/// <summary>
/// Create a SequenceRangeGrouping by passing RangeID,Start and End Index.
/// and validate created SequenceRange.
/// </summary>
/// <param name="nodeName">Xml Node name for different inputs.</param>
static void CreateSequenceRangeGrouping(string nodeName)
{
// Get values from xml.
string expectedRangeIDs = Utility._xmlUtil.GetTextValue(
nodeName, Constants.IDNode);
string expectedStartIndex = Utility._xmlUtil.GetTextValue(
nodeName, Constants.StartNode);
string expectedEndIndex = Utility._xmlUtil.GetTextValue(
nodeName, Constants.EndNode);
string expectedSequenceRangeCount = Utility._xmlUtil.GetTextValue(
nodeName, Constants.SequenceRangeCountNode);
string actualRangeStarts = string.Empty;
string actualRangeEnds = string.Empty;
string actualRangeIDs = string.Empty;
string[] rangeIDs = expectedRangeIDs.Split(',');
string[] rangeStarts = expectedStartIndex.Split(',');
string[] rangeEnds = expectedEndIndex.Split(',');
SequenceRangeGrouping seqRangeGrouping = new SequenceRangeGrouping();
List <ISequenceRange> rangeList = null;
// Create a SequenceRange and add to SequenceRangeList.
for (int i = 0; i < rangeIDs.Length; i++)
{
SequenceRange seqRange = new SequenceRange(rangeIDs[i],
long.Parse(rangeStarts[i]), long.Parse(rangeEnds[i]));
seqRangeGrouping.Add(seqRange);
}
IEnumerable <string> rangeGroupIds = seqRangeGrouping.GroupIDs;
string rangeID = string.Empty;
foreach (string groupID in rangeGroupIds)
{
rangeID = groupID;
// Get SequenceRangeIds.
rangeList = seqRangeGrouping.GetGroup(rangeID);
// Validate created SequenceRanges.
foreach (ISequenceRange seqRange in rangeList)
{
actualRangeIDs = string.Concat(actualRangeIDs, seqRange.ID.ToString(), ",");
actualRangeStarts = string.Concat(actualRangeStarts, seqRange.Start.ToString(), ",");
actualRangeEnds = string.Concat(actualRangeEnds, seqRange.End.ToString(), ",");
}
}
Assert.AreEqual(expectedSequenceRangeCount, rangeList.Count.ToString());
Assert.AreEqual(expectedRangeIDs,
actualRangeIDs.Substring(0, actualRangeIDs.Length - 1));
Assert.AreEqual(expectedStartIndex,
actualRangeStarts.Substring(0,
actualRangeStarts.Length - 1));
Assert.AreEqual(expectedEndIndex,
actualRangeEnds.Substring(0, actualRangeEnds.Length - 1));
Console.WriteLine(
"SequenceRange BVT : Successfully validated the SequenceStart, SequenceID and SequenceEnd.");
}
public void ValidateFlatten()
{
// Get values from xml.
string expectedRangeIDs = utilityObj.xmlUtil.GetTextValue(
Constants.SmallSizeBedNodeName, Constants.IDNode);
string expectedStartIndex = utilityObj.xmlUtil.GetTextValue(
Constants.SmallSizeBedNodeName, Constants.StartNode);
string expectedEndIndex = utilityObj.xmlUtil.GetTextValue(
Constants.SmallSizeBedNodeName, Constants.EndNode);
string expectedSequenceRangeCount = utilityObj.xmlUtil.GetTextValue(
Constants.SmallSizeBedNodeName, Constants.SequenceRangeCountNode);
string[] rangeIDs = expectedRangeIDs.Split(',');
string[] rangeStarts = expectedStartIndex.Split(',');
string[] rangeEnds = expectedEndIndex.Split(',');
SequenceRangeGrouping seqRangeGrouping = new SequenceRangeGrouping();
List <ISequenceRange> rangeList = null;
// Create a SequenceRange and add to SequenceRangeList.
for (int i = 0; i < rangeIDs.Length; i++)
{
SequenceRange seqRange = new SequenceRange(rangeIDs[i],
long.Parse(rangeStarts[i], (IFormatProvider)null),
long.Parse(rangeEnds[i], (IFormatProvider)null));
seqRangeGrouping.Add(seqRange);
}
//Convert SequenceRangeGroup to SequenceRangeList.
rangeList = seqRangeGrouping.Flatten();
int j = 0;
// Validate created SequenceRanges.
