ParseError
structuralClustalParseError = addErrorMessage (Expect "\"mLocARNA\"") (newErrorMessage structuralClustalErrorMessage structuralClustalErrorSourcePosition)

structuralClustalErrorMessage :: Message
structuralClustalErrorMessage = SysUnExpect "\"i\""

structuralClustalErrorSourcePosition :: SourcePos
structuralClustalErrorSourcePosition = newPos "genParserStructuralClustalAlignment" 1 1

structuralClustalExample :: String
structuralClustalExample = "mLocARNA --- multiple Local (and global) Alignment of RNA --- LocARNA 1.8.0\nCopyright Sebastian Will\n\nCompute pair probs ...\nPerform progressive alignment ...\n\n\n\nAB001721.1/2735-2851  CCCGGUGACUAUAGAGAGAGGGCCACACCCGUUCCCAUCCCGAACACGGAAGUUAAGCCUCUCAUCGCUGAUGGUACUAUGUGGUUCGCUGCAUGGGAGAGUAGGACGUUGCCGGGU\ngi|451991584:1-117    CCCGGUGACUAUAGAGAGAGGGCCACACCCGUUCCCAUCCCGAACACGGAAGUUAAGCCUCUCAUCGCUGAUGGUACUAUGUGGUUCGCUGCAUGGGAGAGUAGGACGUUGCCGGGU\nalifold               (((((((((....(.(((.(((.....))).))).)...(((....)))..(((..(((((((((.((.(.(((.(((....))))))).))))))))).))..)))))))))))). (-38.30 = -38.30 +   0.00)\n"
                           
structuralClustalResult :: StructuralClustalAlignment
structuralClustalResult = StructuralClustalAlignment [ClustalAlignmentEntry (T.pack "AB001721.1/2735-2851") (T.pack "CCCGGUGACUAUAGAGAGAGGGCCACACCCGUUCCCAUCCCGAACACGGAAGUUAAGCCUCUCAUCGCUGAUGGUACUAUGUGGUUCGCUGCAUGGGAGAGUAGGACGUUGCCGGGU"),ClustalAlignmentEntry (T.pack "gi|451991584:1-117") (T.pack "CCCGGUGACUAUAGAGAGAGGGCCACACCCGUUCCCAUCCCGAACACGGAAGUUAAGCCUCUCAUCGCUGAUGGUACUAUGUGGUUCGCUGCAUGGGAGAGUAGGACGUUGCCGGGU")] (T.pack  "(((((((((....(.(((.(((.....))).))).)...(((....)))..(((..(((((((((.((.(.(((.(((....))))))).))))))))).))..)))))))))))).") (-38.30)

structuralClustalExample2 :: String
structuralClustalExample2 = "mLocARNA --- multiple Local (and global) Alignment of RNA --- LocARNA 1.9.0\nCopyright Sebastian Will\n\nCompute pair probs ...\nCompute pairwise alignments ... \nPerform progressive alignment ...\n\n\n\nAARQ02000011.1/391-585   -AAUUGAAUAGAAGCGCCAGAACUGAUUGGGACGAAAAUGCUUG-AAGGUGAAAUCCCUGAAAAGUA-UCGAUCAGUUGACGAGGAGGAGAUUAAUCGAAGUUUCGGCGGGAGUCUCCCG\nCP006940.1:755039-755234 CAAUUGAAUAGAAGCGCCAGAACUGAUUGGGACGAAAAUGCUUG-AAGGUGAAAUCCCUGAAAAGUA-UCGAUCAGUUGACGAGGAGGAGAUUAAUCGAAGUUUCGGCGGGAGUCUCCCG\nAM263198.1:720654-720850 CAAUUAAAUAGAAGCGCCAGAACUGAUUGGGACGAAAAUACUUG-AAGGUGAAAUUCCUGAAAAGUA-ACGGUCAGUUGACGAGGAGGAGAUUAAUCGAAAGUUCGGCGGGAGUCUCCCG\nAL596166.1:50733-50929   CAACUGAAUAGAAGCGCCAGAACUGAUUGGGACGAAAAUGCUUA-AAGGUGAAAUUCCUGGAAAGUAAACAAUCAGUUGACGAGGAGGAGAUUAAUCGAAAUUUCGGCGGGAGUCUCCCG\nFR687253.1:714343-714539 CAACUGAAUAGAAGCGCCAGAACUGAUCGGAUCGAAAUUACUUUCUAGGUGAAAUUCCU-AAAAGUAACGGGUCAGUUGACGAGGAGGAGAUUAAUCGAAGUUUCGGCGGGAGUCUCCCG\n\nAARQ02000011.1/391-585   GCUGU-GCAUGCAGUCGUUAAGUCUUACUUACAAAUCAUUUGGGUGACCAAGUGGACAGAGUAGUAAUGAAACAUGCUU\nCP006940.1:755039-755234 GCUGU-GCAUGCAGUCGUUAAGUCUUACUUACAAAUCAUUUGGGUGACCAAGUGGACAGAGUAGUAAUGAAAUAUGCUU\nAM263198.1:720654-720850 GCUGUAGCAUGCAGUCGUUAAGUCUUACUUACAAAACAUUUGGGUGACCAAAUGGACAGAGUAGUAAUGAAAUAUGUGU\nAL596166.1:50733-50929   GCUGU-GCAUGCAGUCGUUAAGUCUUACUUACAAAUCAUUUGGGUGACCAAGUGGACAGAGUAGUAAUGAAACAUGUGC\nFR687253.1:714343-714539 GCUGU-GCAUGCAGUCGUUAAGUCUUACUUACAAAUCAUUUGGGUGACCAAGUGGACAGAGUAGUAAUGAAACAUGCGC\n\nalifold                  .............(((((..((((((((((........(((((...(((.......)))...))))).))))))))))......(.(((((((..((((....))))....)))))))))\n                         )).)).(((((...((((((....((((((.....((((((((....))))))))...))))))))))))..))))).. (-68.86 = -47.45 + -21.41)\n"

