/// <summary>
/// Initializes a new instance of the GenBankParser class.
/// </summary>
/// <param name="filename">Name of the File.</param>
public GenBankParser(string filename)
{
if (string.IsNullOrEmpty(filename))
{
throw new InvalidDataException();
}
Filename = filename;
LocationBuilder = new LocationBuilder();
}
/// <summary>
/// Initializes a new instance of the GenBankParser class.
/// </summary>
/// <param name="filename">Name of the File.</param>
public GenBankParser(string filename)
{
if (string.IsNullOrEmpty(filename))
{
throw new InvalidDataException();
}
Filename = filename;
LocationBuilder = new LocationBuilder();
}
/// <summary>
/// Default constructor chooses default encoding based on alphabet.
/// </summary>
public GenBankParser()
{
LocationBuilder = new LocationBuilder();
}
/// <summary>
/// Validate general Location builder.
/// </summary>
/// <param name="operatorPam">Different operator parameter name</param>
/// <param name="nodeName">Different location string node name</param>
/// <param name="isOperator">True if operator else false.</param>
private void ValidateLocationBuilder(string nodeName,
LocationOperatorParameter operatorPam, bool isOperator)
{
// Get Values from XML node.
string locationString = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.LocationStringValue);
string locationStartPosition = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.LoocationStartNode);
string locationEndPosition = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.LoocationEndNode);
string locationSeperatorNode = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.LocationSeperatorNode);
string expectedLocationString = string.Empty;
string sublocationStartPosition = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.SubLocationStart);
string sublocationEndPosition = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.SubLocationEnd);
string sublocationSeperatorNode = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.SubLocationSeperator);
string subLocationsCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.SubLocationCount);
// Build a new location
ILocationBuilder locationBuilderObj = new LocationBuilder();
ILocation location = locationBuilderObj.GetLocation(locationString);
expectedLocationString = locationBuilderObj.GetLocationString(location);
// Validate constructed location starts,end and location string.
Assert.AreEqual(locationStartPosition, location.LocationStart.ToString((IFormatProvider) null));
Assert.AreEqual(locationString, expectedLocationString);
Assert.AreEqual(locationEndPosition, location.LocationEnd.ToString((IFormatProvider) null));
switch (operatorPam)
{
case LocationOperatorParameter.Join:
Assert.AreEqual(LocationOperator.Join, location.Operator);
break;
case LocationOperatorParameter.Complement:
Assert.AreEqual(LocationOperator.Complement, location.Operator);
break;
case LocationOperatorParameter.Order:
Assert.AreEqual(LocationOperator.Order, location.Operator);
break;
default:
Assert.AreEqual(LocationOperator.None, location.Operator);
Assert.AreEqual(locationSeperatorNode,
location.Separator.ToString(null));
Assert.IsTrue(string.IsNullOrEmpty(location.Accession));
Assert.IsNotNull(location.SubLocations);
break;
}
if (isOperator)
{
Assert.IsTrue(string.IsNullOrEmpty(location.Separator));
Assert.AreEqual(sublocationEndPosition,
location.SubLocations[0].LocationEnd.ToString((IFormatProvider) null));
Assert.AreEqual(sublocationSeperatorNode,
location.SubLocations[0].Separator.ToString(null));
Assert.AreEqual(Convert.ToInt32(subLocationsCount, null),
location.SubLocations.Count);
Assert.AreEqual(sublocationStartPosition,
location.SubLocations[0].LocationStart.ToString((IFormatProvider) null));
Assert.AreEqual(LocationOperator.None,
location.SubLocations[0].Operator);
Assert.AreEqual(0,
location.SubLocations[0].SubLocations.Count);
}
}
/// <summary>
/// Default constructor.
/// </summary>
public GenBankFormatter()
{
LocationBuilder = new LocationBuilder();
}
/// <summary>
/// Constructor for setting the encoding.
/// </summary>
/// <param name="encoding">The encoding to use for parsed ISequence objects.</param>
public GenBankParser(IEncoding encoding)
: base(encoding)
{
LocationBuilder = new LocationBuilder();
}
/// <summary>
/// Validate PrecursorRNA features
/// </summary>
/// <param name="nodeName">XML node name</param>
/// <param name="genMetadata">GenBank Metadata</param>
private void ValidateGenBankPrecursorRNAFeature(string nodeName,
GenBankMetadata genMetadata)
{
// Get Values from XML node.
string expectedLocation = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.Location);
string expectedAllele = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.AlleleNode);
string featureCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.QualifierCount);
string expectedDbReference = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.DbReferenceNode);
string geneSymbol = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.GeneSymbol);
string expectedCitation = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.CitationNode);
string expectedExperiment = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ExperimentNode);
string expectedFunction = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.FunctionNode);
string expectedGeneSynonym = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.GeneSynonymNode);
string expectedInference = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.InferenceNode);
string expectedLabel = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.LabelNode);
string expectedLocusTag = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.LocusTagNode);
string expectedNote = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.Note);
string expectedOldLocusTag = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.OldLocusTagNode);
string expectedMap = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.GenbankMapNode);
List<PrecursorRna> precursorRNAFeatureList =
genMetadata.Features.PrecursorRNAs;
var locBuilder = new LocationBuilder();
// Create a copy of Precursor RNA feature.
PrecursorRna clonePrecursorRNA =
precursorRNAFeatureList[0].Clone();
// Validate Precursor RNA qualifiers.
Assert.AreEqual(precursorRNAFeatureList.Count.ToString((IFormatProvider) null),
featureCount);
Assert.AreEqual(clonePrecursorRNA.GeneSymbol,
geneSymbol);
Assert.AreEqual(clonePrecursorRNA.DatabaseCrossReference[0],
expectedDbReference);
Assert.AreEqual(precursorRNAFeatureList[0].Allele,
expectedAllele);
Assert.AreEqual(precursorRNAFeatureList[0].Citation[0],
expectedCitation);
Assert.AreEqual(precursorRNAFeatureList[0].Experiment[0],
expectedExperiment);
Assert.AreEqual(precursorRNAFeatureList[0].GenomicMapPosition,
expectedMap);
Assert.AreEqual(precursorRNAFeatureList[0].GeneSynonym[0],
expectedGeneSynonym);
Assert.AreEqual(precursorRNAFeatureList[0].Inference[0],
expectedInference);
Assert.AreEqual(precursorRNAFeatureList[0].Label, expectedLabel);
Assert.AreEqual(locBuilder.GetLocationString(
genMetadata.Features.PrecursorRNAs[0].Location),
expectedLocation);
Assert.AreEqual(precursorRNAFeatureList[0].Note[0],
expectedNote);
Assert.AreEqual(precursorRNAFeatureList[0].OldLocusTag[0],
expectedOldLocusTag);
Assert.AreEqual(precursorRNAFeatureList[0].LocusTag[0],
expectedLocusTag);
Assert.AreEqual(precursorRNAFeatureList[0].Function[0],
expectedFunction);
Assert.IsTrue(string.IsNullOrEmpty(precursorRNAFeatureList[0].StandardName));
Assert.IsFalse(string.IsNullOrEmpty(precursorRNAFeatureList[0].Product.ToString()));
Assert.IsTrue(string.IsNullOrEmpty(precursorRNAFeatureList[0].Operon));
Assert.IsFalse(precursorRNAFeatureList[0].TransSplicing);
// Create a new Precursor RNA and validate the same.
var precursorRNA = new PrecursorRna(expectedLocation);
var precursorRNAWithILoc = new PrecursorRna(
genMetadata.Features.PrecursorRNAs[0].Location);
// Set qualifiers and validate them.
precursorRNA.Allele = expectedAllele;
precursorRNA.GeneSymbol = geneSymbol;
precursorRNAWithILoc.GenomicMapPosition = expectedMap;
Assert.AreEqual(precursorRNA.GeneSymbol, geneSymbol);
Assert.AreEqual(precursorRNA.Allele, expectedAllele);
Assert.AreEqual(precursorRNAWithILoc.GenomicMapPosition, expectedMap);
}
public void ValidateCompareGenBankLocationsObject()
{
// Get Values from XML node.
string locationFirstInput = utilityObj.xmlUtil.GetTextValue(
Constants.CompareLocationsNode, Constants.Location1Node);
string locationSecondInput = utilityObj.xmlUtil.GetTextValue(
Constants.CompareLocationsNode, Constants.Location2Node);
string locationThirdInput = utilityObj.xmlUtil.GetTextValue(
Constants.CompareLocationsNode, Constants.Location3Node);
// Create two location instance.
