public void PhylipParsePrimates()
{
string filepath = @"TestUtils\Phylip\primates.phy";
Assert.IsTrue(File.Exists(filepath));
IList<Dictionary<string, string>> expectedOutput = new List<Dictionary<string, string>>();
Dictionary<string, string> expectedAlignment = new Dictionary<string, string>();
expectedAlignment["Mouse"] = "ACCAAAAAAACATCCAAACACCAACCCCAGCCCTTACGCAATAGCCATACAAAGAATATT"
+ "ATACTACTAAAAACTCAAATTAACTCTTTAATCTTTATACAACATTCCACCAACCTATCC"
+ "ACACAAAAAAACTCATATTTATCTAAATACGAACTTCACACAACCTTAACACATAAACAT"
+ "ACCCCAGCCCAACACCCTTCCACAAATCCTTAATATACGCACCATAAATAAC";
expectedAlignment["Bovine"] = "ACCAAACCTGTCCCCACCATCTAACACCAACCCACATATACAAGCTAAACCAAAAATACC"
+ "ATACAACCATAAATAAGACTAATCTATTAAAATAACCCATTACGATACAAAATCCCTTTC"
+ "GTCTAGATACAAACCACAACACACAATTAATACACACCACAATTACAATACTAAACTCCC"
+ "ATCCCACCAAATCACCCTCCATCAAATCCACAAATTACACAACCATTAACCC";
expectedAlignment["Lemur"] = "ACCAAACTAACATCTAACAACTACCTCCAACTCTAAAAAAGCACTCTTACCAAACCCATC"
+ "ACAACTCTATCAACCTAACCAAACTATCAACATGCCCTCTCCTAATTAAAAACATTGCCA"
+ "CACTAAACCTACACACCTCATCACCATTAACGCATAACTCCTCAGTCATATCTACTACAC"
+ "ACCCTAACAATTTATCCCTCCCATAATCCAAAAACTCCATAAACACAAATTC";
expectedAlignment["Tarsier"] = "ATCTACCTTATCTCCCCCAATCAATACCAACCTAAAAACTCTACAATTAAAAACCCCACC"
+ "GCTCAATTACTAGCAAAAATAGACATTCAACTCCTCCCATCATAACATAAAACATTCCTC"
+ "GCTCCAATAAACACATCACAATCCCAATAACGCATATACCTAAATACATCATTTAATAAT"
+ "AATACTCCAACTCCCATAACACAGCATACATAAACTCCATAAGTTTGAACAC";
expectedAlignment["Squir Monk"] = "ACCCCAGCAACTCGTTGTGACCAACATCAATCCAAAATTAGCAAACGTACCAACAATCTC"
+ "CCAAATTTAAAAACACATCCTACCTTTACAATTAATAACCATTGTCTAGATATACCCCTA"
+ "AAATAAATGAATATAAACCCTCGCCGATAACATA-ACCCCTAAAATCAAGACATCCTCTC"
+ "ACAACGCCAAACCCCCCTCTCATAACTCTACAAAATACACAATCACCAACAC";
expectedAlignment["Jpn Macaq"] = "ACTCCACCTGCTCACCTCATCCACTACTACTCCTCAAGCAATACATAAACTAAAAACTTC"
+ "TCACCTCTAATACTACACACCACTCCTGAAATCAATGCCCTCCACTAAAAAACATCACCA"
+ "GCCCAAACAAACACCTATCTACCCCCCCGGTCCACGCCCCTAACTCCATCATTCCCCCTC"
+ "AATACATCAAACAATTCCCCCCAATACCCACAAACTGCATAAGCAAACAGAC";
expectedAlignment["Rhesus Mac"] = "ACTTCACCCGTTCACCTCATCCACTACTACTCCTCAAGCGATACATAAATCAAAAACTTC"
+ "TCACCTCCAATACTACGCACCGCTCCTAAAATCAATGCCCCCCACCAAAAAACATCACCA"