foreach (ISequenceRange seqRange in rangeList)
{
Assert.AreEqual(rangeStarts[j], seqRange.Start.ToString((IFormatProvider)null));
Assert.AreEqual(rangeEnds[j], seqRange.End.ToString((IFormatProvider)null));
Assert.AreEqual(rangeIDs[j], seqRange.ID.ToString((IFormatProvider)null));
j++;
}
Assert.AreEqual(expectedSequenceRangeCount, rangeList.Count.ToString((IFormatProvider)null));
Console.WriteLine(
"SequenceRange BVT : Successfully validated the SequenceStart,SequenceID and SequenceEnd.");
}
/// <summary>
/// Formats the Range/RangeGroup for different test cases based
/// on Additional parameter
/// </summary>
/// <param name="nodeName">Xml Node name</param>
/// <param name="addParam">Additional parameter</param>
private void FormatterGeneralTestCases(string nodeName,
AdditionalParameters addParam)
{
IList <ISequenceRange> rangeList = new List <ISequenceRange>();
var rangeGroup = new SequenceRangeGrouping();
// Gets the file name.
string filePath = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FilePathNode).TestDir();
// Condition to check if Parse() happens before Format()
switch (addParam)
{
case AdditionalParameters.ParseRangeGroup:
var initialParserGroupObj = new BedParser();
rangeGroup =
initialParserGroupObj.ParseRangeGrouping(filePath);
break;
case AdditionalParameters.ParseRange:
var initialParserObj = new BedParser();
rangeList = initialParserObj.ParseRange(filePath);
break;
default:
// Gets all the expected values from xml.
string expectedID = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.IDNode);
string expectedStart = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.StartNode);
string expectedEnd = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.EndNode);
string[] expectedIDs = expectedID.Split(',');
string[] expectedStarts = expectedStart.Split(',');
string[] expectedEnds = expectedEnd.Split(',');
// Gets the Range Group or Range based on the additional parameter
switch (addParam)
{
case AdditionalParameters.RangeGroupTextWriter:
case AdditionalParameters.RangeGroupFileName:
for (int i = 0; i < expectedIDs.Length; i++)
{
var rangeObj1 = new SequenceRange(expectedIDs[i],
long.Parse(expectedStarts[i], null),
long.Parse(expectedEnds[i], null));
rangeGroup.Add(rangeObj1);
}
break;
default:
for (int i = 0; i < expectedIDs.Length; i++)
{
var rangeObj2 = new SequenceRange(expectedIDs[i],
long.Parse(expectedStarts[i], null),
long.Parse(expectedEnds[i], null));
rangeList.Add(rangeObj2);
}
break;
}
break;
}
var formatterObj = new BedFormatter();
// Gets the Range list/Range Group based on the parameters.
switch (addParam)
{
case AdditionalParameters.RangeFileName:
case AdditionalParameters.ParseRange:
formatterObj.Format(rangeList, Constants.BedTempFileName);
break;
case AdditionalParameters.RangeTextWriter:
using (var txtWriter =
File.Create(Constants.BedTempFileName))
{
formatterObj.Format(txtWriter, rangeList);
}
break;
case AdditionalParameters.RangeGroupFileName:
case AdditionalParameters.ParseRangeGroup:
formatterObj.Format(rangeGroup, Constants.BedTempFileName);
break;
case AdditionalParameters.RangeGroupTextWriter:
using (var txtWriter =
File.Create(Constants.BedTempFileName))
{
formatterObj.Format(txtWriter, rangeGroup);
}
break;
default:
break;
}
// Reparse to validate the results
var parserObj = new BedParser();
IList <ISequenceRange> newRangeList =
parserObj.ParseRange(Constants.BedTempFileName);
// Validation of all the properties.
for (int i = 0; i < rangeList.Count; i++)
{
Assert.AreEqual(rangeList[i].ID, newRangeList[i].ID);
Assert.AreEqual(rangeList[i].Start, newRangeList[i].Start);
Assert.AreEqual(rangeList[i].End, newRangeList[i].End);
// Validation of all metadata information.
