public void GenBankProperties()
{
ISequenceParser parser = new GenBankParser();
Assert.AreEqual(parser.Name, Resource.GENBANK_NAME);
Assert.AreEqual(parser.Description, Resource.GENBANKPARSER_DESCRIPTION);
Assert.AreEqual(parser.SupportedFileTypes, Resource.GENBANK_FILEEXTENSION);
ISequenceFormatter formatter = new GenBankFormatter();
Assert.AreEqual(formatter.Name, Resource.GENBANK_NAME);
Assert.AreEqual(formatter.Description, Resource.GENBANKFORMATTER_DESCRIPTION);
Assert.AreEqual(formatter.SupportedFileTypes, Resource.GENBANK_FILEEXTENSION);
}
public void GenBankFormatterValidateReadAndWriteMultipleDBLinks()
{
// Create a Sequence with all attributes.
// parse and update the properties instead of parsing entire file.
string tempFileName = Path.GetTempFileName();
ISequenceParser parser1 = new GenBankParser();
using (parser1.Open(_genBankFile_WithMultipleDBLines))
{
var orgSeq = parser1.Parse().First();
ISequenceFormatter formatter = new GenBankFormatter();
using (formatter.Open(tempFileName))
{
formatter.Format(orgSeq);
formatter.Close();
}
}
var same = CompareFiles(tempFileName, _genBankFile_WithMultipleDBLines);
File.Delete(tempFileName);
Assert.IsTrue(same);
ApplicationLog.WriteLine("GenBank Formatter: Successful read->write loop");
}
public void TestGenBankWhenUserSetsDnaAlphabet()
{
// set correct alphabet and parse
ISequenceParser parser = new GenBankParser();
parser.Alphabet = Alphabets.DNA;
ISequence seq = parser.Parse(_singleDnaSeqGenBankFilename).FirstOrDefault();
Assert.AreEqual(Alphabets.DNA, seq.Alphabet);
// format
ISequenceFormatter formatter = new GenBankFormatter();
formatter.Format(seq, TempGenBankFileName);
string actual = string.Empty;
using (StreamReader reader = new StreamReader(TempGenBankFileName))
{
actual = reader.ReadToEnd();
}
File.Delete(TempGenBankFileName);
// test the formatting
Assert.AreEqual(_singleDnaSeqGenBankFileExpectedOutput.Replace(" ", "").Replace("\r\n", Environment.NewLine), actual.Replace(" ", ""));
}
public void TestGenBankForManyFiles()
{
// parser and formatter will be used for all files in input dir
// iterate through the files in input dir, parsing and formatting each; write results
// to log file
DirectoryInfo inputDirInfo = new DirectoryInfo(_genBankDataPath);
foreach (FileInfo fileInfo in inputDirInfo.GetFiles("*.gbk"))
{
ApplicationLog.WriteLine("Parsing file {0}...{1}", fileInfo.FullName, Environment.NewLine);
IEnumerable<ISequence> seqList = new GenBankParser().Parse(fileInfo.FullName);
ISequenceFormatter formatter = new GenBankFormatter();
using (formatter.Open(TempGenBankFileName))
{
(formatter as GenBankFormatter).Format(seqList.ToList());
}
using (var reader = new StreamReader(TempGenBankFileName))
{
string actual = reader.ReadToEnd();
}
File.Delete(TempGenBankFileName);
}
}
/// <summary>
/// Validate addition of GenBank features.
