/// <summary>
/// Method which will export a parsed BED file
/// </summary>
/// <param name="e">Event Arguments</param>
private void DoExportRangeSequence(InputSequenceRangeSelectionEventArg e)
{
Stream sequenceWriter = null;
//todo: Below line used hard coded BEDFormatter, have to get it from args later on
ISequenceRangeFormatter formatter = new BedFormatter();
var saveDialog = new SaveFileDialog { Filter = "BED Files|*.BED" };
try
{
if (e.Sequences[0].GroupIDs.Any())
{
if (saveDialog.ShowDialog() == DialogResult.OK)
{
// Get a textwriter to the file which will append text to it.
sequenceWriter = File.OpenWrite(saveDialog.FileName);
formatter.Format(sequenceWriter, e.Sequences[0]);
}
}
else
{
MessageBox.Show(
Resources.EMPTY_SEQUENCE_RANGE,
Resources.CAPTION,
MessageBoxButtons.OK,
MessageBoxIcon.Error);
}
}
catch (Exception ex)
{
MessageBox.Show(ex.Message, Resources.CAPTION, MessageBoxButtons.OK, MessageBoxIcon.Error);
}
finally
{
if (sequenceWriter != null)
{
sequenceWriter.Close();
}
}
}
public void SubtractTest()
{
var direc = System.IO.Path.Combine ("TestUtils", "BED", "Subtract");
string refSeqRangefile = System.IO.Path.Combine (direc, "Subtract_ref.BED");
string querySeqRangefile = System.IO.Path.Combine (direc, "Subtract_query.BED");
string resultfilepath = "tmp_mergeresult.bed";
BedParser parser = new BedParser();
BedFormatter formatter = new BedFormatter();
SequenceRangeGrouping result = null;
bool resultvalue = false;
SequenceRangeGrouping refSeqRange = parser.ParseRangeGrouping(refSeqRangefile);
SequenceRangeGrouping querySeqRange = parser.ParseRangeGrouping(querySeqRangefile);
string expectedresultpath = System.IO.Path.Combine (direc, "Result_Subtract_minoverlap1.BED");
result = refSeqRange.Subtract(querySeqRange, 1, SubtractOutputType.IntervalsWithNoOverlap);
formatter.Format(result, resultfilepath);
resultvalue = CompareBEDOutput(resultfilepath, expectedresultpath);
Assert.IsTrue(resultvalue);
resultvalue = ValidateParentSeqRange(result, refSeqRange, querySeqRange, true);
Assert.IsTrue(resultvalue);
expectedresultpath = System.IO.Path.Combine (direc, "Result_Subtract_minoverlap0.BED");
result = refSeqRange.Subtract(querySeqRange, 0, SubtractOutputType.IntervalsWithNoOverlap);
formatter.Format(result, resultfilepath);
resultvalue = CompareBEDOutput(resultfilepath, expectedresultpath);
Assert.IsTrue(resultvalue);
resultvalue = ValidateParentSeqRange(result, refSeqRange, querySeqRange, true);
Assert.IsTrue(resultvalue);
expectedresultpath = System.IO.Path.Combine (direc, "Result_Subtract_minoverlap1.BED");
result = refSeqRange.Subtract(querySeqRange, 1, SubtractOutputType.IntervalsWithNoOverlap, true);
formatter.Format(result, resultfilepath);
resultvalue = CompareBEDOutput(resultfilepath, expectedresultpath);
Assert.IsTrue(resultvalue);
resultvalue = ValidateParentSeqRange(result, refSeqRange, querySeqRange, true);
Assert.IsTrue(resultvalue);
expectedresultpath = System.IO.Path.Combine (direc, "Result_Subtract_minoverlap0.BED");
result = refSeqRange.Subtract(querySeqRange, 0, SubtractOutputType.IntervalsWithNoOverlap, true);
formatter.Format(result, resultfilepath);
resultvalue = CompareBEDOutput(resultfilepath, expectedresultpath);
Assert.IsTrue(resultvalue);
resultvalue = ValidateParentSeqRange(result, refSeqRange, querySeqRange, true);
Assert.IsTrue(resultvalue);
expectedresultpath = System.IO.Path.Combine (direc, "Result_Subtract_minoverlap1.BED");