structuralClustalResult2 :: StructuralClustalAlignment
structuralClustalResult2 = StructuralClustalAlignment [ClustalAlignmentEntry (T.pack "AARQ02000011.1/391-585") (T.pack "-AAUUGAAUAGAAGCGCCAGAACUGAUUGGGACGAAAAUGCUUG-AAGGUGAAAUCCCUGAAAAGUA-UCGAUCAGUUGACGAGGAGGAGAUUAAUCGAAGUUUCGGCGGGAGUCUCCCGGCUGU-GCAUGCAGUCGUUAAGUCUUACUUACAAAUCAUUUGGGUGACCAAGUGGACAGAGUAGUAAUGAAACAUGCUU"),ClustalAlignmentEntry (T.pack "CP006940.1:755039-755234") (T.pack "CAAUUGAAUAGAAGCGCCAGAACUGAUUGGGACGAAAAUGCUUG-AAGGUGAAAUCCCUGAAAAGUA-UCGAUCAGUUGACGAGGAGGAGAUUAAUCGAAGUUUCGGCGGGAGUCUCCCGGCUGU-GCAUGCAGUCGUUAAGUCUUACUUACAAAUCAUUUGGGUGACCAAGUGGACAGAGUAGUAAUGAAAUAUGCUU"),ClustalAlignmentEntry (T.pack "AM263198.1:720654-720850") (T.pack "CAAUUAAAUAGAAGCGCCAGAACUGAUUGGGACGAAAAUACUUG-AAGGUGAAAUUCCUGAAAAGUA-ACGGUCAGUUGACGAGGAGGAGAUUAAUCGAAAGUUCGGCGGGAGUCUCCCGGCUGUAGCAUGCAGUCGUUAAGUCUUACUUACAAAACAUUUGGGUGACCAAAUGGACAGAGUAGUAAUGAAAUAUGUGU"),ClustalAlignmentEntry (T.pack "AL596166.1:50733-50929") (T.pack "CAACUGAAUAGAAGCGCCAGAACUGAUUGGGACGAAAAUGCUUA-AAGGUGAAAUUCCUGGAAAGUAAACAAUCAGUUGACGAGGAGGAGAUUAAUCGAAAUUUCGGCGGGAGUCUCCCGGCUGU-GCAUGCAGUCGUUAAGUCUUACUUACAAAUCAUUUGGGUGACCAAGUGGACAGAGUAGUAAUGAAACAUGUGC"),ClustalAlignmentEntry (T.pack "FR687253.1:714343-714539") (T.pack "CAACUGAAUAGAAGCGCCAGAACUGAUCGGAUCGAAAUUACUUUCUAGGUGAAAUUCCU-AAAAGUAACGGGUCAGUUGACGAGGAGGAGAUUAAUCGAAGUUUCGGCGGGAGUCUCCCGGCUGU-GCAUGCAGUCGUUAAGUCUUACUUACAAAUCAUUUGGGUGACCAAGUGGACAGAGUAGUAAUGAAACAUGCGC")] (T.pack  ".............(((((..((((((((((........(((((...(((.......)))...))))).))))))))))......(.(((((((..((((....))))....))))))))))).)).(((((...((((((....((((((.....((((((((....))))))))...))))))))))))..)))))..") (-68.86)