/// <summary>
/// Extracts sequence from genbank file.
/// </summary>
/// <param name="id">
/// Accession id of the sequence in ncbi (remote id).
/// </param>
/// <returns>
/// The <see cref="Stream"/>.
/// </returns>
private static ISequence GetGenBankSequence(string id)
{
Stream fileStream = GetResponseStream(GetEfetchParamsString("gbwithparts") + id);
ISequenceParser parser = new GenBankParser();
return parser.ParseOne(fileStream);
}
/// <summary>
/// Validate GenBank Features clonning.
/// </summary>
/// <param name="nodeName">xml node name.</param>
/// <param name="featureName">Name of the GenBank feature</param>
private void ValidateGenBankFeaturesClonning(string nodeName, FeatureGroup featureName)
{
// Get Values from XML node.
string filePath = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FilePathNode);
string expectedExonFeatureCount = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ExonCount);
string expectedExonGeneSymbol = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ExonGeneSymbol);
string expectedExonNumber = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ExonNumber);
string expectedMiscDiffCount = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.MiscQualifiersCount);
string expectedGeneSymbol = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.GeneSymbol);
string expectedIntronGeneSymbol = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.IntronGeneSymbol);
string expectedIntronNumber = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.IntronNumber);
string expectedVariationReplace = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.VariationReplace);
// Parse a GenBank file.
ISequenceParser parserObj = new GenBankParser();
{
ISequence seq = parserObj.ParseOne(filePath);
Assert.IsNotNull(seq);
var metadata = seq.Metadata[Constants.GenBank] as GenBankMetadata;
Assert.IsNotNull(metadata);
// Validate cloned GenBank feature.
switch (featureName)
{
case FeatureGroup.Exon:
List<Exon> exonFeatureList = metadata.Features.Exons;
// Validate Exon feature before clonning.
Assert.AreEqual(exonFeatureList.Count.ToString((IFormatProvider) null), expectedExonFeatureCount);
Assert.AreEqual(exonFeatureList[0].GeneSymbol, expectedExonGeneSymbol);
Assert.AreEqual(exonFeatureList[0].Number, expectedExonNumber);
// Clone Exon feature.
Exon clonedExons = exonFeatureList[0].Clone();
// Validate Exon feature after clonning.
Assert.AreEqual(clonedExons.GeneSymbol, expectedExonGeneSymbol);
Assert.AreEqual(clonedExons.Number, expectedExonNumber);
break;
case FeatureGroup.miscDifference:
// Validate Misc Difference feature before clonning.
List<MiscDifference> miscDifferenceFeatureList = metadata.Features.MiscDifferences;
Assert.AreEqual(miscDifferenceFeatureList.Count.ToString((IFormatProvider) null), expectedMiscDiffCount);
Assert.AreEqual(miscDifferenceFeatureList[0].GeneSymbol, expectedGeneSymbol);
// Clone Misc Difference feature
MiscDifference clonedMiscDifferences = miscDifferenceFeatureList[0].Clone();
// Validate Misc Difference feature after clonning.
Assert.AreEqual(clonedMiscDifferences.GeneSymbol, expectedGeneSymbol);
break;
case FeatureGroup.Intron:
// Validate Intron feature before clonning.
List<Intron> intronFeatureList = metadata.Features.Introns;
Assert.AreEqual(intronFeatureList[0].GeneSymbol, expectedIntronGeneSymbol);
Assert.AreEqual(intronFeatureList[0].Number, expectedIntronNumber);
// Clone Intron feature.
Intron clonedIntrons = intronFeatureList[0].Clone();
// Validate Intron feature after clonning.
Assert.AreEqual(clonedIntrons.GeneSymbol, expectedIntronGeneSymbol);
Assert.AreEqual(clonedIntrons.Number, expectedIntronNumber);
break;
case FeatureGroup.variation:
// Validate Variation feature before clonning.
List<Variation> variationFeatureList = metadata.Features.Variations;
Assert.AreEqual(variationFeatureList[0].Replace, expectedVariationReplace);
// Clone Variation feature.