+ "ACCCAAACAAACACCTACCCATCCCCCCGGTTCACGCCTCAAACTCCATCATTCCCCCTC"
+ "AATACATCAAACAATTCCCCCCAATACCCACAAACTACATAAACAAACAAAC";
expectedAlignment["Crab-E.Mac"] = "ACCCCACCTACCCGCCTCGTCCGCTACTGCTTCTCAAACAATATATAGACCAACAACTTC"
+ "TCACCTTTAACACTACATATCACTCCTGAGCTTAACACCCTCCGCTAAAAAACACCACTA"
+ "ACCCAAACAAACACCTATCTATCCCCCCGGTCCACGCCCCAAACCCCGCTATTCCCCCCT"
+ "AATACACCAAACAATTTTCTCCAACACCCACAAACTGTATAAACAAACAAAC";
expectedAlignment["BarbMacaq"] = "ACCCTATCTATCTACCTCACCCGCCACCACCCCCCAAACAACACACAAACCAACAACTTT"
+ "TTATCTTTAGCACCACACATCACCCCCAAAAGCAATACCCTTCACCAAAAAGCACCATCA"
+ "AATCAAACAAACACCTATTTATTCCCCTAATTCACGTCCCAAATCCCATTATCTCTCCCC"
+ "AACATACCAAACAATTCTCCCTAATATACACAAACCACGCAAACAAACAAAC";
expectedAlignment["Gibbon"] = "ACTATACCCACCCAACTCGACCTACACCAATCCCCACATAGCACACAGACCAACAACCTC"
+ "CCACCTTCCATACCAAGCCCCGACTTTACCGCCAACGCACCTCATCAAAACATACCTACA"
+ "ACACAAACAAATGCCCCCCCACCCTCCTTCTTCAAGCCCACTAGACCATCCTACCTTCCT"
+ "AGCACGCCAAGCTCTCTACCATCAAACGCACAACTTACACATACAGAACCAC";
expectedAlignment["Orang"] = "ACCCCACCCGTCTACACCAGCCAACACCAACCCCCACCTACTATACCAACCAATAACCTC"
+ "TCAACCCCTAAACCAAACACTATCCCCAAAACCAACACACTCTACCAAAATACACCCCCA"
+ "ATTCACATCCGCACACCCCCACCCCCCCTGCCCACGTCCATCCCATCACCCTCTCCTCCC"
+ "AACACCCTAAGCCACCTTCCTCAAAATCCAAAACCCACACAACCGAAACAAC";
expectedAlignment["Gorilla"] = "ACCCCATTTATCCATAAAAACCAACACCAACCCCCATCTAACACACAAACTAATGACCCC"
+ "CCACCCTCAAAGCCAAACACCAACCCTATAATCAATACGCCTTATCAAAACACACCCCCA"
+ "ACATAAACCCACGCACCCCCACCCCTTCCGCCCATGCTCACCACATCATCTCTCCCCTTC"
+ "AACACCTCAATCCACCTCCCCCCAAATACACAATTCACACAAACAATACCAC";
expectedAlignment["Chimp"] = "ACCCCATCCACCCATACAAACCAACATTACCCTCCATCCAATATACAAACTAACAACCTC"
+ "CCACTCTTCAGACCGAACACCAATCTCACAACCAACACGCCCCGTCAAAACACCCCTTCA"
+ "GCACAAATTCATACACCCCTACCTTTCCTACCCACGTTCACCACATCATCCCCCCCTCTC"
+ "AACATCTTGACTCGCCTCTCTCCAAACACACAATTCACGCAAACAACGCCAC";
expectedAlignment["Human"] = "ACCCCACTCACCCATACAAACCAACACCACTCTCCACCTAATATACAAATTAATAACCTC"
+ "CCACCTTCAGAACTGAACGCCAATCTCATAACCAACACACCCCATCAAAGCACCCCTCCA"
+ "ACACAAACCCGCACACCTCCACCCCCCTCGTCTACGCTTACCACGTCATCCCTCCCTCTC"
+ "AACACCTTAACTCACCTTCTCCCAAACGCACAATTCGCACACACAACGCCAC";
expectedOutput.Add(expectedAlignment);
IList<ISequenceAlignment> actualOutput = null;