result = refSeqRange.Subtract(querySeqRange, 1, SubtractOutputType.IntervalsWithNoOverlap, false);
formatter.Format(result, resultfilepath);
resultvalue = CompareBEDOutput(resultfilepath, expectedresultpath);
Assert.IsTrue(resultvalue);
resultvalue = ValidateParentSeqRange(result, refSeqRange, querySeqRange, false);
Assert.IsTrue(resultvalue);
expectedresultpath = System.IO.Path.Combine (direc, "Result_Subtract_minoverlap0.BED");
result = refSeqRange.Subtract(querySeqRange, 0, SubtractOutputType.IntervalsWithNoOverlap, false);
formatter.Format(result, resultfilepath);
resultvalue = CompareBEDOutput(resultfilepath, expectedresultpath);
Assert.IsTrue(resultvalue);
resultvalue = ValidateParentSeqRange(result, refSeqRange, querySeqRange, false);
Assert.IsTrue(resultvalue);
expectedresultpath = System.IO.Path.Combine (direc, "Result_Subtract_minoverlap0_NOnOverlappingPieces.BED");
result = refSeqRange.Subtract(querySeqRange, 0, SubtractOutputType.NonOverlappingPiecesOfIntervals, true);
formatter.Format(result, resultfilepath);
resultvalue = CompareBEDOutput(resultfilepath, expectedresultpath);
Assert.IsTrue(resultvalue);
resultvalue = ValidateParentSeqRange(result, refSeqRange, querySeqRange, true);
Assert.IsTrue(resultvalue);
expectedresultpath = System.IO.Path.Combine (direc, "Result_Subtract_minoverlap1_NOnOverlappingPieces.BED");
result = refSeqRange.Subtract(querySeqRange, 1, SubtractOutputType.NonOverlappingPiecesOfIntervals, true);
formatter.Format(result, resultfilepath);
resultvalue = CompareBEDOutput(resultfilepath, expectedresultpath);
Assert.IsTrue(resultvalue);
resultvalue = ValidateParentSeqRange(result, refSeqRange, querySeqRange, true);
Assert.IsTrue(resultvalue);
}
public void IntersectOperationTest()
{
string resultfilepath = "tmp_mergeresult.bed";
string expectedresultpath = string.Empty;
BedParser parser = new BedParser();
BedFormatter formatter = new BedFormatter();
SequenceRangeGrouping result = null;
bool resultvalue = false;
resultfilepath = "tmp_mergeresult.bed";
string direc = Path.Combine("TestUtils", "BED", "Intersect");
string reffile = Path.Combine(direc, @"Intersect_ref.BED");
string queryFile = Path.Combine(direc, "Intersect_query.BED");
SequenceRangeGrouping refSeqRange = parser.ParseRangeGrouping(reffile);
SequenceRangeGrouping querySeqRange = parser.ParseRangeGrouping(queryFile);
expectedresultpath = Path.Combine(direc, "Result_Intersect_MinOverlap1_OverLappingBases.BED");
result = refSeqRange.Intersect(querySeqRange, 1, IntersectOutputType.OverlappingPiecesOfIntervals);
formatter.Format(result, resultfilepath);
resultvalue = CompareBEDOutput(resultfilepath, expectedresultpath);
Assert.IsTrue(resultvalue);
resultvalue = ValidateParentSeqRange(result, refSeqRange, querySeqRange, true);
Assert.IsTrue(resultvalue);
expectedresultpath = Path.Combine(direc, "Result_Intersect_MinOverlap1.BED");
result = refSeqRange.Intersect(querySeqRange, 1, IntersectOutputType.OverlappingIntervals);
formatter.Format(result, resultfilepath);
resultvalue = CompareBEDOutput(resultfilepath, expectedresultpath);
Assert.IsTrue(resultvalue);
resultvalue = ValidateParentSeqRange(result, refSeqRange, querySeqRange, false);
Assert.IsTrue(resultvalue);
expectedresultpath = Path.Combine(direc, "Result_Intersect_MinOverlap0_OverLappingBases.BED");
result = refSeqRange.Intersect(querySeqRange, 0, IntersectOutputType.OverlappingPiecesOfIntervals);
formatter.Format(result, resultfilepath);