Variation clonedVariations = variationFeatureList[0].Clone();
// Validate Intron feature after clonning.
Assert.AreEqual(clonedVariations.Replace, expectedVariationReplace);
break;
default:
break;
}
}
}
/// <summary>
/// Validate GenBank Citation referenced present in GenBank Metadata.
/// </summary>
/// <param name="nodeName">xml node name.</param>
/// <param name="featureName">Feature Name</param>
private void ValidateCitationReferenced(string nodeName,
FeatureGroup featureName)
{
// Get Values from XML node.
string filePath = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.FilePathNode);
string expectedCitationReferenced = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.citationReferencedCount);
string expectedmRNACitationReferenced = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.citationReferencedCount);
string expectedExonACitationReferenced = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ExonCitationReferencedCount);
string expectedIntronCitationReferenced = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.IntronCitationReferencedCount);
string expectedpromoterCitationReferenced = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.PromotersCitationReferencedCount);
// Parse a GenBank file.
ISequenceParser parserObj = new GenBankParser();
{
ISequence seq = parserObj.ParseOne(filePath);
var metadata =
seq.Metadata[Constants.GenBank] as GenBankMetadata;
List<CitationReference> citationReferenceList;
// Get a list citationReferenced present in GenBank file.
switch (featureName)
{
case FeatureGroup.CDS:
FeatureItem cds =
metadata.Features.CodingSequences[0];
citationReferenceList =
metadata.GetCitationsReferredInFeature(cds);
// Validate citation referenced present in CDS features.
Assert.AreEqual(citationReferenceList.Count.ToString((IFormatProvider) null),
expectedCitationReferenced);
break;
case FeatureGroup.mRNA:
FeatureItem mRNA = metadata.Features.MessengerRNAs[0];
citationReferenceList = metadata.GetCitationsReferredInFeature(mRNA);
// Validate citation referenced present in mRNA features.
Assert.AreEqual(citationReferenceList.Count.ToString((IFormatProvider) null),
expectedmRNACitationReferenced);
break;
case FeatureGroup.Exon:
FeatureItem exon = metadata.Features.Exons[0];
citationReferenceList =
metadata.GetCitationsReferredInFeature(exon);
// Validate citation referenced present in Exons features.
Assert.AreEqual(citationReferenceList.Count.ToString((IFormatProvider) null),
expectedExonACitationReferenced);
break;
case FeatureGroup.Intron:
FeatureItem introns = metadata.Features.Introns[0];
citationReferenceList =
metadata.GetCitationsReferredInFeature(introns);
// Validate citation referenced present in Introns features.
Assert.AreEqual(citationReferenceList.Count.ToString((IFormatProvider) null),
expectedIntronCitationReferenced);
break;
case FeatureGroup.Promoter:
FeatureItem promoter = metadata.Features.Promoters[0];
citationReferenceList =
metadata.GetCitationsReferredInFeature(promoter);
// Validate citation referenced present in Promoters features.
Assert.AreEqual(citationReferenceList.Count.ToString((IFormatProvider) null),
expectedpromoterCitationReferenced);
break;
default:
break;
}
}
}
/// <summary>
/// Validate GenBank features with specified range.
/// </summary>
/// <param name="nodeName">xml node name.</param>
private void ValidateGetFeatures(string nodeName)
{
// Get Values from XML node.
string filePath = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.FilePathNode);
string expectedFirstRangeStartPoint = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.FirstRangeStartPoint);
string expectedSecondRangeStartPoint = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.SecondRangeStartPoint);
string expectedFirstRangeEndPoint = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.FirstRangeEndPoint);
string expectedSecondRangeEndPoint = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.SecondRangeEndPoint);
string expectedCountWithinSecondRange = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.SecondRangeCount);
string expectedCountWithinFirstRange = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.FirstRangeCount);
string expectedQualifierName = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.CDSKey);
string expectedQualifiers = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.QualifiersCount);
string firstFeaturesCount = string.Empty;
string secodFeaturesCount = string.Empty;
// Parse a GenBank file.