ISequenceAlignmentParser parser = new PhylipParser();
using (parser.Open(filepath))
{
actualOutput = parser.Parse().ToList();
}
CompareOutput(actualOutput, expectedOutput);
}
public void PhylipParse()
{
string filepath = @"TestUtils\Phylip\dna.phy";
Assert.IsTrue(File.Exists(filepath));
IList<Dictionary<string, string>> expectedOutput = new List<Dictionary<string, string>>();
Dictionary<string, string> expectedAlignment = new Dictionary<string, string>();
expectedAlignment["Cow"] = "ATGGCATATCCCATACAACTAGGATTCCAAGATGCAACATCACCAATCATAGAAGAACTA"
+ "CTTCACTTTCATGACCACACGCTAATAATTGTCTTCTTAATTAGCTCATTAGTACTTTAC"
+ "ATTATTTCACTAATACTAACGACAAAGCTGACCCATACAAGCACGATAGATGCACAAGAA"
+ "GTAGAGACAATCTGAACCATTCTGCCCGCCATCATCTTAATTCTAATTGCTCTTCCTTCT"
+ "TTACGAATTCTATACATAATAGATGAAATCAATAACCCATCTCTTACAGTAAAAACCATA"
+ "GGACATCAGTGATACTGAAGCTATGAGTATACAGATTATGAGGACTTAAGCTTCGACTCC"
+ "TACATAATTCCAACATCAGAATTAAAGCCAGGGGAGCTACGACTATTAGAAGTCGATAAT"
+ "CGAGTTGTACTACCAATAGAAATAACAATCCGAATGTTAGTCTCCTCTGAAGACGTATTA"
+ "CACTCATGAGCTGTGCCCTCTCTAGGACTAAAAACAGACGCAATCCCAGGCCGTCTAAAC"
+ "CAAACAACCCTTATATCGTCCCGTCCAGGCTTATATTACGGTCAATGCTCAGAAATTTGC"
+ "GGGTCAAACCACAGTTTCATACCCATTGTCCTTGAGTTAGTCCCACTAAAGTACTTTGAA"
+ "AAATGATCTGCGTCAATATTA---------------------TAA";
expectedAlignment["Carp"] = "ATGGCACACCCAACGCAACTAGGTTTCAAGGACGCGGCCATACCCGTTATAGAGGAACTT"
+ "CTTCACTTCCACGACCACGCATTAATAATTGTGCTCCTAATTAGCACTTTAGTTTTATAT"
+ "ATTATTACTGCAATGGTATCAACTAAACTTACTAATAAATATATTCTAGACTCCCAAGAA"
+ "ATCGAAATCGTATGAACCATTCTACCAGCCGTCATTTTAGTACTAATCGCCCTGCCCTCC"
+ "CTACGCATCCTGTACCTTATAGACGAAATTAACGACCCTCACCTGACAATTAAAGCAATA"
+ "GGACACCAATGATACTGAAGTTACGAGTATACAGACTATGAAAATCTAGGATTCGACTCC"
+ "TATATAGTACCAACCCAAGACCTTGCCCCCGGACAATTCCGACTTCTGGAAACAGACCAC"
+ "CGAATAGTTGTTCCAATAGAATCCCCAGTCCGTGTCCTAGTATCTGCTGAAGACGTGCTA"
+ "CATTCTTGAGCTGTTCCATCCCTTGGCGTAAAAATGGACGCAGTCCCAGGACGACTAAAT"
+ "CAAGCCGCCTTTATTGCCTCACGCCCAGGGGTCTTTTACGGACAATGCTCTGAAATTTGT"
+ "GGAGCTAATCACAGCTTTATACCAATTGTAGTTGAAGCAGTACCTCTCGAACACTTCGAA"
+ "AACTGATCCTCATTAATACTAGAAGACGCCTCGCTAGGAAGCTAA";
expectedAlignment["Chicken"] = "ATGGCCAACCACTCCCAACTAGGCTTTCAAGACGCCTCATCCCCCATCATAGAAGAGCTC"