ILocationBuilder locBuilder = new LocationBuilder();
ILocation loc1 = locBuilder.GetLocation(locationFirstInput);
object loc2 = locBuilder.GetLocation(locationSecondInput);
object loc3 = locBuilder.GetLocation(locationThirdInput);
// Compare first and second location instances.
Assert.AreEqual(0, loc1.CompareTo(loc2));
// Compare first and third location which are not identical.
Assert.AreEqual(-1, loc1.CompareTo(loc3));
// Compare first and null location.
Assert.AreEqual(1, loc1.CompareTo(null));
ApplicationLog.WriteLine(
"GenBank Features P1: Successfully validated the GenBank Features");
}
/// <summary>
/// Validate StemLoop features
/// </summary>
/// <param name="nodeName">XML node name</param>
/// <param name="genMetadata">GenBank Metadata</param>
private void ValidateGenBankStemLoopFeature(string nodeName,
GenBankMetadata genMetadata)
{
// Get Values from XML node.
string expectedLocation = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.Location);
string expectedAllele = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.AlleleNode);
string featureCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.QualifierCount);
string expectedDbReference = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.DbReferenceNode);
string geneSymbol = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.GeneSymbol);
string expectedCitation = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.CitationNode);
string expectedExperiment = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ExperimentNode);
string expectedFunction = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.FunctionNode);
string expectedGeneSynonym = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.GeneSynonymNode);
string expectedInference = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.InferenceNode);
string expectedLabel = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.LabelNode);
string expectedLocusTag = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.LocusTagNode);
string expectedNote = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.Note);
string expectedOldLocusTag = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.OldLocusTagNode);
string expectedMap = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.GenbankMapNode);
List<StemLoop> sLoopFeatureList = genMetadata.Features.StemLoops;
var locBuilder = new LocationBuilder();
// Create a copy of StemLoop feature.
StemLoop cloneSLoop = sLoopFeatureList[0].Clone();
// Validate transit peptide qualifiers.
Assert.AreEqual(sLoopFeatureList.Count.ToString((IFormatProvider) null),
featureCount);
Assert.AreEqual(cloneSLoop.GeneSymbol, geneSymbol);
Assert.AreEqual(cloneSLoop.DatabaseCrossReference[0],
expectedDbReference);
Assert.AreEqual(sLoopFeatureList[0].Allele,
expectedAllele);
Assert.AreEqual(sLoopFeatureList[0].Citation[0],
expectedCitation);
Assert.AreEqual(sLoopFeatureList[0].Experiment[0],
expectedExperiment);
Assert.AreEqual(sLoopFeatureList[0].GenomicMapPosition,
expectedMap);
Assert.AreEqual(sLoopFeatureList[0].GeneSynonym[0],
expectedGeneSynonym);
Assert.AreEqual(sLoopFeatureList[0].Inference[0],
expectedInference);
Assert.AreEqual(sLoopFeatureList[0].Label,
expectedLabel);
Assert.AreEqual(locBuilder.GetLocationString(
genMetadata.Features.StemLoops[0].Location),
expectedLocation);
Assert.AreEqual(sLoopFeatureList[0].Note[0],
expectedNote);
Assert.AreEqual(sLoopFeatureList[0].OldLocusTag[0],
expectedOldLocusTag);
Assert.AreEqual(sLoopFeatureList[0].LocusTag[0],
expectedLocusTag);
Assert.AreEqual(sLoopFeatureList[0].Function[0],
expectedFunction);
Assert.IsTrue(string.IsNullOrEmpty(sLoopFeatureList[0].Operon));
Assert.IsTrue(string.IsNullOrEmpty(sLoopFeatureList[0].StandardName));
// Create a new StemLoop and validate the same.
var stemLoop = new StemLoop(expectedLocation);
var stemLoopWithILoc = new StemLoop(
genMetadata.Features.StemLoops[0].Location);
// Set qualifiers and validate them.
stemLoop.Allele = expectedAllele;
stemLoop.GeneSymbol = geneSymbol;
stemLoopWithILoc.GenomicMapPosition = expectedMap;
Assert.AreEqual(stemLoop.GeneSymbol, geneSymbol);
Assert.AreEqual(stemLoop.Allele, expectedAllele);
Assert.AreEqual(stemLoopWithILoc.GenomicMapPosition,
expectedMap);
}
/// <summary>
/// Validate ModifiedBase features
/// </summary>
/// <param name="nodeName">XML node name</param>
/// <param name="genMetadata">GenBank Metadata</param>
private void ValidateGenBankModifiedBaseFeature(string nodeName,
GenBankMetadata genMetadata)
{
// Get Values from XML node.
string expectedLocation = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.Location);
string expectedAllele = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.AlleleNode);
string featureCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.QualifierCount);
string expectedDbReference = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.DbReferenceNode);
string geneSymbol = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.GeneSymbol);
string expectedCitation = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.CitationNode);
string expectedExperiment = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ExperimentNode);
string expectedGeneSynonym = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.GeneSynonymNode);
string expectedInference = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.InferenceNode);
string expectedLabel = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.LabelNode);
string expectedLocusTag = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.LocusTagNode);
string expectedNote = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.Note);
string expectedOldLocusTag = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.OldLocusTagNode);
string expectedMap = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.GenbankMapNode);
List<ModifiedBase> modifiedBaseFeatureList =
genMetadata.Features.ModifiedBases;
var locBuilder = new LocationBuilder();
// Create a copy of Modified base feature.
ModifiedBase cloneModifiedBase = modifiedBaseFeatureList[0].Clone();
// Validate Modified Base qualifiers.
Assert.AreEqual(modifiedBaseFeatureList.Count.ToString((IFormatProvider) null),
featureCount);
Assert.AreEqual(cloneModifiedBase.GeneSymbol,
geneSymbol);
Assert.AreEqual(cloneModifiedBase.DatabaseCrossReference[0],
expectedDbReference);
Assert.AreEqual(modifiedBaseFeatureList[0].Allele,
expectedAllele);
Assert.AreEqual(modifiedBaseFeatureList[0].Citation[0],
expectedCitation);
Assert.AreEqual(modifiedBaseFeatureList[0].Experiment[0],
expectedExperiment);
Assert.AreEqual(modifiedBaseFeatureList[0].GenomicMapPosition,
expectedMap);
Assert.AreEqual(modifiedBaseFeatureList[0].GeneSynonym[0],
expectedGeneSynonym);
Assert.AreEqual(modifiedBaseFeatureList[0].Inference[0],
expectedInference);
Assert.AreEqual(modifiedBaseFeatureList[0].Label,
expectedLabel);
Assert.AreEqual(locBuilder.GetLocationString(
genMetadata.Features.ModifiedBases[0].Location),
expectedLocation);
Assert.AreEqual(modifiedBaseFeatureList[0].Note[0],
expectedNote);
Assert.AreEqual(modifiedBaseFeatureList[0].OldLocusTag[0],
expectedOldLocusTag);
Assert.AreEqual(modifiedBaseFeatureList[0].LocusTag[0],
expectedLocusTag);
Assert.IsFalse(string.IsNullOrEmpty(modifiedBaseFeatureList[0].ModifiedNucleotideBase.ToString()));
// Create a new ModifiedBase and validate the same.
var modifiedBase = new ModifiedBase(expectedLocation);
var modifiedBaseWithILoc = new ModifiedBase(
genMetadata.Features.ModifiedBases[0].Location);
// Set qualifiers and validate them.
modifiedBase.Allele = expectedAllele;
modifiedBase.GeneSymbol = geneSymbol;
modifiedBaseWithILoc.GenomicMapPosition = expectedMap;
Assert.AreEqual(modifiedBase.GeneSymbol, geneSymbol);
Assert.AreEqual(modifiedBase.Allele, expectedAllele);
Assert.AreEqual(modifiedBaseWithILoc.GenomicMapPosition,
expectedMap);
}
/// <summary>
/// Validate TrnsitPeptide features
/// </summary>
/// <param name="nodeName">XML node name</param>
/// <param name="genMetadata">GenBank Metadata</param>
private void ValidateGenBankTrnsitPeptideFeature(string nodeName,
GenBankMetadata genMetadata)
{
// Get Values from XML node.
string expectedLocation = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.Location);
string expectedAllele = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.AlleleNode);
string featureCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.QualifierCount);
string expectedDbReference = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.DbReferenceNode);
string geneSymbol = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.GeneSymbol);
string expectedCitation = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.CitationNode);
string expectedExperiment = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ExperimentNode);
string expectedFunction = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.FunctionNode);
string expectedGeneSynonym = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.GeneSynonymNode);
string expectedInference = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.InferenceNode);
string expectedLabel = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.LabelNode);
string expectedLocusTag = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.LocusTagNode);
string expectedNote = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.Note);
string expectedOldLocusTag = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.OldLocusTagNode);
string expectedMap = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.GenbankMapNode);
List<TransitPeptide> tansitPeptideFeatureList =
genMetadata.Features.TransitPeptides;
var locBuilder = new LocationBuilder();
// Create a copy of transit peptide features.