if (rangeList[i].Metadata.Count > 0)
{
if (rangeList[i].Metadata.ContainsKey("Name"))
{
Assert.AreEqual(rangeList[i].Metadata["Name"],
newRangeList[i].Metadata["Name"]);
}
if (rangeList[i].Metadata.ContainsKey("Score"))
{
Assert.AreEqual(rangeList[i].Metadata["Score"],
newRangeList[i].Metadata["Score"]);
}
if (rangeList[i].Metadata.ContainsKey("Strand"))
{
Assert.AreEqual(rangeList[i].Metadata["Strand"],
newRangeList[i].Metadata["Strand"]);
}
if (rangeList[i].Metadata.ContainsKey("ThickStart"))
{
Assert.AreEqual(rangeList[i].Metadata["ThickStart"],
newRangeList[i].Metadata["ThickStart"]);
}
if (rangeList[i].Metadata.ContainsKey("ThickEnd"))
{
Assert.AreEqual(rangeList[i].Metadata["ThickEnd"],
newRangeList[i].Metadata["ThickEnd"]);
}
if (rangeList[i].Metadata.ContainsKey("ItemRGB"))
{
Assert.AreEqual(rangeList[i].Metadata["ItemRGB"],
newRangeList[i].Metadata["ItemRGB"]);
}
if (rangeList[i].Metadata.ContainsKey("BlockCount"))
{
Assert.AreEqual(rangeList[i].Metadata["BlockCount"],
newRangeList[i].Metadata["BlockCount"]);
}
if (rangeList[i].Metadata.ContainsKey("BlockSizes"))
{
Assert.AreEqual(rangeList[i].Metadata["BlockSizes"],
newRangeList[i].Metadata["BlockSizes"]);
}
if (rangeList[i].Metadata.ContainsKey("BlockStarts"))
{
Assert.AreEqual(rangeList[i].Metadata["BlockStarts"],
newRangeList[i].Metadata["BlockStarts"]);
}
ApplicationLog.WriteLine(
"Bed Formatter BVT: Successfully validated all the metadata information");
}
}
ApplicationLog.WriteLine(
"Bed Formatter BVT: Successfully validated the ID, Start and End Ranges");
// Cleanup the file.
if (File.Exists(Constants.BedTempFileName))
{
File.Delete(Constants.BedTempFileName);
}
}
/// <summary>
/// Formats the Range/RangeGroup for different test cases based
/// on Additional parameter
/// </summary>
/// <param name="nodeName">Xml Node name</param>
/// <param name="addParam">Additional parameter</param>
void FormatterGeneralTestCases(string nodeName,
AdditionalParameters addParam)
{
IList <ISequenceRange> rangeList = new List <ISequenceRange>();
SequenceRangeGrouping rangeGroup = new SequenceRangeGrouping();
// Gets the file name.
string filePath = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.FilePathNode);
// Condition to check if Parse() happens before Format()
switch (addParam)
{
case AdditionalParameters.ParseRangeGroup:
case AdditionalParameters.ParseRangeGroupTextWriter:
BedParser initialParserGroupObj = new BedParser();
rangeGroup =
initialParserGroupObj.ParseRangeGrouping(filePath);
break;
case AdditionalParameters.ParseRange:
case AdditionalParameters.ParseRangeTextWriter:
BedParser initialParserObj = new BedParser();
rangeList = initialParserObj.ParseRange(filePath);
break;
default:
// Gets all the expected values from xml.
string expectedID = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.IDNode);
string expectedStart = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.StartNode);
string expectedEnd = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.EndNode);
string[] expectedIDs = expectedID.Split(',');
string[] expectedStarts = expectedStart.Split(',');
string[] expectedEnds = expectedEnd.Split(',');
// Gets the Range Group or Range based on the additional parameter
switch (addParam)
{
case AdditionalParameters.RangeGroupTextWriter:
case AdditionalParameters.RangeGroupFileName:
for (int i = 0; i < expectedIDs.Length; i++)
{
SequenceRange rangeObj1 =
new SequenceRange(expectedIDs[i],
long.Parse(expectedStarts[i], (IFormatProvider)null),
long.Parse(expectedEnds[i], (IFormatProvider)null));
rangeGroup.Add(rangeObj1);
}
break;
default:
for (int i = 0; i < expectedIDs.Length; i++)
{
SequenceRange rangeObj2 =
new SequenceRange(expectedIDs[i],
long.Parse(expectedStarts[i], (IFormatProvider)null),
long.Parse(expectedEnds[i], (IFormatProvider)null));
rangeList.Add(rangeObj2);
}
break;
}
break;
}
BedFormatter formatterObj = new BedFormatter();
// Gets the Range list/Range Group based on the parameters.
switch (addParam)
{
case AdditionalParameters.RangeFileName:
case AdditionalParameters.ParseRange:
formatterObj.Format(rangeList, Constants.BedTempFileName);
break;
case AdditionalParameters.RangeTextWriter:
case AdditionalParameters.ParseRangeTextWriter:
using (TextWriter txtWriter =
new StreamWriter(Constants.BedTempFileName))
{
formatterObj.Format(rangeList, txtWriter);
}
break;
case AdditionalParameters.RangeGroupFileName:
case AdditionalParameters.ParseRangeGroup:
formatterObj.Format(rangeGroup, Constants.BedTempFileName);
break;
case AdditionalParameters.RangeGroupTextWriter:
case AdditionalParameters.ParseRangeGroupTextWriter:
using (TextWriter txtWriter =
new StreamWriter(Constants.BedTempFileName))
{
formatterObj.Format(rangeGroup, txtWriter);
}
break;
default:
break;
}
// Reparse to validate the results
BedParser parserObj = new BedParser();
IList <ISequenceRange> newRangeList =
parserObj.ParseRange(Constants.BedTempFileName);
// Validation of all the properties.