resultvalue = CompareBEDOutput(resultfilepath, expectedresultpath);
Assert.IsTrue(resultvalue);
resultvalue = ValidateParentSeqRange(result, refSeqRange, querySeqRange, true);
Assert.IsTrue(resultvalue);
expectedresultpath = Path.Combine(direc, "Result_Intersect_MinOverlap0.BED");
result = refSeqRange.Intersect(querySeqRange, 0, IntersectOutputType.OverlappingIntervals);
formatter.Format(result, resultfilepath);
resultvalue = CompareBEDOutput(resultfilepath, expectedresultpath);
Assert.IsTrue(resultvalue);
resultvalue = ValidateParentSeqRange(result, refSeqRange, querySeqRange, false);
Assert.IsTrue(resultvalue);
expectedresultpath = Path.Combine(direc, "Result_Intersect_MinOverlap1_OverLappingBases.BED");
result = refSeqRange.Intersect(querySeqRange, 1, IntersectOutputType.OverlappingPiecesOfIntervals, true);
formatter.Format(result, resultfilepath);
resultvalue = CompareBEDOutput(resultfilepath, expectedresultpath);
Assert.IsTrue(resultvalue);
resultvalue = ValidateParentSeqRange(result, refSeqRange, querySeqRange, true);
Assert.IsTrue(resultvalue);
expectedresultpath = Path.Combine(direc, "Result_Intersect_MinOverlap1.BED");
result = refSeqRange.Intersect(querySeqRange, 1, IntersectOutputType.OverlappingIntervals, true);
formatter.Format(result, resultfilepath);
resultvalue = CompareBEDOutput(resultfilepath, expectedresultpath);
Assert.IsTrue(resultvalue);
resultvalue = ValidateParentSeqRange(result, refSeqRange, querySeqRange, true);
Assert.IsTrue(resultvalue);
expectedresultpath = Path.Combine(direc, "Result_Intersect_MinOverlap0_OverLappingBases.BED");
result = refSeqRange.Intersect(querySeqRange, 0, IntersectOutputType.OverlappingPiecesOfIntervals, true);
formatter.Format(result, resultfilepath);
resultvalue = CompareBEDOutput(resultfilepath, expectedresultpath);
Assert.IsTrue(resultvalue);
resultvalue = ValidateParentSeqRange(result, refSeqRange, querySeqRange, true);
Assert.IsTrue(resultvalue);
expectedresultpath = Path.Combine(direc, "Result_Intersect_MinOverlap0.BED");
result = refSeqRange.Intersect(querySeqRange, 0, IntersectOutputType.OverlappingIntervals, true);
formatter.Format(result, resultfilepath);
resultvalue = CompareBEDOutput(resultfilepath, expectedresultpath);
Assert.IsTrue(resultvalue);
resultvalue = ValidateParentSeqRange(result, refSeqRange, querySeqRange, true);
Assert.IsTrue(resultvalue);
File.Delete(resultfilepath);
}
public void MergeOperationTest()
{
string direc = Path.Combine ("TestUtils", "BED", "Merge");
string filepath = Path.Combine(direc, "Merge_single.BED");
string resultfilepath = "tmp_mergeresult.bed";
string expectedresultpath = Path.Combine(direc, "Result_Merge_Single_MinLength0.BED");
BedParser parser = new BedParser();
BedFormatter formatter = new BedFormatter();
SequenceRangeGrouping seqGrouping = null;
SequenceRangeGrouping result = null;
bool resultvalue = false;
resultfilepath = "tmp_mergeresult.bed";
expectedresultpath = Path.Combine(direc, "Result_Merge_Single_MinLength0.BED");
seqGrouping = parser.ParseRangeGrouping(filepath);
result = seqGrouping.MergeOverlaps();
formatter.Format(result, resultfilepath);
resultvalue = CompareBEDOutput(resultfilepath, expectedresultpath);
Assert.IsTrue(resultvalue);
resultvalue = ValidateParentSeqRange(result, seqGrouping, null, false);
Assert.IsTrue(resultvalue);
expectedresultpath = Path.Combine(direc, "Result_Merge_Single_MinLength0.BED");
result = seqGrouping.MergeOverlaps(0, true);
formatter.Format(result, resultfilepath);