TransitPeptide cloneTransit = tansitPeptideFeatureList[0].Clone();
// Validate transit peptide qualifiers.
Assert.AreEqual(tansitPeptideFeatureList.Count.ToString((IFormatProvider) null), featureCount);
Assert.AreEqual(cloneTransit.GeneSymbol, geneSymbol);
Assert.AreEqual(cloneTransit.DatabaseCrossReference[0],
expectedDbReference);
Assert.AreEqual(tansitPeptideFeatureList[0].Allele,
expectedAllele);
Assert.AreEqual(tansitPeptideFeatureList[0].Citation[0],
expectedCitation);
Assert.AreEqual(tansitPeptideFeatureList[0].Experiment[0],
expectedExperiment);
Assert.AreEqual(tansitPeptideFeatureList[0].GenomicMapPosition,
expectedMap);
Assert.AreEqual(tansitPeptideFeatureList[0].GeneSynonym[0],
expectedGeneSynonym);
Assert.AreEqual(tansitPeptideFeatureList[0].Inference[0],
expectedInference);
Assert.AreEqual(tansitPeptideFeatureList[0].Label,
expectedLabel);
Assert.AreEqual(locBuilder.GetLocationString(
genMetadata.Features.TransitPeptides[0].Location),
expectedLocation);
Assert.AreEqual(tansitPeptideFeatureList[0].Note[0],
expectedNote);
Assert.AreEqual(tansitPeptideFeatureList[0].OldLocusTag[0],
expectedOldLocusTag);
Assert.AreEqual(tansitPeptideFeatureList[0].LocusTag[0],
expectedLocusTag);
Assert.AreEqual(tansitPeptideFeatureList[0].Function[0],
expectedFunction);
// Create a new TransitPeptide and validate the same.
var tPeptide = new TransitPeptide(expectedLocation);
var tPeptideWithILoc = new TransitPeptide(
genMetadata.Features.TransitPeptides[0].Location);
// Set qualifiers and validate them.
tPeptide.Allele = expectedAllele;
tPeptide.GeneSymbol = geneSymbol;
tPeptideWithILoc.GenomicMapPosition = expectedMap;
Assert.AreEqual(tPeptide.GeneSymbol, geneSymbol);
Assert.AreEqual(tPeptide.Allele, expectedAllele);
Assert.AreEqual(tPeptideWithILoc.GenomicMapPosition,
expectedMap);
}
/// <summary>
/// Validate GenBank Promoter feature qualifiers.
/// </summary>
/// <param name="nodeName">xml node name.</param>
private void ValidateGenBankPromoterFeatureQualifiers(string nodeName)
{
// Get Values from XML node.
string filePath = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.FilePathNode);
string expectedPromoterComplement = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.PromoterComplement);
string expectedPromoterCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.PromoterCount);
// Parse a GenBank file.
ISequenceParser parserObj = new GenBankParser();
{
IEnumerable<ISequence> seqList = parserObj.Parse(filePath);
var locBuilder = new LocationBuilder();
// Validate Misc feature all qualifiers.
var metadata =
(GenBankMetadata) seqList.ElementAt(0).Metadata[Constants.GenBank];
List<Promoter> promotersFeatureList =
metadata.Features.Promoters;
Assert.AreEqual(locBuilder.GetLocationString(
metadata.Features.Promoters[0].Location),
expectedPromoterComplement);
Assert.AreEqual(promotersFeatureList.Count.ToString((IFormatProvider) null),
expectedPromoterCount);
Assert.IsTrue(string.IsNullOrEmpty(promotersFeatureList[0].GeneSymbol));
Assert.IsTrue(string.IsNullOrEmpty(promotersFeatureList[0].Allele));
Assert.IsFalse(string.IsNullOrEmpty(promotersFeatureList[0].Citation.ToString()));
Assert.IsFalse(string.IsNullOrEmpty(promotersFeatureList[0].Experiment.ToString()));
Assert.IsFalse(string.IsNullOrEmpty(promotersFeatureList[0].Function.ToString()));
Assert.IsFalse(string.IsNullOrEmpty(promotersFeatureList[0].GeneSynonym.ToString()));
Assert.IsTrue(string.IsNullOrEmpty(promotersFeatureList[0].GenomicMapPosition));
Assert.IsFalse(string.IsNullOrEmpty(promotersFeatureList[0].Inference.ToString()));
Assert.IsTrue(string.IsNullOrEmpty(promotersFeatureList[0].Label));
Assert.IsFalse(string.IsNullOrEmpty(promotersFeatureList[0].OldLocusTag.ToString()));
Assert.IsFalse(promotersFeatureList[0].Pseudo);
Assert.IsTrue(string.IsNullOrEmpty(promotersFeatureList[0].StandardName));
// Log VSTest GUI.
ApplicationLog.WriteLine(
"GenBank Features P1: Successfully validated the GenBank Features");
}
}
/// <summary>
/// Validate GenBank tRNA features.
/// </summary>
/// <param name="nodeName">xml node name.</param>
private void ValidateGenBanktRNAFeatureQualifiers(string nodeName)
{
// Get Values from XML node.
string filePath = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.FilePathNode);
string tRNAsCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.tRNACount);
string tRNAGeneSymbol = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.TRNAGeneSymbol);
string tRNAComplement = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.TRNAComplement);
string tRNADBCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.CDSCodonStart);
// Parse a GenBank file.
ISequenceParser parserObj = new GenBankParser();
{
IEnumerable<ISequence> seqList = parserObj.Parse(filePath);
var locBuilder = new LocationBuilder();
var metadata =
(GenBankMetadata) seqList.ElementAt(0).Metadata[Constants.GenBank];
List<TransferRna> tRANsList =
metadata.Features.TransferRNAs;
Assert.AreEqual(tRANsList.Count.ToString((IFormatProvider) null),
tRNAsCount);
Assert.AreEqual(tRANsList[0].GeneSymbol.ToString(null),
tRNAGeneSymbol);
Assert.AreEqual(tRANsList[0].DatabaseCrossReference.Count,
Convert.ToInt32(tRNADBCount, null));
Assert.IsTrue(string.IsNullOrEmpty(tRANsList[0].Allele));
Assert.IsFalse(string.IsNullOrEmpty(tRANsList[0].Citation.ToString()));
Assert.IsFalse(string.IsNullOrEmpty(tRANsList[0].Experiment.ToString()));
Assert.IsFalse(string.IsNullOrEmpty(tRANsList[0].Function.ToString()));
Assert.IsFalse(string.IsNullOrEmpty(tRANsList[0].GeneSynonym.ToString()));
Assert.IsTrue(string.IsNullOrEmpty(tRANsList[0].GenomicMapPosition));
Assert.IsFalse(string.IsNullOrEmpty(tRANsList[0].Inference.ToString()));
Assert.IsTrue(string.IsNullOrEmpty(tRANsList[0].Label));
Assert.AreEqual(locBuilder.GetLocationString(
metadata.Features.TransferRNAs[0].Location),
tRNAComplement);
Assert.IsFalse(string.IsNullOrEmpty(tRANsList[0].Note.ToString()));
Assert.IsFalse(string.IsNullOrEmpty(tRANsList[0].OldLocusTag.ToString()));
Assert.IsFalse(tRANsList[0].Pseudo);
Assert.IsTrue(string.IsNullOrEmpty(tRANsList[0].StandardName));
Assert.IsFalse(tRANsList[0].TransSplicing);
// Log VSTest GUI.