/// </summary>
/// <param name="nodeName">xml node name.</param>
private void ValidateAdditionGenBankFeatures(string nodeName)
{
// Get Values from XML node.
string filePath = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.FilePathNode);
string alphabetName = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.AlphabetNameNode);
string expectedSequence = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ExpectedSequenceNode);
string addFirstKey = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.FirstKey);
string addSecondKey = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.SecondKey);
string addFirstLocation = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.FirstLocation);
string addSecondLocation = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.SecondLocation);
string addFirstQualifier = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.FirstQualifier);
string addSecondQualifier = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.SecondQualifier);
ISequenceParser parser1 = new GenBankParser();
{
IEnumerable<ISequence> seqList1 = parser1.Parse(filePath);
var localBuilderObj = new LocationBuilder();
string tempFileName = Path.GetTempFileName();
string expectedUpdatedSequence =
expectedSequence.Replace("\r", "").Replace("\n", "").Replace(" ", "");
var orgSeq = new Sequence(Utility.GetAlphabet(alphabetName),
expectedUpdatedSequence);
orgSeq.ID = seqList1.ElementAt(0).ID;
orgSeq.Metadata.Add(Constants.GenBank,
seqList1.ElementAt(0).Metadata[Constants.GenBank]);
ISequenceFormatter formatterObj = new GenBankFormatter();
{
formatterObj.Format(orgSeq, tempFileName);
// parse GenBank file.
var parserObj = new GenBankParser();
{
IEnumerable<ISequence> seqList = parserObj.Parse(tempFileName);
ISequence seq = seqList.ElementAt(0);
var metadata = (GenBankMetadata) seq.Metadata[Constants.GenBank];
// Add a new features to Genbank features list.
metadata.Features = new SequenceFeatures();
var feature = new FeatureItem(addFirstKey, addFirstLocation);
var qualifierValues = new List<string>();
qualifierValues.Add(addFirstQualifier);
qualifierValues.Add(addFirstQualifier);
feature.Qualifiers.Add(addFirstQualifier, qualifierValues);
metadata.Features.All.Add(feature);
feature = new FeatureItem(addSecondKey, addSecondLocation);
qualifierValues = new List<string>();
qualifierValues.Add(addSecondQualifier);
qualifierValues.Add(addSecondQualifier);
feature.Qualifiers.Add(addSecondQualifier, qualifierValues);
metadata.Features.All.Add(feature);
// Validate added GenBank features.
Assert.AreEqual(metadata.Features.All[0].Key.ToString(null), addFirstKey);
Assert.AreEqual(
localBuilderObj.GetLocationString(metadata.Features.All[0].Location),
addFirstLocation);
Assert.AreEqual(metadata.Features.All[1].Key.ToString(null), addSecondKey);
Assert.AreEqual(localBuilderObj.GetLocationString(metadata.Features.All[1].Location),
addSecondLocation);
parserObj.Close();
}
File.Delete(tempFileName);
}
}
}
public void TestGenBankWhenParsingOne()
{
// parse
ISequenceParser parser = new GenBankParser();
ISequence seq = parser.Parse(_singleProteinSeqGenBankFilename).FirstOrDefault();
// test the non-metadata properties
Assert.AreEqual(Alphabets.DNA, seq.Alphabet);
Assert.AreEqual("SCU49845", seq.ID);
// test the metadata that is tricky to parse, and will not be tested implicitly by