resultvalue = CompareBEDOutput(resultfilepath, expectedresultpath);
Assert.IsTrue(resultvalue);
resultvalue = ValidateParentSeqRange(result, seqGrouping, null, true);
Assert.IsTrue(resultvalue);
expectedresultpath = Path.Combine(direc, "Result_Merge_Single_MinLength0.BED");
result = seqGrouping.MergeOverlaps(0, false);
formatter.Format(result, resultfilepath);
resultvalue = CompareBEDOutput(resultfilepath, expectedresultpath);
Assert.IsTrue(resultvalue);
resultvalue = ValidateParentSeqRange(result, seqGrouping, null, false);
Assert.IsTrue(resultvalue);
expectedresultpath = Path.Combine(direc, "Result_Merge_Single_MinLength0.BED");
result = seqGrouping.MergeOverlaps(0);
formatter.Format(result, resultfilepath);
resultvalue = CompareBEDOutput(resultfilepath, expectedresultpath);
Assert.IsTrue(resultvalue);
resultvalue = ValidateParentSeqRange(result, seqGrouping, null, false);
Assert.IsTrue(resultvalue);
expectedresultpath = Path.Combine(direc, "Result_Merge_Single_MinLength0.BED");
result = seqGrouping.MergeOverlaps(0, true);
formatter.Format(result, resultfilepath);
resultvalue = CompareBEDOutput(resultfilepath, expectedresultpath);
Assert.IsTrue(resultvalue);
resultvalue = ValidateParentSeqRange(result, seqGrouping, null, true);
Assert.IsTrue(resultvalue);
expectedresultpath = Path.Combine(direc, "Result_Merge_Single_MinLength0.BED");
result = seqGrouping.MergeOverlaps(0, false);
formatter.Format(result, resultfilepath);
resultvalue = CompareBEDOutput(resultfilepath, expectedresultpath);
Assert.IsTrue(resultvalue);
resultvalue = ValidateParentSeqRange(result, seqGrouping, null, false);
Assert.IsTrue(resultvalue);
expectedresultpath = Path.Combine(direc, "Result_Merge_Single_MinLength1.BED");
result = seqGrouping.MergeOverlaps(1);
formatter.Format(result, resultfilepath);
resultvalue = CompareBEDOutput(resultfilepath, expectedresultpath);
Assert.IsTrue(resultvalue);
resultvalue = ValidateParentSeqRange(result, seqGrouping, null, false);
Assert.IsTrue(resultvalue);
expectedresultpath = Path.Combine(direc, "Result_Merge_Single_MinLength-1.BED");
result = seqGrouping.MergeOverlaps(-1);
formatter.Format(result, resultfilepath);
resultvalue = CompareBEDOutput(resultfilepath, expectedresultpath);
Assert.IsTrue(resultvalue);
resultvalue = ValidateParentSeqRange(result, seqGrouping, null, false);
Assert.IsTrue(resultvalue);
expectedresultpath = Path.Combine(direc, "Result_Merge_Single_MinLength-3.BED");
result = seqGrouping.MergeOverlaps(-3);
formatter.Format(result, resultfilepath);
resultvalue = CompareBEDOutput(resultfilepath, expectedresultpath);
Assert.IsTrue(resultvalue);
resultvalue = ValidateParentSeqRange(result, seqGrouping, null, false);
Assert.IsTrue(resultvalue);
string firstFile = Path.Combine(direc, "Merge_twofiles_1.BED");
string secondFile = Path.Combine(direc, "Merge_twofiles_2.BED");
SequenceRangeGrouping refSeqRange = parser.ParseRangeGrouping(firstFile);
SequenceRangeGrouping querySeqRange = parser.ParseRangeGrouping(secondFile);
expectedresultpath = Path.Combine(direc, "Result_Merge_Two_MinLength0.BED");
result = refSeqRange.MergeOverlaps(querySeqRange);
formatter.Format(result, resultfilepath);
resultvalue = CompareBEDOutput(resultfilepath, expectedresultpath);
Assert.IsTrue(resultvalue);
resultvalue = ValidateParentSeqRange(result, refSeqRange, querySeqRange, false);
Assert.IsTrue(resultvalue);
result = refSeqRange.MergeOverlaps(querySeqRange, 0, false);
formatter.Format(result, resultfilepath);