ApplicationLog.WriteLine(
"GenBank Features P1: Successfully validated the GenBank Features");
}
}
public void InValidateGenBankLocations()
{
// Build a location with invalid values
ILocationBuilder locBuilder = new LocationBuilder();
ILocation loc = null;
try
{
loc = locBuilder.GetLocation(null);
Assert.Fail();
}
catch (ArgumentNullException)
{
Assert.IsNull(loc);
ApplicationLog.WriteLine(
"GenBankFeatures P2 : Validated the expected exception");
}
try
{
loc = locBuilder.GetLocation("Invalid");
Assert.Fail();
}
catch (ArgumentException)
{
Assert.IsNull(loc);
ApplicationLog.WriteLine(
"GenBankFeatures P2 : Validated the expected exception");
}
}
/// <summary>
/// Validate GenBank GCSignal features
/// </summary>
/// <param name="nodeName">XML node name</param>
/// <param name="genMetadata">GenBank Metadata</param>
private void ValidateGenBankGCSignalFeature(string nodeName,
GenBankMetadata genMetadata)
{
// Get Values from XML node.
string expectedLocation = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.Location);
string expectedAllele = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.AlleleNode);
string featureCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.QualifierCount);
string expectedDbReference = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.DbReferenceNode);
string geneSymbol = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.GeneSymbol);
string expectedCitation = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.CitationNode);
string expectedExperiment = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ExperimentNode);
string expectedGeneSynonym = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.GeneSynonymNode);
string expectedInference = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.InferenceNode);
string expectedLabel = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.LabelNode);
string expectedLocusTag = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.LocusTagNode);
string expectedNote = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.Note);
string expectedOldLocusTag = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.OldLocusTagNode);
string expectedMap = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.GenbankMapNode);
List<GcSingal> gcSignalFeatureList = genMetadata.Features.GCSignals;
var locBuilder = new LocationBuilder();
// Create a copy of GC_Signal feature.
GcSingal cloneGCSignal = gcSignalFeatureList[0].Clone();
// Validate GC_Signal qualifiers.
Assert.AreEqual(gcSignalFeatureList.Count.ToString((IFormatProvider) null),
featureCount);
Assert.AreEqual(cloneGCSignal.GeneSymbol,
geneSymbol);
Assert.AreEqual(cloneGCSignal.DatabaseCrossReference[0],
expectedDbReference);
Assert.AreEqual(gcSignalFeatureList[0].Allele,
expectedAllele);
Assert.AreEqual(gcSignalFeatureList[0].Citation[0],
expectedCitation);
Assert.AreEqual(gcSignalFeatureList[0].Experiment[0],
expectedExperiment);
Assert.AreEqual(gcSignalFeatureList[0].GenomicMapPosition,
expectedMap);
Assert.AreEqual(gcSignalFeatureList[0].GeneSynonym[0],
expectedGeneSynonym);
Assert.AreEqual(gcSignalFeatureList[0].Inference[0],
expectedInference);
Assert.AreEqual(gcSignalFeatureList[0].Label,
expectedLabel);
Assert.AreEqual(locBuilder.GetLocationString(
genMetadata.Features.GCSignals[0].Location),
expectedLocation);
Assert.AreEqual(gcSignalFeatureList[0].Note[0],
expectedNote);
Assert.AreEqual(gcSignalFeatureList[0].OldLocusTag[0],
expectedOldLocusTag);
Assert.AreEqual(gcSignalFeatureList[0].LocusTag[0],
expectedLocusTag);
// Create a new GCSignal and validate the same.
var gcSignal = new GcSingal(expectedLocation);
var gcSignalWithILoc = new GcSingal(
genMetadata.Features.GCSignals[0].Location);
// Set qualifiers and validate them.
gcSignal.Allele = expectedAllele;
gcSignal.GeneSymbol = geneSymbol;
gcSignalWithILoc.GenomicMapPosition = expectedMap;
Assert.AreEqual(gcSignal.GeneSymbol, geneSymbol);
Assert.AreEqual(gcSignal.Allele, expectedAllele);
Assert.AreEqual(gcSignalWithILoc.GenomicMapPosition,
expectedMap);
}
public void InValidateSubSequenceWithComplimentOperator()
{
// Get Values from XML node.
string sequence = utilityObj.xmlUtil.GetTextValue(
Constants.InvalidLocationWithComplementOperatorNode,
Constants.ExpectedSequence);
string location = utilityObj.xmlUtil.GetTextValue(
Constants.InvalidLocationWithComplementOperatorNode,
Constants.Location);
string alphabet = utilityObj.xmlUtil.GetTextValue(
Constants.InvalidLocationWithComplementOperatorNode,
Constants.AlphabetNameNode);
// Create a sequence object.
ISequence seqObj = new Sequence(Utility.GetAlphabet(alphabet),
sequence);
// Build a location.
ILocationBuilder locBuilder = new LocationBuilder();
ILocation loc = locBuilder.GetLocation(location);
LocationResolver locResolver = new LocationResolver();
// Get sequence using location of the sequence with operator.
try
{
loc.GetSubSequence(seqObj);
Assert.Fail();
}
catch (ArgumentException)
{
LogExceptionMessage();
}
// Validate sub sequence exception for an invalid sequence.
try
{
locResolver.GetSubSequence(loc, null);
Assert.Fail();
}
catch (ArgumentNullException)
{
LogExceptionMessage();
}
// Validate GetSubSequence method with null location.
try
{
locResolver.GetSubSequence(null, seqObj);
Assert.Fail();
}
catch (ArgumentNullException)
{
LogExceptionMessage();
}
// Validate sub sequence exception for an invalid sequence.
try
{
locResolver.GetSubSequence(loc, null, null);
Assert.Fail();
}
catch (ArgumentNullException)
{
LogExceptionMessage();
}
// Validate GetSubSequence method with null location.
try
{
locResolver.GetSubSequence(null, seqObj, null);
Assert.Fail();
}
catch (ArgumentNullException)
{
LogExceptionMessage();
}
// Validate GetSubSequence method with null location.
try
{
loc.GetSubSequence(null);
Assert.Fail();
}
catch (ArgumentNullException)
{
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"GenBankFeatures P2 : Validate the exception successfully"));
}
}
/// <summary>
/// Validate GenBank LTR features
/// </summary>
/// <param name="nodeName">XML node name</param>
/// <param name="genMetadata">GenBank Metadata</param>
private void ValidateGenBankLTRFeature(string nodeName,
GenBankMetadata genMetadata)
{
// Get Values from XML node.
string expectedLocation = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.Location);
string expectedAllele = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.AlleleNode);
string featureCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.QualifierCount);
string expectedDbReference = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.DbReferenceNode);
string geneSymbol = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.GeneSymbol);
string expectedCitation = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.CitationNode);
string expectedExperiment = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ExperimentNode);
string expectedFunction = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.FunctionNode);
string expectedGeneSynonym = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.GeneSynonymNode);
string expectedInference = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.InferenceNode);
string expectedLabel = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.LabelNode);
string expectedLocusTag = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.LocusTagNode);
string expectedNote = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.Note);
string expectedOldLocusTag = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.OldLocusTagNode);
string expectedMap = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.GenbankMapNode);
List<LongTerminalRepeat> LTRFeatureList =
genMetadata.Features.LongTerminalRepeats;
var locBuilder = new LocationBuilder();
// Create a copy of Long Terminal Repeat feature.
LongTerminalRepeat cloneLTR = LTRFeatureList[0].Clone();
// Validate Long Terminal Repeat qualifiers.
Assert.AreEqual(LTRFeatureList.Count.ToString((IFormatProvider) null),
featureCount);
Assert.AreEqual(cloneLTR.GeneSymbol, geneSymbol);
Assert.AreEqual(cloneLTR.DatabaseCrossReference[0],
expectedDbReference);
Assert.AreEqual(LTRFeatureList[0].Allele,
expectedAllele);
Assert.AreEqual(LTRFeatureList[0].Citation[0],
expectedCitation);
Assert.AreEqual(LTRFeatureList[0].Experiment[0],
expectedExperiment);
Assert.AreEqual(LTRFeatureList[0].GenomicMapPosition,
expectedMap);
Assert.AreEqual(LTRFeatureList[0].GeneSynonym[0],
expectedGeneSynonym);
Assert.AreEqual(LTRFeatureList[0].Inference[0],
expectedInference);
Assert.AreEqual(LTRFeatureList[0].Label,
expectedLabel);
Assert.AreEqual(locBuilder.GetLocationString(
genMetadata.Features.LongTerminalRepeats[0].Location),
expectedLocation);
Assert.AreEqual(LTRFeatureList[0].Note[0],
expectedNote);
Assert.AreEqual(LTRFeatureList[0].OldLocusTag[0],
expectedOldLocusTag);
Assert.AreEqual(LTRFeatureList[0].LocusTag[0],
expectedLocusTag);
Assert.AreEqual(LTRFeatureList[0].Function[0],
expectedFunction);
Assert.IsTrue(string.IsNullOrEmpty(LTRFeatureList[0].StandardName));
// Create a new LTR and validate.
var ltr =
new LongTerminalRepeat(expectedLocation);
var ltrWithILoc = new LongTerminalRepeat(
genMetadata.Features.LongTerminalRepeats[0].Location);
// Set qualifiers and validate them.
ltr.Allele = expectedAllele;
ltr.GeneSymbol = geneSymbol;
ltrWithILoc.GenomicMapPosition = expectedMap;
Assert.AreEqual(ltr.GeneSymbol, geneSymbol);
Assert.AreEqual(ltr.Allele, expectedAllele);
Assert.AreEqual(ltrWithILoc.GenomicMapPosition,
expectedMap);
}
/// <summary>
/// Gives out string array of metadata and features just below metadata.
