/// <summary>
/// Try Parse Sequence File.
/// </summary>
/// <param name="fileName">The fileName.</param>
/// <param name="alphabet">The Alphabet.</param>
/// <param name="sequences">List of sequences.</param>
/// <returns>True if Parsed sequence properly.</returns>
private static bool TryParseSequenceFile(string fileName, IAlphabet alphabet, out IList <ISequence> sequences)
{
// Read the first line.
string firstLine;
using (var reader = new StreamReader(fileName))
{
firstLine = reader.ReadLine();
}
// Attempt to discover the format.
if (ValidateFastaFormat(firstLine))
{
var parse = new FastAParser {
Alphabet = alphabet
};
using (parse.Open(fileName))
{
sequences = parse.Parse().ToList();
}
return(true);
}
if (ValidatePhylipFormat(firstLine))
{
var parse = new PhylipParser {
Alphabet = alphabet
};
using (parse.Open(fileName))
{
sequences = ConvertAlignedSequenceToSequence(parse.Parse());
}
return(true);
}
if (ValidateTabFormat(firstLine))
{
var parse = new FieldTextFileParser {
Alphabet = alphabet
};
using (parse.Open(fileName))
{
sequences = parse.Parse().ToList();
return(true);
}
}
sequences = null;
return(false);
}
public void ValidatePhylipParserProperties()
{
PhylipParser parser = new PhylipParser();
Assert.AreEqual(
utilityObj.xmlUtil.GetTextValue(Constants.PhylipPropertyNode,
Constants.PhylipDescriptionNode),
parser.Description);
Assert.AreEqual(
utilityObj.xmlUtil.GetTextValue(Constants.PhylipPropertyNode,
Constants.PhylipNameNode),
parser.Name);
Assert.AreEqual(null, parser.Alphabet);
}
/// <summary>
/// General method to invalidate Phylip parser
/// </summary>
/// <param name="nodeName">xml node name.</param>
/// <param name="method">Phylip Parser method parameters</param>
void InvalidatePhylipParserTestCases(
string nodeName,
ParserTestAttributes method)
{
try
{
string filePath = utilityObj.xmlUtil.GetTextValue(
nodeName,
Constants.FilePathNode);
PhylipParser parser = new PhylipParser();
switch (method)
{
case ParserTestAttributes.Parse:
parser.Parse(filePath);
break;
case ParserTestAttributes.ParseOne:
parser.ParseOne(filePath);
break;
default:
break;
}
Assert.Fail();
}
catch (InvalidDataException)
{
ApplicationLog.WriteLine(
"Phylip Parser P2 : All the features validated successfully.");
Console.WriteLine(
"Phylip Parser P2 : All the features validated successfully.");
}
catch (FormatException)
{
ApplicationLog.WriteLine(
"Phylip Parser P2 : All the features validated successfully.");
Console.WriteLine(
"Phylip Parser P2 : All the features validated successfully.");
}
}
public void ValidatePhylipParserProperties()
{
PhylipParser parser = new PhylipParser(Encodings.Ncbi4NA);
Assert.AreEqual(
Utility._xmlUtil.GetTextValue(Constants.PhylipPropertyNode,
Constants.PhylipDescriptionNode),
parser.Description);
Assert.AreEqual(
Utility._xmlUtil.GetTextValue(Constants.PhylipPropertyNode,
Constants.PhylipNameNode),
parser.Name);
Assert.AreEqual(
Utility._xmlUtil.GetTextValue(Constants.PhylipPropertyNode,
Constants.PhylipFileTypesNode),
parser.FileTypes);
Assert.AreEqual(null, parser.Alphabet);
Assert.AreEqual(
Utility._xmlUtil.GetTextValue(Constants.PhylipPropertyNode,
Constants.PhylipEncodingNode),
parser.Encoding.ToString());
}
/// <summary>
/// Try Parse Sequence File.