for (int i = 0; i < rangeList.Count; i++)
{
Assert.AreEqual(rangeList[0].ID, newRangeList[0].ID);
Assert.AreEqual(rangeList[0].Start, newRangeList[0].Start);
Assert.AreEqual(rangeList[0].End, newRangeList[0].End);
}
ApplicationLog.WriteLine(
"Bed Formatter P1: Successfully validated the ID, Start and End Ranges");
Console.WriteLine(
"Bed Formatter P1: Successfully validated the ID, Start and End Ranges");
// Cleanup the file.
if (File.Exists(Constants.BedTempFileName))
{
File.Delete(Constants.BedTempFileName);
}
}
/// <summary>
/// Formats the Range/RangeGroup for different test cases based
/// on Additional parameter
/// </summary>
/// <param name="nodeName">Xml Node name</param>
/// <param name="addParam">Additional parameter</param>
private void FormatterGeneralTestCases(string nodeName,
AdditionalParameters addParam)
{
IList<ISequenceRange> rangeList = new List<ISequenceRange>();
var rangeGroup = new SequenceRangeGrouping();
// Gets the file name.
string filePath = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.FilePathNode);
// Condition to check if Parse() happens before Format()
switch (addParam)
{
case AdditionalParameters.ParseRangeGroup:
case AdditionalParameters.ParseRangeGroupTextWriter:
var initialParserGroupObj = new BedParser();
rangeGroup =
initialParserGroupObj.ParseRangeGrouping(filePath);
break;
case AdditionalParameters.ParseRange:
case AdditionalParameters.ParseRangeTextWriter:
var initialParserObj = new BedParser();
rangeList = initialParserObj.ParseRange(filePath);
break;
default:
// Gets all the expected values from xml.
string expectedID = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.IDNode);
string expectedStart = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.StartNode);
string expectedEnd = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.EndNode);
string[] expectedIDs = expectedID.Split(',');
string[] expectedStarts = expectedStart.Split(',');
string[] expectedEnds = expectedEnd.Split(',');
// Gets the Range Group or Range based on the additional parameter
switch (addParam)
{
case AdditionalParameters.RangeGroupTextWriter:
case AdditionalParameters.RangeGroupFileName:
for (int i = 0; i < expectedIDs.Length; i++)
{
var rangeObj1 =
new SequenceRange(expectedIDs[i],
long.Parse(expectedStarts[i], null),
long.Parse(expectedEnds[i], null));
rangeGroup.Add(rangeObj1);
}
break;
default:
for (int i = 0; i < expectedIDs.Length; i++)
{
var rangeObj2 =
new SequenceRange(expectedIDs[i],
long.Parse(expectedStarts[i], null),
long.Parse(expectedEnds[i], null));
rangeList.Add(rangeObj2);
}
break;
}
break;
}
var formatterObj = new BedFormatter();
// Gets the Range list/Range Group based on the parameters.
switch (addParam)
{
case AdditionalParameters.RangeFileName:
case AdditionalParameters.ParseRange:
formatterObj.Format(rangeList, Constants.BedTempFileName);
break;
case AdditionalParameters.RangeTextWriter:
case AdditionalParameters.ParseRangeTextWriter:
using (var txtWriter = File.Create(Constants.BedTempFileName))
{
formatterObj.Format(txtWriter, rangeList);
}
break;
case AdditionalParameters.RangeGroupFileName:
case AdditionalParameters.ParseRangeGroup:
formatterObj.Format(rangeGroup, Constants.BedTempFileName);
break;
case AdditionalParameters.RangeGroupTextWriter:
case AdditionalParameters.ParseRangeGroupTextWriter:
using (var txtWriter = File.Create(Constants.BedTempFileName))
{
formatterObj.Format(txtWriter, rangeGroup);
}
break;
default:
break;
}
// Reparse to validate the results
var parserObj = new BedParser();
IList<ISequenceRange> newRangeList =
parserObj.ParseRange(Constants.BedTempFileName);
// Validation of all the properties.
for (int i = 0; i < rangeList.Count; i++)
{
Assert.AreEqual(rangeList[0].ID, newRangeList[0].ID);
Assert.AreEqual(rangeList[0].Start, newRangeList[0].Start);
Assert.AreEqual(rangeList[0].End, newRangeList[0].End);
}
ApplicationLog.WriteLine(
"Bed Formatter P1: Successfully validated the ID, Start and End Ranges");
// Cleanup the file.
if (File.Exists(Constants.BedTempFileName))
File.Delete(Constants.BedTempFileName);
}
/// <summary>
/// Create a SequenceRangeGrouping by passing RangeID,Start and End Index.