// testing the formatting
GenBankMetadata metadata = (GenBankMetadata)seq.Metadata["GenBank"];
Assert.AreEqual(metadata.Locus.Strand, SequenceStrandType.None);
Assert.AreEqual("none", metadata.Locus.StrandTopology.ToString().ToLower(CultureInfo.CurrentCulture));
Assert.AreEqual("PLN", metadata.Locus.DivisionCode.ToString());
Assert.AreEqual(DateTime.Parse("21-JUN-1999", (IFormatProvider)null), metadata.Locus.Date);
Assert.AreEqual("1", metadata.Version.Version);
Assert.AreEqual("1293613", metadata.Version.GiNumber);
// test that we're correctly putting all types of metadata in the right places
Assert.AreEqual(1, seq.Metadata.Count);
IList<CitationReference> referenceList = metadata.References;
Assert.AreEqual(3, referenceList.Count);
IList<FeatureItem> featureList = metadata.Features.All;
Assert.AreEqual(6, featureList.Count);
Assert.AreEqual(4, featureList[0].Qualifiers.Count);
Assert.AreEqual(5, featureList[1].Qualifiers.Count);
Assert.AreEqual(1, featureList[2].Qualifiers.Count);
// test the sequence string
string expected = @"gatcctccatatacaacggtatctccacctcaggtttagatctcaacaacggaaccattgccgacatgagacagttaggtatcgtcgagagttacaagctaaaacgagcagtagtcagctctgcatctgaagccgctgaagttctactaagggtggataacatcatccgtgcaagaccaagaaccgccaatagacaacatatgtaacatatttaggatatacctcgaaaataataaaccgccacactgtcattattataattagaaacagaacgcaaaaattatccactatataattcaaagacgcgaaaaaaaaagaacaacgcgtcatagaacttttggcaattcgcgtcacaaataaattttggcaacttatgtttcctcttcgagcagtactcgagccctgtctcaagaatgtaataatacccatcgtaggtatggttaaagatagcatctccacaacctcaaagctccttgccgagagtcgccctcctttgtcgagtaattttcacttttcatatgagaacttattttcttattctttactctcacatcctgtagtgattgacactgcaacagccaccatcactagaagaacagaacaattacttaatagaaaaattatatcttcctcgaaacgatttcctgcttccaacatctacgtatatcaagaagcattcacttaccatgacacagcttcagatttcattattgctgacagctactatatcactactccatctagtagtggccacgccctatgaggcatatcctatcggaaaacaataccccccagtggcaagagtcaatgaatcgtttacatttcaaatttccaatgatacctataaatcgtctgtagacaagacagctcaaataacatacaattgcttcgacttaccgagctggctttcgtttgactctagttctagaacgttctcaggtgaaccttcttctgacttactatctgatgcgaacaccacgttgtatttcaatgtaatactcgagggtacggactctgccgacagcacgtctttgaacaatacataccaatttgttgttacaaaccgtccatccatctcgctatcgtcagatttcaatctattggcgttgttaaaaaactatggttatactaacggcaaaaacgctctgaaactagatcctaatgaagtcttcaacgtgacttttgaccgttcaatgttcactaacgaagaatccattgtgtcgtattacggacgttctcagttgtataatgcgccgttacccaattggctgttcttcgattctggcgagttgaagtttactgggacggcaccggtgataaactcggcgattgctccagaaacaagctacagttttgtcatcatcgctacagacattgaaggattttctgccgttgaggtagaattcgaattagtcatcggggctcaccagttaactacctctattcaaaatagtttgataatcaacgttactgacacaggtaacgtttcatatgacttacctctaaactatgtttatctcgatgacgatcctatttcttctgataaattgggttctataaacttattggatgctccagactgggtggcattagataatgctaccatttccgggtctgtcccagatgaattactcggtaagaactccaatcctgccaatttttctgtgtccatttatgatacttatggtgatgtgatttatttcaacttcgaagttgtctccacaacggatttgtttgccattagttctcttcccaatattaacgctacaaggggtgaatggttctcctactattttttgccttctcagtttacagactacgtgaatacaaacgtttcattagagtttactaattcaagccaagaccatgactgggtgaaattccaatcatctaatttaacattagctggagaagtgcccaagaatttcgacaagctttcattaggtttgaaagcgaaccaaggttcacaatctcaagagctatattttaacatcattggcatggattcaaagataactcactcaaaccacagtgcgaatgcaacgtccacaagaagttctcaccactccacctcaacaagttcttacacatcttctacttacactgcaaaaatttcttctacctccgctgctgctacttcttctgctccagcagcgctgccagcagccaataaaacttcatctcacaataaaaaagcagtagcaattgcgtgcggtgttgctatcccattaggcgttatcctagtagctctcatttgcttcctaatattctggagacgcagaagggaaaatccagacgatgaaaacttaccgcatgctattagtggacctgatttgaataatcctgcaaataaaccaaatcaagaaaacgctacacctttgaacaacccctttgatgatgatgcttcctcgtacgatgatacttcaatagcaagaagattggctgctttgaacactttgaaattggataaccactctgccactgaatctgatatttccagcgtggatgaaaagagagattctctatcaggtatgaatacatacaatgatcagttccaatcccaaagtaaagaagaattattagcaaaacccccagtacagcctccagagagcccgttctttgacccacagaataggtcttcttctgtgtatatggatagtgaaccagcagtaaataaatcctggcgatatactggcaacctgtcaccagtctctgatattgtcagagacagttacggatcacaaaaaactgttgatacagaaaaacttttcgatttagaagcaccagagaaggaaaaacgtacgtcaagggatgtcactatgtcttcactggacccttggaacagcaatattagcccttctcccgtaagaaaatcagtaacaccatcaccatataacgtaacgaagcatcgtaaccgccacttacaaaatattcaagactctcaaagcggtaaaaacggaatcactcccacaacaatgtcaacttcatcttctgacgattttgttccggttaaagatggtgaaaatttttgctgggtccatagcatggaaccagacagaagaccaagtaagaaaaggttagtagatttttcaaataagagtaatgtcaatgttggtcaagttaaggacattcacggacgcatcccagaaatgctgtgattatacgcaacgatattttgcttaattttattttcctgttttattttttattagtggtttacagataccctatattttatttagtttttatacttagagacatttaattttaattccattcttcaaatttcatttttgcacttaaaacaaagatccaaaaatgctctcgccctcttcatattgagaatacactccattcaaaattttgtcgtcaccgctgattaatttttcactaaactgatgaataatcaaaggccccacgtcagaaccgactaaagaagtgagttttattttaggaggttgaaaaccattattgtctggtaaattttcatcttcttgacatttaacccagtttgaatccctttcaatttctgctttttcctccaaactatcgaccctcctgtttctgtccaacttatgtcctagttccaattcgatcgcattaataactgcttcaaatgttattgtgtcatcgttgactttaggtaatttctccaaatgcataatcaaactatttaaggaagatcggaattcgtcgaacacttcagtttccgtaatgatctgatcgtctttatccacatgttgtaattcactaaaatctaaaacgtatttttcaatgcataaatcgttctttttattaataatgcagatggaaaatctgtaaacgtgcgttaatttagaaagaacatccagtataagttcttctatatagtcaattaaagcaggatgcctattaatgggaacgaactgcggcaagttgaatgactggtaagtagtgtagtcgaatgactgaggtgggtatacatttctataaaataaaatcaaattaatgtagcattttaagtataccctcagccacttctctacccatctattcataaagctgacgcaacgattactattttttttttcttcttggatctcagtcgtcgcaaaaacgtataccttctttttccgaccttttttttagctttctggaaaagtttatattagttaaacagggtctagtcttagtgtgaaagctagtggtttcgattgactgatattaagaaagtggaaattaaattagtagtgtagacgtatatgcatatgtatttctcgcctgtttatgtttctacgtacttttgatttatagcaaggggaaaagaaatacatactattttttggtaaaggtgaaagcataatgtaaaagctagaataaaatggacgaaataaagagaggcttagttcatcttttttccaaaaagcacccaatgataataactaaaatgaaaaggatttgccatctgtcagcaacatcagttgtgtgagcaataataaaatcatcacctccgttgcctttagcgcgtttgtcgtttgtatcttccgtaattttagtcttatcaatgggaatcataaattttccaatgaattagcaatttcgtccaattctttttgagcttcttcatatttgctttggaattcttcgcacttcttttcccattcatctctttcttcttccaaagcaacgatccttctacccatttgctcagagttcaaatcggcctctttcagtttatccattgcttccttcagtttggcttcactgtcttctagctgttgttctagatcctggtttttcttggtgtagttctcattattagatctcaagttattggagtcttcagccaattgctttgtatcagacaattgactctctaacttctccacttcactgtcgagttgctcgtttttagcggacaaagatttaatctcgttttctttttcagtgttagattgctctaattctttgagctgttctctcagctcctcatatttttcttgccatgactcagattctaattttaagctattcaatttctctttgatc";
Assert.AreEqual(expected, new string(seq.Select(a => (char)a).ToArray()));
// format
ISequenceFormatter formatter = new GenBankFormatter();
formatter.Format(seq, TempGenBankFileName);
string actual = string.Empty;
using (StreamReader reader = new StreamReader(TempGenBankFileName))
{
actual = reader.ReadToEnd();
}
File.Delete(TempGenBankFileName);
// test the formatting
Assert.AreEqual(_singleProteinSeqGenBankFileExpectedOutput.Replace(" ", "").Replace("\r\n", Environment.NewLine), actual.Replace(" ", ""));
}
/// <summary>
/// Validate GenBank features.