+ "GTTGAATTCCACGACCACGCCCTGATAGTCGCACTAGCAATTTGCAGCTTAGTACTCTAC"
+ "CTTCTAACTCTTATACTTATAGAAAAACTATCA---TCAAACACCGTAGATGCCCAAGAA"
+ "GTTGAACTAATCTGAACCATCCTACCCGCTATTGTCCTAGTCCTGCTTGCCCTCCCCTCC"
+ "CTCCAAATCCTCTACATAATAGACGAAATCGACGAACCTGATCTCACCCTAAAAGCCATC"
+ "GGACACCAATGATACTGAACCTATGAATACACAGACTTCAAGGACCTCTCATTTGACTCC"
+ "TACATAACCCCAACAACAGACCTCCCCCTAGGCCACTTCCGCCTACTAGAAGTCGACCAT"
+ "CGCATTGTAATCCCCATAGAATCCCCCATTCGAGTAATCATCACCGCTGATGACGTCCTC"
+ "CACTCATGAGCCGTACCCGCCCTCGGGGTAAAAACAGACGCAATCCCTGGACGACTAAAT"
+ "CAAACCTCCTTCATCACCACTCGACCAGGAGTGTTTTACGGACAATGCTCAGAAATCTGC"
+ "GGAGCTAACCACAGCTACATACCCATTGTAGTAGAGTCTACCCCCCTAAAACACTTTGAA"
+ "GCCTGATCCTCACTA------------------CTGTCATCTTAA";
expectedAlignment["Human"] = "ATGGCACATGCAGCGCAAGTAGGTCTACAAGACGCTACTTCCCCTATCATAGAAGAGCTT"
+ "ATCACCTTTCATGATCACGCCCTCATAATCATTTTCCTTATCTGCTTCCTAGTCCTGTAT"
+ "GCCCTTTTCCTAACACTCACAACAAAACTAACTAATACTAACATCTCAGACGCTCAGGAA"
+ "ATAGAAACCGTCTGAACTATCCTGCCCGCCATCATCCTAGTCCTCATCGCCCTCCCATCC"
+ "CTACGCATCCTTTACATAACAGACGAGGTCAACGATCCCTCCCTTACCATCAAATCAATT"
+ "GGCCACCAATGGTACTGAACCTACGAGTACACCGACTACGGCGGACTAATCTTCAACTCC"
+ "TACATACTTCCCCCATTATTCCTAGAACCAGGCGACCTGCGACTCCTTGACGTTGACAAT"
+ "CGAGTAGTACTCCCGATTGAAGCCCCCATTCGTATAATAATTACATCACAAGACGTCTTG"
+ "CACTCATGAGCTGTCCCCACATTAGGCTTAAAAACAGATGCAATTCCCGGACGTCTAAAC"
+ "CAAACCACTTTCACCGCTACACGACCGGGGGTATACTACGGTCAATGCTCTGAAATCTGT"
+ "GGAGCAAACCACAGTTTCATGCCCATCGTCCTAGAATTAATTCCCCTAAAAATCTTTGAA"
+ "ATA---------------------GGGCCCGTATTTACCCTATAG";
expectedAlignment["Loach"] = "ATGGCACATCCCACACAATTAGGATTCCAAGACGCGGCCTCACCCGTAATAGAAGAACTT"
+ "CTTCACTTCCATGACCATGCCCTAATAATTGTATTTTTGATTAGCGCCCTAGTACTTTAT"
+ "GTTATTATTACAACCGTCTCAACAAAACTCACTAACATATATATTTTGGACTCACAAGAA"
+ "ATTGAAATCGTATGAACTGTGCTCCCTGCCCTAATCCTCATTTTAATCGCCCTCCCCTCA"
+ "CTACGAATTCTATATCTTATAGACGAGATTAATGACCCCCACCTAACAATTAAGGCCATG"
+ "GGGCACCAATGATACTGAAGCTACGAGTATACTGATTATGAAAACTTAAGTTTTGACTCC"
+ "TACATAATCCCCACCCAGGACCTAACCCCTGGACAATTCCGGCTACTAGAGACAGACCAC"
+ "CGAATGGTTGTTCCCATAGAATCCCCTATTCGCATTCTTGTTTCCGCCGAAGATGTACTA"
+ "CACTCCTGGGCCCTTCCAGCCATGGGGGTAAAGATAGACGCGGTCCCAGGACGCCTTAAC"
+ "CAAACCGCCTTTATTGCCTCCCGCCCCGGGGTATTCTATGGGCAATGCTCAGAAATCTGT"