/// and validate created SequenceRange.
/// </summary>
/// <param name="nodeName">Xml Node name for different inputs.</param>
private void CreateSequenceRangeGrouping(string nodeName)
{
// Get values from xml.
string expectedRangeIDs = this.utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.IDNode);
string expectedStartIndex = this.utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.StartNode);
string expectedEndIndex = this.utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.EndNode);
string expectedSequenceRangeCount = this.utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.SequenceRangeCountNode);
string[] rangeIDs = expectedRangeIDs.Split(',');
string[] rangeStarts = expectedStartIndex.Split(',');
string[] rangeEnds = expectedEndIndex.Split(',');
var seqRangeGrouping = new SequenceRangeGrouping();
List<ISequenceRange> rangeList = null;
// Create a SequenceRange and add to SequenceRangeList.
for (int i = 0; i < rangeIDs.Length; i++)
{
var seqRange = new SequenceRange(rangeIDs[i],
long.Parse(rangeStarts[i], null), long.Parse(rangeEnds[i], null));
seqRangeGrouping.Add(seqRange);
}
IEnumerable<string> rangeGroupIds = seqRangeGrouping.GroupIDs;
string rangeID = string.Empty;
int j = 0;
foreach (string groupID in rangeGroupIds)
{
rangeID = groupID;
// Get SequenceRangeIds.
rangeList = seqRangeGrouping.GetGroup(rangeID);
// Validate created SequenceRanges.
foreach (ISequenceRange seqRange in rangeList)
{
Assert.AreEqual(rangeStarts[j], seqRange.Start.ToString((IFormatProvider) null));
Assert.AreEqual(rangeEnds[j], seqRange.End.ToString((IFormatProvider) null));
Assert.AreEqual(rangeIDs[j], seqRange.ID.ToString(null));
j++;
}
}
Assert.AreEqual(expectedSequenceRangeCount,
rangeList.Count.ToString((IFormatProvider) null));
ApplicationLog.WriteLine(
"SequenceRange BVT : Successfully validated the SequenceStart, SequenceID and SequenceEnd.");
}
public void ValidateFlatten()
{
// Get values from xml.
string expectedRangeIDs = this.utilityObj.xmlUtil.GetTextValue(
Constants.SmallSizeBedNodeName, Constants.IDNode);
string expectedStartIndex = this.utilityObj.xmlUtil.GetTextValue(
Constants.SmallSizeBedNodeName, Constants.StartNode);
string expectedEndIndex = this.utilityObj.xmlUtil.GetTextValue(
Constants.SmallSizeBedNodeName, Constants.EndNode);
string expectedSequenceRangeCount = this.utilityObj.xmlUtil.GetTextValue(
Constants.SmallSizeBedNodeName, Constants.SequenceRangeCountNode);
string[] rangeIDs = expectedRangeIDs.Split(',');
string[] rangeStarts = expectedStartIndex.Split(',');
string[] rangeEnds = expectedEndIndex.Split(',');
var seqRangeGrouping = new SequenceRangeGrouping();
List<ISequenceRange> rangeList = null;
// Create a SequenceRange and add to SequenceRangeList.
for (int i = 0; i < rangeIDs.Length; i++)
{
var seqRange = new SequenceRange(rangeIDs[i],
long.Parse(rangeStarts[i], null),
long.Parse(rangeEnds[i], null));
seqRangeGrouping.Add(seqRange);
}
//Convert SequenceRangeGroup to SequenceRangeList.
rangeList = seqRangeGrouping.Flatten();
int j = 0;
// Validate created SequenceRanges.
foreach (ISequenceRange seqRange in rangeList)
{
Assert.AreEqual(rangeStarts[j], seqRange.Start.ToString((IFormatProvider) null));
Assert.AreEqual(rangeEnds[j], seqRange.End.ToString((IFormatProvider) null));
Assert.AreEqual(rangeIDs[j], seqRange.ID.ToString(null));
j++;
}
Assert.AreEqual(expectedSequenceRangeCount, rangeList.Count.ToString((IFormatProvider) null));
ApplicationLog.WriteLine("SequenceRange BVT : Successfully validated the SequenceStart,SequenceID and SequenceEnd.");
}