/// </summary>
/// <param name="nodeName">xml node name.</param>
/// <param name="methodName">Name of the method</param>
private void ValidateGenBankFeatures(string nodeName,
string methodName)
{
// Get Values from XML node.
string filePath = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.FilePathNode);
string alphabetName = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.AlphabetNameNode);
string expectedSequence = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ExpectedSequenceNode);
string mRNAFeatureCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.mRNACount);
string exonFeatureCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ExonCount);
string intronFeatureCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.IntronCount);
string cdsFeatureCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.CDSCount);
string allFeaturesCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.GenBankFeaturesCount);
string expectedCDSKey = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.CDSKey);
string expectedIntronKey = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.IntronKey);
string expectedExonKey = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ExonKey);
string mRNAKey = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.mRNAKey);
string sourceKeyName = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.SourceKey);
string proteinKey = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ProteinKeyName);
string tempFileName = Path.GetTempFileName();
ISequenceParser parserObj = new GenBankParser();
IEnumerable<ISequence> sequenceList = parserObj.Parse(filePath);
if (sequenceList.Count() == 1)
{
string expectedUpdatedSequence =
expectedSequence.Replace("\r", "").Replace("\n", "").Replace(" ", "");
var orgSeq = new Sequence(Utility.GetAlphabet(alphabetName), expectedUpdatedSequence);
orgSeq.ID = sequenceList.ElementAt(0).ID;
orgSeq.Metadata.Add(Constants.GenBank,
sequenceList.ElementAt(0).Metadata[Constants.GenBank]);
ISequenceFormatter formatterObj = new GenBankFormatter();
formatterObj.Format(orgSeq, tempFileName);
}
else
{
string expectedUpdatedSequence =
expectedSequence.Replace("\r", "").Replace("\n", "").Replace(" ", "");
var orgSeq =
new Sequence(Utility.GetAlphabet(alphabetName), expectedUpdatedSequence)
{
ID = sequenceList.ElementAt(1).ID
};
orgSeq.Metadata.Add(Constants.GenBank,
sequenceList.ElementAt(1).Metadata[Constants.GenBank]);
ISequenceFormatter formatterObj = new GenBankFormatter();
formatterObj.Format(orgSeq, tempFileName);
}
// parse a temporary file.
var tempParserObj = new GenBankParser();
{
IEnumerable<ISequence> tempFileSeqList = tempParserObj.Parse(tempFileName);
ISequence sequence = tempFileSeqList.ElementAt(0);
var metadata = (GenBankMetadata) sequence.Metadata[Constants.GenBank];
// Validate formatted temporary file GenBank Features.