resultvalue = CompareBEDOutput(resultfilepath, expectedresultpath);
Assert.IsTrue(resultvalue);
resultvalue = ValidateParentSeqRange(result, refSeqRange, querySeqRange, false);
Assert.IsTrue(resultvalue);
result = refSeqRange.MergeOverlaps(querySeqRange, 0, true);
formatter.Format(result, resultfilepath);
resultvalue = CompareBEDOutput(resultfilepath, expectedresultpath);
Assert.IsTrue(resultvalue);
resultvalue = ValidateParentSeqRange(result, refSeqRange, querySeqRange, true);
Assert.IsTrue(resultvalue);
result = refSeqRange.MergeOverlaps(querySeqRange, 0);
formatter.Format(result, resultfilepath);
resultvalue = CompareBEDOutput(resultfilepath, expectedresultpath);
Assert.IsTrue(resultvalue);
resultvalue = ValidateParentSeqRange(result, refSeqRange, querySeqRange, false);
Assert.IsTrue(resultvalue);
result = refSeqRange.MergeOverlaps(querySeqRange, 0, true);
formatter.Format(result, resultfilepath);
resultvalue = CompareBEDOutput(resultfilepath, expectedresultpath);
Assert.IsTrue(resultvalue);
resultvalue = ValidateParentSeqRange(result, refSeqRange, querySeqRange, true);
Assert.IsTrue(resultvalue);
result = refSeqRange.MergeOverlaps(querySeqRange, 0, false);
formatter.Format(result, resultfilepath);
resultvalue = CompareBEDOutput(resultfilepath, expectedresultpath);
Assert.IsTrue(resultvalue);
resultvalue = ValidateParentSeqRange(result, refSeqRange, querySeqRange, false);
Assert.IsTrue(resultvalue);
expectedresultpath = Path.Combine(direc, "Result_Merge_Two_MinLength1.BED");
result = refSeqRange.MergeOverlaps(querySeqRange, 1, true);
formatter.Format(result, resultfilepath);
resultvalue = CompareBEDOutput(resultfilepath, expectedresultpath);
Assert.IsTrue(resultvalue);
resultvalue = ValidateParentSeqRange(result, refSeqRange, querySeqRange, true);
Assert.IsTrue(resultvalue);
expectedresultpath = Path.Combine(direc, "Result_Merge_Two_MinLength-1.BED");
result = refSeqRange.MergeOverlaps(querySeqRange, -1, true);
formatter.Format(result, resultfilepath);
resultvalue = CompareBEDOutput(resultfilepath, expectedresultpath);
Assert.IsTrue(resultvalue);
resultvalue = ValidateParentSeqRange(result, refSeqRange, querySeqRange, true);
Assert.IsTrue(resultvalue);
expectedresultpath = Path.Combine(direc, "Result_Merge_Two_MinLength-3.BED");
result = refSeqRange.MergeOverlaps(querySeqRange, -3, true);
formatter.Format(result, resultfilepath);
resultvalue = CompareBEDOutput(resultfilepath, expectedresultpath);
Assert.IsTrue(resultvalue);
resultvalue = ValidateParentSeqRange(result, refSeqRange, querySeqRange, true);
Assert.IsTrue(resultvalue);
expectedresultpath = Path.Combine(direc, "Result_Merge_Two_MinLength2.BED");
result = refSeqRange.MergeOverlaps(querySeqRange, 2, true);
formatter.Format(result, resultfilepath);
resultvalue = CompareBEDOutput(resultfilepath, expectedresultpath);
Assert.IsTrue(resultvalue);
resultvalue = ValidateParentSeqRange(result, refSeqRange, querySeqRange, true);
Assert.IsTrue(resultvalue);
expectedresultpath = Path.Combine(direc, "Result_Merge_Two_MinLength6.BED");
result = refSeqRange.MergeOverlaps(querySeqRange, 6, true);
formatter.Format(result, resultfilepath);
resultvalue = CompareBEDOutput(resultfilepath, expectedresultpath);
Assert.IsTrue(resultvalue);
resultvalue = ValidateParentSeqRange(result, refSeqRange, querySeqRange, true);
Assert.IsTrue(resultvalue);
File.Delete(resultfilepath);
}
/// <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);
}