ISequenceParser parserObj = new GenBankParser();
{
ISequence seq = parserObj.ParseOne(filePath);
var metadata = seq.Metadata[Constants.GenBank] as GenBankMetadata;
// Validate GetFeature within specified range.
List<FeatureItem> features =
metadata.GetFeatures(Convert.ToInt32(
expectedFirstRangeStartPoint, null), Convert.ToInt32(
expectedFirstRangeEndPoint, null));
firstFeaturesCount = metadata.GetFeatures(Convert.ToInt32(
expectedFirstRangeStartPoint, null), Convert.ToInt32(
expectedFirstRangeEndPoint, null)).Count.ToString((IFormatProvider) null);
secodFeaturesCount = metadata.GetFeatures(Convert.ToInt32(
expectedSecondRangeStartPoint, null), Convert.ToInt32(
expectedSecondRangeEndPoint, null)).Count.ToString((IFormatProvider) null);
// Validate GenBank features count within specified range.
Assert.AreEqual(firstFeaturesCount, expectedCountWithinFirstRange);
Assert.AreEqual(secodFeaturesCount, expectedCountWithinSecondRange);
Assert.AreEqual(features.Count.ToString((IFormatProvider) null), firstFeaturesCount);
Assert.AreEqual(features[1].Qualifiers.Count.ToString((IFormatProvider) null),
expectedQualifiers);
Assert.AreEqual(features[1].Key.ToString(null), expectedQualifierName);
}
}
public void ValidateGenBankLocationStartAndEndRange()
{
// Get Values from XML node.
string filePath = utilityObj.xmlUtil.GetTextValue(
Constants.GenBankRepeatRegionQualifiersNode,
Constants.FilePathNode);
bool startLocResult = false;
bool endLocResult = false;
bool rangeLocResult = false;
// Parse a GenBank file.
ISequenceParser parserObj = new GenBankParser();
{
ISequence sequence = parserObj.ParseOne(filePath);
ILocationResolver locResolver = new LocationResolver();
// Validate Start,End and Range of Gene feature location.
var metadata =
(GenBankMetadata) sequence.Metadata[Constants.GenBank];
startLocResult =
locResolver.IsInStart(metadata.Features.Genes[0].Location, 289);
endLocResult =
locResolver.IsInEnd(metadata.Features.Genes[0].Location, 1647);
rangeLocResult =
locResolver.IsInRange(metadata.Features.Genes[0].Location, 300);
Assert.IsTrue(startLocResult);
Assert.IsTrue(endLocResult);
Assert.IsTrue(rangeLocResult);
// Log VSTest GUI.
ApplicationLog.WriteLine(
"GenBank Features P1: Successfully validated the location resolver Gene feature start End and IsInRange methods");
}
}
public void ValidateGenBankSubSequence()
{
// Get Values from XML node.
string filePath = utilityObj.xmlUtil.GetTextValue(
Constants.GenBankRepeatRegionQualifiersNode,
Constants.FilePathNode);
string expectedSubSequence = utilityObj.xmlUtil.GetTextValue(
Constants.GenBankRepeatRegionQualifiersNode,
Constants.ExpectedFeatureSubSequence);
// Parse a GenBank file.
ISequenceParser parserObj = new GenBankParser();
{
ISequence sequence = parserObj.ParseOne(filePath);
ILocationResolver locResolver = new LocationResolver();
// Get repeatregion subsequence.
var metadata =
(GenBankMetadata) sequence.Metadata[Constants.GenBank];
ISequence subSeq = locResolver.GetSubSequence(
metadata.Features.RepeatRegions[0].Location, sequence);
var sequenceString = new string(subSeq.Select(a => (char) a).ToArray());
// Validate repeat region subsequence.
Assert.AreEqual(sequenceString, expectedSubSequence);
// Log VSTest GUI.
ApplicationLog.WriteLine(
"GenBank Features P1: Successfully validated the GenBank subSequence");
}
}