/// </summary>
/// <param name="metadata">GenBank Metadata</param>
/// <returns>string array of metadata</returns>
public static string[,] GenBankMetadataToRange(GenBankMetadata metadata)
{
List<string[]> excelData = new List<string[]>();
List<string> excelRow = new List<string>();
// Add the metadata headers
excelRow.Add(Properties.Resources.GenbankMetadataHeader);
excelData.Add(excelRow.ToArray());
excelRow.Clear();
if (metadata.Locus != null)
{
excelData.Add(new[] { Properties.Resources.GenbankMetadataLocus });
AddNameValuePair(excelData, 1, Properties.Resources.GenbankMetadataName, metadata.Locus.Name);
AddNameValuePair(excelData, 1, Properties.Resources.GenbankMetadataSeqLength, metadata.Locus.SequenceLength.ToString());
AddNameValuePair(excelData, 1, Properties.Resources.GenbankMetadataSeqType, metadata.Locus.SequenceType);
AddNameValuePair(excelData, 1, Properties.Resources.GenbankMetadataStrandType, Helper.GetStrandType(metadata.Locus.Strand));
AddNameValuePair(excelData, 1, Properties.Resources.GenbankMetadataMoleculeType, metadata.Locus.MoleculeType.ToString());
AddNameValuePair(excelData, 1, Properties.Resources.GenbankMetadataStrandTopology, Helper.GetStrandTopology(metadata.Locus.StrandTopology));
AddNameValuePair(excelData, 1, Properties.Resources.GenbankMetadataDivisionCode, metadata.Locus.DivisionCode.ToString());
AddNameValuePair(excelData, 1, Properties.Resources.GenbankMetadataDate, metadata.Locus.Date.ToString("dd-MMM-yyyy").ToUpper());
}
if (!string.IsNullOrWhiteSpace(metadata.Definition))
{
AddNameValuePair(excelData, 0, Properties.Resources.GenbankMetadataDefinition, "", metadata.Definition);
}
if (metadata.Accession != null)
{
string secondaryAccession = string.Empty;
foreach (string accession2 in metadata.Accession.Secondary)
{
secondaryAccession += accession2 == null ? " " : " " + accession2;
}
AddNameValuePair(excelData, 0, Properties.Resources.GenbankMetadataAccession, "", metadata.Accession.Primary + secondaryAccession);
}
if (metadata.DbLinks != null)
{
foreach (var link in metadata.DbLinks)
{
string linkNumbers = string.Empty;
foreach (string linkNumber in link.Numbers)
{
linkNumbers += linkNumber + ",";
}
AddNameValuePair(excelData, 0, Properties.Resources.GenbankMetadataDBLink, "", link.Type.ToString() + ":" + linkNumbers);
}
}
if (!string.IsNullOrWhiteSpace(metadata.DbSource))
{
AddNameValuePair(excelData, 0, Properties.Resources.GenbankMetadataDBSource, "", metadata.DbSource);
}
if (metadata.Version != null)
{
AddNameValuePair(excelData, 0, Properties.Resources.GenbankMetadataVersion, "", (metadata.Version.Accession ?? string.Empty) + "." +
(metadata.Version.Version ?? string.Empty) + " " + Properties.Resources.GenbankMetadataGI + (metadata.Version.GiNumber ?? string.Empty));
}
if (metadata.Segment != null)
{
AddNameValuePair(excelData, 0, Properties.Resources.GenbankMetadataSegment, "", metadata.Segment.Current + " of " + metadata.Segment.Count);
}
AddNameValuePair(excelData, 0, Properties.Resources.GenbankMetadataKeywords, "", metadata.Keywords);
if (metadata.Source != null)
{
AddNameValuePair(excelData, 0, Properties.Resources.GenbankMetadataSource, "", metadata.Source.CommonName ?? string.Empty);
AddNameValuePair(excelData, 1, Properties.Resources.GenbankMetadataOrganism, (metadata.Source.Organism.Genus ?? string.Empty) + " " + (metadata.Source.Organism.Species ?? string.Empty));
AddNameValuePair(excelData, 1, Properties.Resources.GenbankMetadataClassLevels, metadata.Source.Organism.ClassLevels ?? string.Empty);
}
foreach (CitationReference reference in metadata.References)
{
AddNameValuePair(excelData, 0, Properties.Resources.GenbankMetadataReference, "", reference.Number.ToString() + " (" + reference.Location + ")");
AddNameValuePair(excelData, 1, Properties.Resources.GenbankMetadataAuthors, reference.Authors);
AddNameValuePair(excelData, 1, Properties.Resources.GenbankMetadataTitle, reference.Title);
AddNameValuePair(excelData, 1, Properties.Resources.GenbankMetadataJournal, reference.Journal);
AddNameValuePair(excelData, 1, Properties.Resources.GenbankMetadataConsortiums, reference.Consortiums);
AddNameValuePair(excelData, 1, Properties.Resources.GenbankMetadataMedLine, reference.Medline);
AddNameValuePair(excelData, 1, Properties.Resources.GenbankMetadataPubMed, reference.PubMed);
AddNameValuePair(excelData, 1, Properties.Resources.GenbankMetadataRemarks, reference.Remarks);
}
if (!string.IsNullOrWhiteSpace(metadata.Primary))
{
AddNameValuePair(excelData, 0, Properties.Resources.GenbankMetadataPrimary, "", metadata.Primary);
}
if (metadata.Comments != null && metadata.Comments.Count > 0)
{
StringBuilder strbuilder = null;
foreach (string str in metadata.Comments)
{
if (strbuilder == null)
{
strbuilder = new StringBuilder();
}
else
{
strbuilder.Append(Environment.NewLine);
}
strbuilder.Append(str);
}
if (strbuilder != null)
{
AddNameValuePair(excelData, 0, Properties.Resources.GenbankMetadataComment, "", strbuilder.ToString());
}
}
if (metadata.Features != null)
{
// Add the metadata headers
excelRow.Add(Properties.Resources.GenbankFeaturesHeader);
excelData.Add(excelRow.ToArray());
excelRow.Clear();
IList<FeatureItem> featureList = metadata.Features.All;
foreach (FeatureItem featureItem in featureList)
{
LocationBuilder locBuilder = new LocationBuilder();
// Add the feature headers
excelRow.Add(featureItem.Key);
//excelRow.Add(""); // skip one column
excelRow.Add(locBuilder.GetLocationString(featureItem.Location));
excelData.Add(excelRow.ToArray());
excelRow.Clear();
foreach (string key in featureItem.Qualifiers.Keys)
{
foreach (string value in featureItem.Qualifiers[key])
{
AddNameValuePair(excelData, 1, key, value);
}
}
}
}
if (!string.IsNullOrWhiteSpace(metadata.BaseCount))
{
AddNameValuePair(excelData, 0, Properties.Resources.GenbankMetadataBaseCount, "", metadata.BaseCount);
}
return ConvertToArray(excelData);
}
/// <summary>
/// Validate GenBank Operon features
/// </summary>
/// <param name="nodeName">XML node name</param>
/// <param name="genMetadata">GenBank Metadata</param>
private void ValidateGenBankOperon(string nodeName,
GenBankMetadata genMetadata)
{
// Get Values from XML node.
string expectedLocation = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.Location);
string expectedAllele = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.AlleleNode);
string featureCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.QualifierCount);
string expectedDbReference = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.DbReferenceNode);
string expectedCitation = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.CitationNode);
string expectedExperiment = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ExperimentNode);
string expectedInference = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.InferenceNode);
string expectedLabel = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.LabelNode);
string expectedNote = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.Note);
string expectedMap = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.GenbankMapNode);
List<OperonRegion> operonFeatureList =
genMetadata.Features.OperonRegions;
var locBuilder = new LocationBuilder();
// Create a copy of Long Terminal Repeat feature.
OperonRegion cloneOperon = operonFeatureList[0].Clone();
// Validate Operon region qualifiers.