Assert.AreEqual(metadata.Features.All.Count,
Convert.ToInt32(allFeaturesCount, null));
Assert.AreEqual(metadata.Features.CodingSequences.Count,
Convert.ToInt32(cdsFeatureCount, null));
Assert.AreEqual(metadata.Features.Exons.Count,
Convert.ToInt32(exonFeatureCount, null));
Assert.AreEqual(metadata.Features.Introns.Count,
Convert.ToInt32(intronFeatureCount, null));
Assert.AreEqual(metadata.Features.MessengerRNAs.Count,
Convert.ToInt32(mRNAFeatureCount, null));
Assert.AreEqual(metadata.Features.Attenuators.Count, 0);
Assert.AreEqual(metadata.Features.CAATSignals.Count, 0);
Assert.AreEqual(metadata.Features.DisplacementLoops.Count, 0);
Assert.AreEqual(metadata.Features.Enhancers.Count, 0);
Assert.AreEqual(metadata.Features.Genes.Count, 0);
if ((0 == string.Compare(methodName, "DNA",
CultureInfo.CurrentCulture, CompareOptions.IgnoreCase))
|| (0 == string.Compare(methodName, "RNA",
CultureInfo.CurrentCulture, CompareOptions.IgnoreCase)))
{
IList<FeatureItem> featureList = metadata.Features.All;
Assert.AreEqual(featureList[0].Key.ToString(null), sourceKeyName);
Assert.AreEqual(featureList[1].Key.ToString(null), mRNAKey);
Assert.AreEqual(featureList[3].Key.ToString(null), expectedCDSKey);
Assert.AreEqual(featureList[5].Key.ToString(null), expectedExonKey);
Assert.AreEqual(featureList[6].Key.ToString(null), expectedIntronKey);
ApplicationLog.WriteLine(
"GenBank Features BVT: Successfully validated the GenBank Features");
ApplicationLog.WriteLine(string.Format(null,
"GenBank Features BVT: Successfully validated the CDS feature '{0}'",
featureList[3].Key.ToString(null)));
ApplicationLog.WriteLine(string.Format(null,
"GenBank Features BVT: Successfully validated the Exon feature '{0}'",
featureList[5].Key.ToString(null)));
}
else
{
IList<FeatureItem> proFeatureList = metadata.Features.All;
Assert.AreEqual(proFeatureList[0].Key.ToString(null), sourceKeyName);
Assert.AreEqual(proFeatureList[1].Key.ToString(null), proteinKey);
Assert.AreEqual(proFeatureList[2].Key.ToString(null), expectedCDSKey);
ApplicationLog.WriteLine(
"GenBank Features BVT: Successfully validated the GenBank Features");
ApplicationLog.WriteLine(string.Format(null,
"GenBank Features BVT: Successfully validated the CDS feature '{0}'",
proFeatureList[2].Key.ToString(null)));
ApplicationLog.WriteLine(string.Format(null,
"GenBank Features BVT: Successfully validated the Source feature '{0}'",
proFeatureList[0].Key.ToString(null)));
}
}
File.Delete(tempFileName);
}
public void GenBankFormatterValidateWriteUsingStream()
{
InitializeXmlVariables();
// Create a Sequence with all attributes.
// Parse and update the properties instead of parsing entire file.
ISequenceParser parser1 = new GenBankParser();
{
IEnumerable<ISequence> seqList1 = parser1.Parse(FilePath);
string tempFileName = Path.GetTempFileName();
GenBankMetadata metadata = null;
ISequence seq = null;
string expectedUpdatedSequence =
ExpectedSequence.Replace("\r", "").Replace("\n", "").Replace(" ", "");
var orgSeq =
new Sequence(Utility.GetAlphabet(AlphabetName), expectedUpdatedSequence);
orgSeq.Metadata.Add("GenBank",
seqList1.ElementAt(0).Metadata["GenBank"]);
orgSeq.ID = seqList1.ElementAt(0).ID;
ISequenceFormatter formatter = new GenBankFormatter();
{
using (formatter.Open(tempFileName))
{
formatter.Format(orgSeq);
}
}
var parserObj = new GenBankParser();
{
IEnumerable<ISequence> seqList = parserObj.Parse(tempFileName);
seq = seqList.ElementAt(0);