/// </summary>
/// <param name="fileName">The fileName.</param>
/// <param name="alphabet">The Alphabet.</param>
/// <param name="sequences">List of sequences.</param>
/// <returns>True if Parsed sequence properly.</returns>
private static bool TryParseSequenceFile(string fileName, IAlphabet alphabet, out IList <ISequence> sequences)
{
using (TextReader reader = new StreamReader(fileName))
{
string firstLine = reader.ReadLine();
if (ValidateFastaFormat(firstLine))
{
using (FastAParser parse = new FastAParser())
{
parse.Alphabet = alphabet;
sequences = parse.Parse().ToList();
}
return(true);
}
else if (ValidatePhylipFormat(firstLine))
{
PhylipParser parse = new PhylipParser();
parse.Alphabet = alphabet;
sequences = ConvertAlignedSequenceToSequence(parse.Parse(fileName));
return(true);
}
else if (ValidateTabFormat(firstLine))
{
using (FieldTextFileParser parse = new FieldTextFileParser(fileName))
{
parse.Alphabet = alphabet;
sequences = parse.Parse().ToList();
return(true);
}
}
else
{
sequences = null;
return(false);
}
}
}
/// <summary>
/// Parsers the Phylip file for different test cases based
/// on Additional parameter
/// </summary>
/// <param name="nodeName">Xml Node name</param>
/// <param name="addParam">Additional parameter</param>
static void ParserGeneralTestCases(string nodeName,
ParserTestAttributes addParam)
{
// Gets the Filename
string filePath = Utility._xmlUtil.GetTextValue(
nodeName, Constants.FilePathNode);
Assert.IsNotEmpty(filePath);
ApplicationLog.WriteLine(string.Format(
"Phylip Parser BVT: Reading the File from location '{0}'", filePath));
Console.WriteLine(string.Format(
"Phylip Parser BVT: Reading the File from location '{0}'", filePath));
// Get the rangelist after parsing.
PhylipParser parserObj = new PhylipParser();
IList <ISequenceAlignment> sequenceAlignmentList = null;
ISequenceAlignment sequenceAlignment = null;
// Gets the SequenceAlignment list based on the parameters.
switch (addParam)
{
case ParserTestAttributes.Parse:
sequenceAlignmentList = parserObj.Parse(filePath);
break;
case ParserTestAttributes.ParseOne:
sequenceAlignment = parserObj.ParseOne(filePath);
break;
case ParserTestAttributes.ParseTextReader:
sequenceAlignmentList = parserObj.Parse(
new StreamReader(filePath));
break;
case ParserTestAttributes.ParseOneTextReader:
sequenceAlignment = parserObj.ParseOne(
new StreamReader(filePath));
break;
case ParserTestAttributes.ParseOneTextReaderReadOnly:
sequenceAlignment = parserObj.ParseOne(
new StreamReader(filePath), false);
break;
case ParserTestAttributes.ParseTextReaderReadOnly:
sequenceAlignmentList = parserObj.Parse(
new StreamReader(filePath), false);
break;
case ParserTestAttributes.ParseReadOnly:
sequenceAlignmentList = parserObj.Parse(filePath,
false);
break;
case ParserTestAttributes.ParseOneReadOnly:
sequenceAlignment = parserObj.ParseOne(filePath,
false);
break;
case ParserTestAttributes.ParseEncoding:
PhylipParser parser =
new PhylipParser(Encodings.Ncbi4NA);
sequenceAlignmentList = parser.Parse(
new StreamReader(filePath), false);
break;
default:
break;
}
// Gets all the expected values from xml.