Assert.AreEqual(operonFeatureList.Count.ToString((IFormatProvider) null),
featureCount);
Assert.AreEqual(cloneOperon.DatabaseCrossReference[0],
expectedDbReference);
Assert.AreEqual(operonFeatureList[0].Allele,
expectedAllele);
Assert.AreEqual(operonFeatureList[0].Citation[0],
expectedCitation);
Assert.AreEqual(operonFeatureList[0].Experiment[0],
expectedExperiment);
Assert.AreEqual(operonFeatureList[0].GenomicMapPosition,
expectedMap);
Assert.AreEqual(operonFeatureList[0].Inference[0],
expectedInference);
Assert.AreEqual(operonFeatureList[0].Label,
expectedLabel);
Assert.AreEqual(locBuilder.GetLocationString(
genMetadata.Features.OperonRegions[0].Location),
expectedLocation);
Assert.AreEqual(operonFeatureList[0].Note[0],
expectedNote);
Assert.IsFalse(string.IsNullOrEmpty(operonFeatureList[0].Function.ToString()));
Assert.AreEqual(operonFeatureList[0].GenomicMapPosition,
expectedMap);
Assert.IsTrue(string.IsNullOrEmpty(operonFeatureList[0].Operon));
Assert.IsFalse(string.IsNullOrEmpty(operonFeatureList[0].Phenotype.ToString()));
Assert.IsTrue(string.IsNullOrEmpty(operonFeatureList[0].StandardName));
Assert.IsFalse(operonFeatureList[0].Pseudo);
// Create a new Operon feature using constructor.
var operonRegion =
new OperonRegion(expectedLocation);
var operonRegionWithLoc = new OperonRegion(
genMetadata.Features.OperonRegions[0].Location);
// Set and validate qualifiers.
operonRegion.Allele = expectedAllele;
operonRegionWithLoc.GenomicMapPosition = expectedMap;
Assert.AreEqual(operonRegionWithLoc.GenomicMapPosition,
expectedMap);
Assert.AreEqual(operonRegion.Allele, expectedAllele);
}
/// <summary>
/// Initializes a new instance of the GenBankFormatter class.
/// </summary>
/// <param name="filename">Name of the File.</param>
public GenBankFormatter(string filename)
{
Filename = filename;
writer = new StreamWriter(filename);
LocationBuilder = new LocationBuilder();
}
/// <summary>
/// Validate GenBank UnsureSequenceRegion features
/// </summary>
/// <param name="nodeName">XML node name</param>
/// <param name="genMetadata">GenBank Metadata</param>
private void ValidateGenBankUnsureSequenceRegion(string nodeName,
GenBankMetadata genMetadata)
{
// Get Values from XML node.
string expectedLocation = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.Location);
string expectedAllele = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.AlleleNode);
string featureCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.QualifierCount);
string expectedDbReference = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.DbReferenceNode);
string geneSymbol = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.GeneSymbol);
string expectedCitation = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.CitationNode);
string expectedExperiment = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ExperimentNode);
string expectedInference = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.InferenceNode);
string expectedLabel = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.LabelNode);
string expectedNote = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.Note);
string expectedMap = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.GenbankMapNode);
List<UnsureSequenceRegion> unsureSeqRegionFeatureList =
genMetadata.Features.UnsureSequenceRegions;
// Create a copy of Unsure Seq Region feature.
UnsureSequenceRegion cloneUnSureSeqRegion =
unsureSeqRegionFeatureList[0].Clone();
var locBuilder = new LocationBuilder();
// Validate Unsure Seq Region qualifiers.
Assert.AreEqual(unsureSeqRegionFeatureList.Count.ToString((IFormatProvider) null)
, featureCount);
Assert.AreEqual(cloneUnSureSeqRegion.DatabaseCrossReference[0],
expectedDbReference);
Assert.AreEqual(cloneUnSureSeqRegion.GeneSymbol,
geneSymbol);
Assert.AreEqual(unsureSeqRegionFeatureList[0].Allele,
expectedAllele);
Assert.AreEqual(unsureSeqRegionFeatureList[0].Citation[0],
expectedCitation);
Assert.AreEqual(unsureSeqRegionFeatureList[0].Experiment[0],
expectedExperiment);
Assert.AreEqual(unsureSeqRegionFeatureList[0].GenomicMapPosition,
expectedMap);
Assert.AreEqual(unsureSeqRegionFeatureList[0].Inference[0],
expectedInference);
Assert.AreEqual(unsureSeqRegionFeatureList[0].Label,
expectedLabel);
Assert.AreEqual(locBuilder.GetLocationString(
genMetadata.Features.UnsureSequenceRegions[0].Location),
expectedLocation);
Assert.AreEqual(unsureSeqRegionFeatureList[0].Note[0],
expectedNote);
Assert.AreEqual(unsureSeqRegionFeatureList[0].GenomicMapPosition,
expectedMap);
Assert.IsFalse(string.IsNullOrEmpty(unsureSeqRegionFeatureList[0].Compare.ToString()));
Assert.IsTrue(string.IsNullOrEmpty(unsureSeqRegionFeatureList[0].Replace));
// Create a new Unsure feature using constructor.
var unsureRegion =
new UnsureSequenceRegion(expectedLocation);
var unsureRegionWithLoc =
new UnsureSequenceRegion(
genMetadata.Features.UnsureSequenceRegions[0].Location);
// Set and validate qualifiers.
unsureRegion.Allele = expectedAllele;
unsureRegionWithLoc.GeneSymbol = geneSymbol;
unsureRegionWithLoc.GenomicMapPosition = expectedMap;
Assert.AreEqual(unsureRegionWithLoc.GenomicMapPosition,
expectedMap);
Assert.AreEqual(unsureRegion.Allele, expectedAllele);
Assert.AreEqual(unsureRegionWithLoc.GeneSymbol,
geneSymbol);
}
/// <summary>
/// Initializes a new instance of the GenBankFormatter class.
/// </summary>
/// <param name="filename">Name of the File.</param>
public GenBankFormatter(string filename)
{
Filename = filename;
writer = new StreamWriter(filename);
LocationBuilder = new LocationBuilder();
}
/// <summary>
/// Validate GenBank RibosomeBindingSite features
/// </summary>
/// <param name="nodeName">XML node name</param>
/// <param name="genMetadata">GenBank Metadata</param>
private void ValidateGenBankRibosomeBindingSite(string nodeName,
GenBankMetadata genMetadata)
{
// Get Values from XML node.
string expectedLocation = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.Location);
string expectedAllele = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.AlleleNode);
string featureCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.QualifierCount);
string expectedDbReference = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.DbReferenceNode);
string geneSymbol = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.GeneSymbol);
string expectedCitation = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.CitationNode);
string expectedExperiment = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ExperimentNode);
string expectedInference = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.InferenceNode);
string expectedLabel = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.LabelNode);
string expectedNote = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.Note);
string expectedMap = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.GenbankMapNode);
List<RibosomeBindingSite> ribosomeSite =
genMetadata.Features.RibosomeBindingSites;
// Create a copy of RibosomeBindigSite Region feature.
RibosomeBindingSite cloneRibosomeSite =
ribosomeSite[0].Clone();
var locBuilder = new LocationBuilder();
// Validate RibosomeBindigSite qualifiers.
Assert.AreEqual(ribosomeSite.Count.ToString((IFormatProvider) null)
, featureCount);
Assert.AreEqual(cloneRibosomeSite.DatabaseCrossReference[0],
expectedDbReference);
Assert.AreEqual(cloneRibosomeSite.GeneSymbol,
geneSymbol);
Assert.AreEqual(ribosomeSite[0].Allele,
expectedAllele);
Assert.AreEqual(ribosomeSite[0].Citation[0],
expectedCitation);
Assert.AreEqual(ribosomeSite[0].Experiment[0],
expectedExperiment);
Assert.AreEqual(ribosomeSite[0].Inference[0],
expectedInference);
Assert.AreEqual(ribosomeSite[0].Label,
expectedLabel);
Assert.AreEqual(locBuilder.GetLocationString(
genMetadata.Features.RibosomeBindingSites[0].Location),
expectedLocation);
Assert.AreEqual(ribosomeSite[0].Note[0],
expectedNote);
Assert.AreEqual(ribosomeSite[0].GenomicMapPosition,
expectedMap);
Assert.IsNotNull(ribosomeSite[0].OldLocusTag[0]);
Assert.IsNotNull(ribosomeSite[0].LocusTag[0]);
Assert.IsNotNull(ribosomeSite[0].StandardName);
// Create a new RibosomeBindingSite feature using constructor.
var ribosomeBindingSite =
new RibosomeBindingSite(expectedLocation);
var ribosomeBindingSiteLoc =
new RibosomeBindingSite(
genMetadata.Features.RibosomeBindingSites[0].Location);
// Set and validate qualifiers.
ribosomeBindingSite.Allele = expectedAllele;
ribosomeBindingSiteLoc.GeneSymbol = geneSymbol;
ribosomeBindingSiteLoc.GenomicMapPosition = expectedMap;
Assert.AreEqual(ribosomeBindingSiteLoc.GenomicMapPosition,
expectedMap);
Assert.AreEqual(ribosomeBindingSite.Allele, expectedAllele);
Assert.AreEqual(ribosomeBindingSiteLoc.GeneSymbol,
geneSymbol);
}
/// <summary>
/// Default constructor.