Assert.AreEqual(Utility.GetAlphabet(AlphabetName), seq.Alphabet);
Assert.AreEqual(SeqId, seq.ID);
ApplicationLog.WriteLine(
"GenBank Formatter BVT: Successfully validated the Alphabet, Molecular type, Sequence ID and Display ID");
// test the metadata that is tricky to parse, and will not be tested implicitly by
// testing the formatting
metadata = (GenBankMetadata) seq.Metadata["GenBank"];
if (metadata.Locus.Strand != SequenceStrandType.None)
{
Assert.AreEqual(StrandType, metadata.Locus.Strand.ToString());
}
}
Assert.AreEqual(StrandTopology.ToUpper(CultureInfo.CurrentCulture),
metadata.Locus.StrandTopology.ToString().ToUpper(CultureInfo.CurrentCulture));
Assert.AreEqual(Div, metadata.Locus.DivisionCode.ToString());
Assert.AreEqual(DateTime.Parse(SequenceDate, null), metadata.Locus.Date);
Assert.AreEqual(Version, metadata.Version.Version.ToString(null));
Assert.AreEqual(PrimaryId, metadata.Version.GiNumber);
ApplicationLog.WriteLine(
"GenBank Formatter BVT: Successfully validated the StrandType, StrandTopology, Division, Date, Version, PrimaryID Properties");
// test the sequence string
Assert.AreEqual(ExpectedSequence, new string(seq.Select(a => (char) a).ToArray()));
ApplicationLog.WriteLine("GenBank Formatter BVT: Successfully validated the Sequence");
File.Delete(tempFileName);
}
}
public void GenBankFormatterWithParseValidateWriteFilePath()
{
InitializeXmlVariables();
// parse
ISequenceParser parserObj = new GenBankParser();
{
IEnumerable<ISequence> seqList = parserObj.Parse(FilePath);
ISequence seq = seqList.ElementAt(0);
string tempFileName = Path.GetTempFileName();
ISequenceFormatter formatter = new GenBankFormatter();
{
formatter.Format(seq, tempFileName);
// parse
ISequenceParser parserObjFromFile = new GenBankParser();
seqList = parserObjFromFile.Parse(tempFileName);
seq = seqList.ElementAt(0);
Assert.AreEqual(Utility.GetAlphabet(AlphabetName), seq.Alphabet);
Assert.AreEqual(SeqId, seq.ID);
ApplicationLog.WriteLine(
"GenBank Formatter BVT: Successfully validated the Alphabet, Molecular type, Sequence ID and Display ID");
// test the metadata that is tricky to parse, and will not be tested implicitly by
// testing the formatting
var metadata =
(GenBankMetadata) seq.Metadata["GenBank"];
if (metadata.Locus.Strand != SequenceStrandType.None)
{
Assert.AreEqual(StrandType,
metadata.Locus.Strand.ToString());
}
Assert.AreEqual(StrandTopology.ToUpper(CultureInfo.CurrentCulture),
metadata.Locus.StrandTopology.ToString().ToUpper(CultureInfo.CurrentCulture));
Assert.AreEqual(Div, metadata.Locus.DivisionCode.ToString());
Assert.AreEqual(DateTime.Parse(SequenceDate, null),
metadata.Locus.Date);
Assert.AreEqual(Version, metadata.Version.Version.ToString(null));
Assert.AreEqual(PrimaryId, metadata.Version.GiNumber);
ApplicationLog.WriteLine(
"GenBank Formatter BVT: Successfully validated the StrandType, StrandTopology, Division, Date, Version, PrimaryID Properties");
// test the sequence string
Assert.AreEqual(ExpectedSequence, new string(seq.Select(a => (char) a).ToArray()));
ApplicationLog.WriteLine(
"GenBank Formatter BVT: Successfully validated the Sequence");
File.Delete(tempFileName);
}
}
}
/// <summary>
/// Validates GenBank Formatter for General test cases.
/// </summary>
/// <param name="seqList">sequence list.</param>
private static void ValidateWriteGeneralTestCases(IEnumerable<ISequence> seqList1)
{
// Create a Sequence with all attributes.