+ "GGAGCAAACCACAGCTTTATACCCATCGTAGTAGAAGCGGTCCCACTATCTCACTTCGAA"
+ "AACTGGTCCACCCTTATACTAAAAGACGCCTCACTAGGAAGCTAA";
expectedAlignment["Mouse"] = "ATGGCCTACCCATTCCAACTTGGTCTACAAGACGCCACATCCCCTATTATAGAAGAGCTA"
+ "ATAAATTTCCATGATCACACACTAATAATTGTTTTCCTAATTAGCTCCTTAGTCCTCTAT"
+ "ATCATCTCGCTAATATTAACAACAAAACTAACACATACAAGCACAATAGATGCACAAGAA"
+ "GTTGAAACCATTTGAACTATTCTACCAGCTGTAATCCTTATCATAATTGCTCTCCCCTCT"
+ "CTACGCATTCTATATATAATAGACGAAATCAACAACCCCGTATTAACCGTTAAAACCATA"
+ "GGGCACCAATGATACTGAAGCTACGAATATACTGACTATGAAGACCTATGCTTTGATTCA"
+ "TATATAATCCCAACAAACGACCTAAAACCTGGTGAACTACGACTGCTAGAAGTTGATAAC"
+ "CGAGTCGTTCTGCCAATAGAACTTCCAATCCGTATATTAATTTCATCTGAAGACGTCCTC"
+ "CACTCATGAGCAGTCCCCTCCCTAGGACTTAAAACTGATGCCATCCCAGGCCGACTAAAT"
+ "CAAGCAACAGTAACATCAAACCGACCAGGGTTATTCTATGGCCAATGCTCTGAAATTTGT"
+ "GGATCTAACCATAGCTTTATGCCCATTGTCCTAGAAATGGTTCCACTAAAATATTTCGAA"
+ "AACTGATCTGCTTCAATAATT---------------------TAA";
expectedAlignment["Rat"] = "ATGGCTTACCCATTTCAACTTGGCTTACAAGACGCTACATCACCTATCATAGAAGAACTT"
+ "ACAAACTTTCATGACCACACCCTAATAATTGTATTCCTCATCAGCTCCCTAGTACTTTAT"
+ "ATTATTTCACTAATACTAACAACAAAACTAACACACACAAGCACAATAGACGCCCAAGAA"
+ "GTAGAAACAATTTGAACAATTCTCCCAGCTGTCATTCTTATTCTAATTGCCCTTCCCTCC"
+ "CTACGAATTCTATACATAATAGACGAGATTAATAACCCAGTTCTAACAGTAAAAACTATA"
+ "GGACACCAATGATACTGAAGCTATGAATATACTGACTATGAAGACCTATGCTTTGACTCC"
+ "TACATAATCCCAACCAATGACCTAAAACCAGGTGAACTTCGTCTATTAGAAGTTGATAAT"
+ "CGGGTAGTCTTACCAATAGAACTTCCAATTCGTATACTAATCTCATCCGAAGACGTCCTG"
+ "CACTCATGAGCCATCCCTTCACTAGGGTTAAAAACCGACGCAATCCCCGGCCGCCTAAAC"
+ "CAAGCTACAGTCACATCAAACCGACCAGGTCTATTCTATGGCCAATGCTCTGAAATTTGC"
+ "GGCTCAAATCACAGCTTCATACCCATTGTACTAGAAATAGTGCCTCTAAAATATTTCGAA"
+ "AACTGATCAGCTTCTATAATT---------------------TAA";
expectedAlignment["Seal"] = "ATGGCATACCCCCTACAAATAGGCCTACAAGATGCAACCTCTCCCATTATAGAGGAGTTA"
+ "CTACACTTCCATGACCACACATTAATAATTGTGTTCCTAATTAGCTCATTAGTACTCTAC"
+ "ATTATCTCACTTATACTAACCACGAAACTCACCCACACAAGTACAATAGACGCACAAGAA"
+ "GTGGAAACGGTGTGAACGATCCTACCCGCTATCATTTTAATTCTCATTGCCCTACCATCA"
+ "TTACGAATCCTCTACATAATGGACGAGATCAATAACCCTTCCTTGACCGTAAAAACTATA"
+ "GGACATCAGTGATACTGAAGCTATGAGTACACAGACTACGAAGACCTGAACTTTGACTCA"
+ "TATATGATCCCCACACAAGAACTAAAGCCCGGAGAACTACGACTGCTAGAAGTAGACAAT"