/// </summary>
public GenBankFormatter()
{
LocationBuilder = new LocationBuilder();
}
/// <summary>
/// Validate GenBank Non Coding RNA features
/// </summary>
/// <param name="nodeName">XML node name</param>
/// <param name="genMetadata">GenBank Metadata</param>
private void ValidateGenBankNonCodingRNA(string nodeName,
GenBankMetadata genMetadata)
{
// Get Values from XML node.
string expectedLocation = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.Location);
string featureCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.QualifierCount);
string expectedLabel = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.LabelNode);
string expectedNonCodingRnaClass = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.NonCodingRnaClassNode);
List<NonCodingRna> nonCodingRNAFeatureList =
genMetadata.Features.NonCodingRNAs;
var locBuilder = new LocationBuilder();
// Create a copy of Non coding RNA feature.
NonCodingRna cloneNonCodingRNA =
nonCodingRNAFeatureList[0].Clone();
// Validate Non Coding RNA Region qualifiers.
Assert.AreEqual(nonCodingRNAFeatureList.Count.ToString((IFormatProvider) null),
featureCount);
Assert.AreEqual(nonCodingRNAFeatureList[0].NonCodingRnaClass,
expectedNonCodingRnaClass);
Assert.AreEqual(cloneNonCodingRNA.Label,
expectedLabel);
Assert.AreEqual(locBuilder.GetLocationString(
genMetadata.Features.NonCodingRNAs[0].Location),
expectedLocation);
// Create a non Coding RNA and validate the same.
var nRNA =
new NonCodingRna(genMetadata.Features.NonCodingRNAs[0].Location);
var nRNAWithLocation =
new NonCodingRna(expectedLocation);
// Set properties
nRNA.NonCodingRnaClass = expectedNonCodingRnaClass;
nRNAWithLocation.NonCodingRnaClass = expectedNonCodingRnaClass;
// Validate created nRNA.
Assert.AreEqual(nRNA.NonCodingRnaClass,
expectedNonCodingRnaClass);
Assert.AreEqual(nRNAWithLocation.NonCodingRnaClass,
expectedNonCodingRnaClass);
}
/// <summary>
/// Default constructor chooses default encoding based on alphabet.
/// </summary>
public GenBankParser()
{
LocationBuilder = new LocationBuilder();
}
/// <summary>
/// Validate GenBank CDS features
/// </summary>
/// <param name="nodeName">XML node name</param>
/// <param name="genMetadata">GenBank Metadata</param>
private void ValidateGenBankCDSFeatures(string nodeName,
GenBankMetadata genMetadata)
{
// Get Values from XML node.
string expectedLocation = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.Location);
string expectedAllele = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.AlleleNode);
string featureCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.QualifierCount);
string expectedDbReference = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.DbReferenceNode);
string geneSymbol = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.GeneSymbol);
string expectedCitation = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.CitationNode);
string expectedExperiment = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ExperimentNode);
string expectedInference = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.InferenceNode);
string expectedLabel = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.LabelNode);
string expectedNote = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.Note);
string expectedMap = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.GenbankMapNode);
string expectedTranslation = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.GenbankTranslationNode);
string expectedCodonStart = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.CodonStartNode);
List<CodingSequence> codingSequenceFeatureList =
genMetadata.Features.CodingSequences;
var locBuilder = new LocationBuilder();
// Create a copy of Coding Seq Region feature.
CodingSequence cloneCDS = codingSequenceFeatureList[0].Clone();
// Validate Unsure Seq Region qualifiers.
Assert.AreEqual(codingSequenceFeatureList.Count.ToString((IFormatProvider) null),
featureCount);
Assert.AreEqual(cloneCDS.DatabaseCrossReference[0],
expectedDbReference);
Assert.AreEqual(cloneCDS.GeneSymbol, geneSymbol);
Assert.AreEqual(codingSequenceFeatureList[0].Allele,
expectedAllele);
Assert.AreEqual(codingSequenceFeatureList[0].Citation[0],
expectedCitation);
Assert.AreEqual(codingSequenceFeatureList[0].Experiment[0],
expectedExperiment);
Assert.AreEqual(codingSequenceFeatureList[0].GenomicMapPosition,
expectedMap);
Assert.AreEqual(codingSequenceFeatureList[0].Inference[0],
expectedInference);
Assert.AreEqual(codingSequenceFeatureList[0].Label,
expectedLabel);
Assert.AreEqual(locBuilder.GetLocationString(
genMetadata.Features.CodingSequences[0].Location),
expectedLocation);
Assert.AreEqual(codingSequenceFeatureList[0].Note[0],
expectedNote);
Assert.AreEqual(codingSequenceFeatureList[0].GenomicMapPosition,
expectedMap);
Assert.AreEqual(codingSequenceFeatureList[0].CodonStart[0],
expectedCodonStart);
Assert.AreEqual(codingSequenceFeatureList[0].Translation,
expectedTranslation);
Assert.IsFalse(string.IsNullOrEmpty(codingSequenceFeatureList[0].Codon.ToString()));
Assert.IsTrue(string.IsNullOrEmpty(codingSequenceFeatureList[0].EnzymeCommissionNumber));
Assert.IsTrue(string.IsNullOrEmpty(codingSequenceFeatureList[0].Number));
Assert.IsTrue(string.IsNullOrEmpty(codingSequenceFeatureList[0].Operon));
Assert.IsFalse(codingSequenceFeatureList[0].Pseudo);
Assert.IsFalse(codingSequenceFeatureList[0].RibosomalSlippage);
Assert.IsTrue(string.IsNullOrEmpty(codingSequenceFeatureList[0].StandardName));
Assert.IsFalse(string.IsNullOrEmpty(codingSequenceFeatureList[0].TranslationalExcept.ToString()));
Assert.IsTrue(string.IsNullOrEmpty(codingSequenceFeatureList[0].TranslationTable));
Assert.IsFalse(codingSequenceFeatureList[0].TransSplicing);
Assert.IsTrue(string.IsNullOrEmpty(codingSequenceFeatureList[0].Exception));
// Create a new CDS feature using constructor.
var cds = new CodingSequence(expectedLocation);
var cdsWithLoc = new CodingSequence(
genMetadata.Features.CodingSequences[0].Location);
Sequence seq = cds.GetTranslation();
Assert.IsNotNull(seq);
// Set and validate qualifiers.
cds.Allele = expectedAllele;
cdsWithLoc.GeneSymbol = geneSymbol;
cdsWithLoc.GenomicMapPosition = expectedMap;
Assert.AreEqual(cdsWithLoc.GenomicMapPosition, expectedMap);
Assert.AreEqual(cds.Allele, expectedAllele);
Assert.AreEqual(cdsWithLoc.GeneSymbol, geneSymbol);
}
/// <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);
}
}
}
/// <summary>
/// Validate Location builder and location resolver.
/// </summary>
/// <param name="nodeName">xml node name.</param>
/// <param name="FeatureOperator">Name of the operator used in a location</param>
/// <param name="isOperator">
/// True if location resolver validation with
/// operator
/// </param>
private void ValidateGenBankLocationResolver(string nodeName,
FeatureOperator operatorName, bool isOperator)
{
// Get Values from XML node.
string sequence = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ExpectedSequence);
string location = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.Location);
string alphabet = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.AlphabetNameNode);
string expectedSeq = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ExpSequenceWithOperator);
// Create a sequence object.
ISequence seqObj = new Sequence(Utility.GetAlphabet(alphabet),
sequence);
ISequence expectedSeqWithLoc;
// Build a location.
ILocationBuilder locBuilder = new LocationBuilder();
ILocation loc = locBuilder.GetLocation(location);
if (isOperator)
{
switch (operatorName)
{
case FeatureOperator.Complement:
loc.Operator = LocationOperator.Complement;
break;
case FeatureOperator.Join:
loc.Operator = LocationOperator.Join;
break;
case FeatureOperator.Order:
loc.Operator = LocationOperator.Order;
break;
default:
break;
}
}
// Get sequence using location of the sequence with operator.
expectedSeqWithLoc = loc.GetSubSequence(seqObj);
var sequenceString = new string(expectedSeqWithLoc.Select(a => (char) a).ToArray());
Assert.AreEqual(expectedSeq, sequenceString);
// Log to VSTest GUI.