// Parse and update the properties instead of parsing entire file.
string expectedUpdatedSequence =
ExpectedSequence.Replace("\r", "").Replace("\n", "").Replace(" ", "");
Sequence orgSeq =
new Sequence(Utility.GetAlphabet(AlphabetName), expectedUpdatedSequence);
orgSeq.Metadata.Add("GenBank",
(GenBankMetadata)seqList1.ElementAt(0).Metadata["GenBank"]);
orgSeq.ID = seqList1.ElementAt(0).ID;
string tempFileName = System.IO.Path.GetTempFileName();
ISequenceFormatter formatter = new GenBankFormatter();
formatter.Format(orgSeq, tempFileName);
// parse
GenBankParser parserObj = new GenBankParser();
IEnumerable<ISequence> seqList = parserObj.Parse(tempFileName);
ISequence seq = seqList.ElementAt(0);
Assert.AreEqual(Utility.GetAlphabet(AlphabetName), seq.Alphabet);
Assert.AreEqual(SeqId, seq.ID);
ApplicationLog.WriteLine(
"GenBank Formatter P1: Successfully validated the Alphabet, Molecular type, Sequence ID and Display ID");
// test the metadata that is tricky to parse, and will not be tested implicitly by
// testing the formatting
GenBankMetadata metadata =
(GenBankMetadata)seq.Metadata["GenBank"];
if (metadata.Locus.Strand != SequenceStrandType.None)
{
Assert.AreEqual(StrandType,
metadata.Locus.Strand.ToString());
}
if (metadata.Locus.Strand != SequenceStrandType.None)
{
Assert.AreEqual(StrandTopology.ToUpper(CultureInfo.CurrentCulture),
metadata.Locus.StrandTopology.ToString().ToUpper(CultureInfo.CurrentCulture));
}
if (metadata.Locus.DivisionCode != SequenceDivisionCode.None)
{
Assert.AreEqual(Div,
metadata.Locus.DivisionCode.ToString());
}
Assert.AreEqual(DateTime.Parse(SequenceDate, null),
metadata.Locus.Date);
if (0 != string.Compare(AlphabetName, "rna",
CultureInfo.CurrentCulture, CompareOptions.IgnoreCase))
{
Assert.AreEqual(Version, metadata.Version.Version.ToString((IFormatProvider)null));
Assert.AreEqual(PrimaryId, metadata.Version.GiNumber);
ApplicationLog.WriteLine(
"GenBank Parser : Successfully validated the StrandType, StrandTopology, Division, Date, Version, PrimaryID Properties");
}
else
{
ApplicationLog.WriteLine(
"GenBank Parser : Successfully validated the StrandType, StrandTopology, Division, Date Properties");
}
string truncatedExpectedSequence =
ExpectedSequence.Replace("\r", "").Replace("\n", "").Replace(" ", "").ToUpper(
CultureInfo.CurrentCulture);
string truncatedActualSequence =
new string(seq.Select(a => (char)a).ToArray()).Replace("\r", "").Replace("\n", "").Replace(" ", "").ToUpper(
CultureInfo.CurrentCulture);
// test the sequence string
Assert.AreEqual(truncatedExpectedSequence, truncatedActualSequence);
ApplicationLog.WriteLine(
"GenBank Formatter P1: Successfully validated the Sequence");
File.Delete(tempFileName);
}
/// <summary>
/// Validates GenBank Formatter for the files which are
/// Parsed using GenBankParser for General test cases.
/// </summary>
private static void ValidateParseWriterGeneralTestCases()
{
Assert.IsTrue(File.Exists(FilePath));
// Logs information to the log file
ApplicationLog.WriteLine(string.Format("GenBank Parser : File Exists in the Path '{0}'.", FilePath));
string tempFileName = Path.GetTempFileName();
// parse
ISequenceParser parserObj = new GenBankParser();
{
IEnumerable<ISequence> seqList = parserObj.Parse(FilePath);
ISequence seq = seqList.ElementAt(0);
ISequenceFormatter formatter = new GenBankFormatter();
{
formatter.Format(seq, tempFileName);
FilePath = tempFileName;
ValidateParserGeneralTestCases();
}
}
}