+ "CGAGTAGTCCTCCCAATAGAAATAACAATCCGCATACTAATCTCATCAGAAGATGTACTC"
+ "CACTCATGAGCCGTACCGTCCCTAGGACTAAAAACTGATGCTATCCCAGGACGACTAAAC"
+ "CAAACAACCCTAATAACCATACGACCAGGACTGTACTACGGTCAATGCTCAGAAATCTGT"
+ "GGTTCAAACCACAGCTTCATACCTATTGTCCTCGAATTGGTCCCACTATCCCACTTCGAG"
+ "AAATGATCTACCTCAATGCTT---------------------TAA";
expectedAlignment["Whale"] = "ATGGCATATCCATTCCAACTAGGTTTCCAAGATGCAGCATCACCCATCATAGAAGAGCTC"
+ "CTACACTTTCACGATCATACACTAATAATCGTTTTTCTAATTAGCTCTTTAGTTCTCTAC"
+ "ATTATTACCCTAATGCTTACAACCAAATTAACACATACTAGTACAATAGACGCCCAAGAA"
+ "GTAGAAACTGTCTGAACTATCCTCCCAGCCATTATCTTAATTTTAATTGCCTTGCCTTCA"
+ "TTACGGATCCTTTACATAATAGACGAAGTCAATAACCCCTCCCTCACTGTAAAAACAATA"
+ "GGTCACCAATGATATTGAAGCTATGAGTATACCGACTACGAAGACCTAAGCTTCGACTCC"
+ "TATATAATCCCAACATCAGACCTAAAGCCAGGAGAACTACGATTATTAGAAGTAGATAAC"
+ "CGAGTTGTCTTACCTATAGAAATAACAATCCGAATATTAGTCTCATCAGAAGACGTACTC"
+ "CACTCATGGGCCGTACCCTCCTTGGGCCTAAAAACAGATGCAATCCCAGGACGCCTAAAC"
+ "CAAACAACCTTAATATCAACACGACCAGGCCTATTTTATGGACAATGCTCAGAGATCTGC"
+ "GGCTCAAACCACAGTTTCATACCAATTGTCCTAGAACTAGTACCCCTAGAAGTCTTTGAA"
+ "AAATGATCTGTATCAATACTA---------------------TAA";
expectedAlignment["Frog"] = "ATGGCACACCCATCACAATTAGGTTTTCAAGACGCAGCCTCTCCAATTATAGAAGAATTA"
+ "CTTCACTTCCACGACCATACCCTCATAGCCGTTTTTCTTATTAGTACGCTAGTTCTTTAC"
+ "ATTATTACTATTATAATAACTACTAAACTAACTAATACAAACCTAATGGACGCACAAGAG"
+ "ATCGAAATAGTGTGAACTATTATACCAGCTATTAGCCTCATCATAATTGCCCTTCCATCC"
+ "CTTCGTATCCTATATTTAATAGATGAAGTTAATGATCCACACTTAACAATTAAAGCAATC"
+ "GGCCACCAATGATACTGAAGCTACGAATATACTAACTATGAGGATCTCTCATTTGACTCT"
+ "TATATAATTCCAACTAATGACCTTACCCCTGGACAATTCCGGCTGCTAGAAGTTGATAAT"
+ "CGAATAGTAGTCCCAATAGAATCTCCAACCCGACTTTTAGTTACAGCCGAAGACGTCCTC"
+ "CACTCGTGAGCTGTACCCTCCTTGGGTGTCAAAACAGATGCAATCCCAGGACGACTTCAT"
+ "CAAACATCATTTATTGCTACTCGTCCGGGAGTATTTTACGGACAATGTTCAGAAATTTGC"
+ "GGAGCAAACCACAGCTTTATACCAATTGTAGTTGAAGCAGTACCGCTAACCGACTTTGAA"
+ "AACTGATCTTCATCAATACTA---GAAGCATCACTA------AGA";
expectedOutput.Add(expectedAlignment);
IList<ISequenceAlignment> actualOutput = null;
ISequenceAlignmentParser parser = new PhylipParser();
using (parser.Open(filepath))
{
actualOutput = parser.Parse().ToList();
}
CompareOutput(actualOutput, expectedOutput);
}