ApplicationLog.WriteLine(string.Format(null,
"GenBankFeatures P1 : Expected sequence is verfied '{0}'.",
sequenceString));
}
public void InValidateSubSequenceWithInvalidAccessionID()
{
// Get Values from XML node.
string sequence = utilityObj.xmlUtil.GetTextValue(
Constants.LocationWithDotOperatorNode,
Constants.ExpectedSequence);
string location = utilityObj.xmlUtil.GetTextValue(
Constants.LocationWithDotOperatorNode,
Constants.Location);
string alphabet = utilityObj.xmlUtil.GetTextValue(
Constants.LocationWithDotOperatorNode,
Constants.AlphabetNameNode);
// Create a sequence object.
ISequence seqObj = new Sequence(Utility.GetAlphabet(alphabet),
sequence);
// Build a location.
ILocationBuilder locBuilder = new LocationBuilder();
ILocation loc = locBuilder.GetLocation(location);
loc.Accession = "Invalid";
// Get sequence using location of the sequence with operator.
try
{
loc.GetSubSequence(seqObj);
Assert.Fail();
}
catch (ArgumentException)
{
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"GenBankFeatures P2 : Validate the exception successfully"));
}
Dictionary<string, ISequence> refSeq = null;
// Validate GetSubSequence method with null location.
try
{
loc.GetSubSequence(null, refSeq);
Assert.Fail();
}
catch (ArgumentNullException)
{
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"GenBankFeatures P2 : Validate the exception successfully"));
}
}
/// <summary>
/// Validate location resolver end data.
/// </summary>
/// <param name="nodeName">xml node name.</param>
private void ValidateLocationEndData(string nodeName)
{
// Get Values from XML node.
string location = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.Location);
string expectedEndData = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.EndData);
string position = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.Position);
bool result = false;
// Build a location.
var locResolver = new LocationResolver();
ILocationBuilder locBuilder = new LocationBuilder();
ILocation loc = locBuilder.GetLocation(location);
loc.EndData = expectedEndData;
// Validate whether mentioned end data is present in the location
// or not.
result = locResolver.IsInEnd(loc, Int32.Parse(position, null));
Assert.IsTrue(result);
// Log to VSTest GUI.
ApplicationLog.WriteLine(string.Format(null,
"GenBankFeatures P1 : Expected sequence is verified"));
}
public void InValidateGenBankLocationPositions()
{
// Get Values from XML node.
string location = utilityObj.xmlUtil.GetTextValue(
Constants.LocationWithEndDataUsingOperatorNode, Constants.Location);
string expectedEndData = utilityObj.xmlUtil.GetTextValue(
Constants.LocationWithEndDataUsingOperatorNode, Constants.EndData);
string expectedStartData = utilityObj.xmlUtil.GetTextValue(
Constants.LocationWithEndDataUsingOperatorNode, Constants.StartData);
string position = utilityObj.xmlUtil.GetTextValue(
Constants.LocationWithEndDataUsingOperatorNode, Constants.Position);
// Build a location.
ILocationBuilder locBuilder = new LocationBuilder();
Location loc = (Location)locBuilder.GetLocation(location);
loc.Resolver = null;
loc.EndData = expectedEndData;
loc.StartData = expectedStartData;
// Validate whether mentioned end data is present in the location
// or not.
try
{
loc.IsInEnd(Int32.Parse(position, (IFormatProvider)null));
Assert.Fail();
}
catch (InvalidOperationException)
{
// Log to VSTest GUI.
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"GenBankFeatures P2 : Expected exception is verified"));
}
try
{
loc.IsInStart(Int32.Parse(position, (IFormatProvider)null));
Assert.Fail();
}
catch (InvalidOperationException)
{
// Log to VSTest GUI.
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"GenBankFeatures P2 : Expected exception is verified"));
}
try
{
loc.IsInRange(Int32.Parse(position, (IFormatProvider)null));
Assert.Fail();
}
catch (InvalidOperationException)
{
// Log to VSTest GUI.
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"GenBankFeatures P2 : Expected exception is verified"));
}
}
public void ValidateAdditionSingleGenBankQualifier()
{
// Get Values from XML node.
string filePath = utilityObj.xmlUtil.GetTextValue(
Constants.MediumSizeRNAGenBankFeaturesNode, Constants.FilePathNode);
string addFirstKey = utilityObj.xmlUtil.GetTextValue(
Constants.MediumSizeRNAGenBankFeaturesNode, Constants.FirstKey);
string addFirstLocation = utilityObj.xmlUtil.GetTextValue(
Constants.MediumSizeRNAGenBankFeaturesNode, Constants.FirstLocation);
string addFirstQualifier = utilityObj.xmlUtil.GetTextValue(
Constants.MediumSizeRNAGenBankFeaturesNode, Constants.FirstQualifier);
string addSecondQualifier = utilityObj.xmlUtil.GetTextValue(
Constants.MediumSizeRNAGenBankFeaturesNode, Constants.SecondQualifier);
// Parse a GenBank file.
ISequenceParser parserObj = new GenBankParser();
{
IEnumerable<ISequence> seqList = parserObj.Parse(filePath);
var locBuilder = new LocationBuilder();
// Validate Minus35Signal feature all qualifiers.
var metadata =
(GenBankMetadata) seqList.ElementAt(0).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);
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(
locBuilder.GetLocationString(metadata.Features.All[0].Location),
addFirstLocation);
}
}
/// <summary>
/// InValidate GenBank location with invalid Start location data.
/// <param name="endData">Start data used for different test cases.</param>
/// </summary>
private static void InValidateLocationStartData(string startData)
{
// Build a location.
LocationResolver locResolver = new LocationResolver();
string location = "123.125";
ILocationBuilder locBuilder = new LocationBuilder();
ILocation loc = locBuilder.GetLocation(location);
// Set Invalid end data Validate GetStart method exception.
loc.StartData = startData;
try
{
locResolver.IsInStart(loc, 124);
Assert.Fail();
}
catch (IndexOutOfRangeException)
{
LogExceptionMessage();
}
catch (FormatException)
{
LogExceptionMessage();
}
}
public void ValidateGenBankRepeatRegionFeatureQualifiers()
{
// Get Values from XML node.
string filePath = utilityObj.xmlUtil.GetTextValue(
Constants.GenBankRepeatRegionQualifiersNode,
Constants.FilePathNode);
string repeatRegionCount = utilityObj.xmlUtil.GetTextValue(
Constants.GenBankRepeatRegionQualifiersNode,
Constants.ThreePrimeUTRCount);
string expectedLocation = utilityObj.xmlUtil.GetTextValue(
Constants.GenBankRepeatRegionQualifiersNode,
Constants.RepeatRegionLocation);
// Parse a GenBank file.
ISequenceParser parserObj = new GenBankParser();
{
IEnumerable<ISequence> seqList = parserObj.Parse(filePath);
var locBuilder = new LocationBuilder();
// Validate RepeatRegion feature all qualifiers.
var metadata =
(GenBankMetadata) seqList.ElementAt(0).Metadata[Constants.GenBank];
List<RepeatRegion> repeatRegionsList =
metadata.Features.RepeatRegions;
Assert.AreEqual(repeatRegionsList.Count.ToString((IFormatProvider) null),
repeatRegionCount);
Assert.IsTrue(string.IsNullOrEmpty(repeatRegionsList[0].GeneSymbol));
Assert.AreEqual(locBuilder.GetLocationString(
metadata.Features.RepeatRegions[0].Location),
expectedLocation);
Assert.IsFalse(string.IsNullOrEmpty(repeatRegionsList[0].DatabaseCrossReference.ToString()));
Assert.IsFalse(string.IsNullOrEmpty(repeatRegionsList[0].Note.ToString()));
Assert.IsTrue(string.IsNullOrEmpty(repeatRegionsList[0].Allele));
Assert.IsFalse(string.IsNullOrEmpty(repeatRegionsList[0].Citation.ToString()));
Assert.IsFalse(string.IsNullOrEmpty(repeatRegionsList[0].Experiment.ToString()));
Assert.IsFalse(string.IsNullOrEmpty(repeatRegionsList[0].GeneSynonym.ToString()));
Assert.IsTrue(string.IsNullOrEmpty(repeatRegionsList[0].GenomicMapPosition));
Assert.IsTrue(string.IsNullOrEmpty(repeatRegionsList[0].Label));
Assert.IsFalse(string.IsNullOrEmpty(repeatRegionsList[0].OldLocusTag.ToString()));
Assert.IsFalse(string.IsNullOrEmpty(repeatRegionsList[0].LocusTag.ToString()));
// Log VSTest GUI.
ApplicationLog.WriteLine(
"GenBank Features P1: Successfully validated the GenBank Features");
}
}