IList <Dictionary <string, string> > expectedAlignmentList =
new List <Dictionary <string, string> >();
Dictionary <string, string> expectedAlignmentObj =
new Dictionary <string, string>();
XmlNode expectedAlignmentNodes = Utility._xmlUtil.GetNode(
nodeName, Constants.ExpectedAlignmentNode);
XmlNodeList alignNodes = expectedAlignmentNodes.ChildNodes;
// Create a ISequenceAlignment List
switch (addParam)
{
case ParserTestAttributes.ParseOne:
case ParserTestAttributes.ParseOneTextReader:
case ParserTestAttributes.ParseOneTextReaderReadOnly:
case ParserTestAttributes.ParseOneReadOnly:
sequenceAlignmentList = new List <ISequenceAlignment>();
sequenceAlignmentList.Add(sequenceAlignment);
break;
default:
break;
}
foreach (XmlNode expectedAlignment in alignNodes)
{
expectedAlignmentObj[expectedAlignment.Name] =
expectedAlignment.InnerText;
}
expectedAlignmentList.Add(expectedAlignmentObj);
Assert.IsTrue(CompareOutput(sequenceAlignmentList,
expectedAlignmentList));
ApplicationLog.WriteLine(
"Phylip Parser BVT: Successfully validated all the Alignment Sequences");
Console.WriteLine(
"Phylip Parser BVT: Successfully validated all the Alignment Sequences");
}
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 (StreamReader reader = File.OpenText(filepath))
{
actualOutput = parser.Parse(reader);
}
CompareOutput(actualOutput, expectedOutput);
}
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 (StreamReader reader = File.OpenText(filepath))
{
actualOutput = parser.Parse(reader);
}
CompareOutput(actualOutput, expectedOutput);
}
/// <summary>
/// Parsers the Phylip file for different test cases based
/// on Additional parameter
/// </summary>
/// <param name="nodeName">Xml Node name</param>
/// <param name="addParam">Additional parameter</param>
void ParserGeneralTestCases(string nodeName, ParserTestAttributes addParam)
{
// Gets the Filename
string filePath = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FilePathNode).TestDir();
Assert.IsFalse(string.IsNullOrEmpty(filePath));
ApplicationLog.WriteLine($"Phylip Parser BVT: Reading the File from location '{filePath}'");
// Get the range list after parsing.
PhylipParser parserObj = new PhylipParser();
IEnumerable <ISequenceAlignment> sequenceAlignmentList = null;
ISequenceAlignment sequenceAlignment = null;
// Gets the SequenceAlignment list based on the parameters.
switch (addParam)
{
case ParserTestAttributes.Parse:
sequenceAlignmentList = parserObj.Parse(filePath);
break;
case ParserTestAttributes.ParseOne:
sequenceAlignment = parserObj.ParseOne(filePath);
break;
case ParserTestAttributes.ParseTextReader:
using (var rdrObj = File.OpenRead(filePath))
{
sequenceAlignmentList = parserObj.Parse(rdrObj).ToList();
}
break;
case ParserTestAttributes.ParseOneTextReader:
using (var rdrObj = File.OpenRead(filePath))
{
sequenceAlignment = parserObj.ParseOne(rdrObj);
}
break;
default:
break;
}
// Gets all the expected values from xml.
var expectedAlignmentList = new List <Dictionary <string, string> >();
var expectedAlignmentObj = new Dictionary <string, string>();
XElement expectedAlignmentNodes = utilityObj.xmlUtil.GetNode(nodeName, Constants.ExpectedAlignmentNode);
IList <XNode> nodes = expectedAlignmentNodes.Nodes().ToList();
//Get all the values from the elements in the node.
foreach (XElement node in nodes)
{
expectedAlignmentObj[node.Name.ToString()] = node.Value;
}
// Create a ISequenceAlignment List
switch (addParam)
{
case ParserTestAttributes.ParseOne:
case ParserTestAttributes.ParseOneTextReader:
sequenceAlignmentList = new List <ISequenceAlignment> {
sequenceAlignment
};
break;
default:
break;
}
expectedAlignmentList.Add(expectedAlignmentObj);
Assert.IsTrue(CompareOutput(sequenceAlignmentList.ToList(), expectedAlignmentList));
ApplicationLog.WriteLine("Phylip Parser BVT: Successfully validated all the Alignment Sequences");
}