/// <summary>
/// Parsers the Bed file for different test cases based
/// on Additional parameter
/// </summary>
/// <param name="nodeName">Xml Node name</param>
/// <param name="addParam">Additional parameter</param>
private void ParserGeneralTestCases(string nodeName,
AdditionalParameters addParam)
{
// Gets the Filename
string filePath = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.FilePathNode);
Assert.IsFalse(string.IsNullOrEmpty(filePath));
ApplicationLog.WriteLine(string.Format(null,
"Bed Parser P1: Reading the File from location '{0}'", filePath));
// Get the rangelist after parsing.
var parserObj = new BedParser();
IList<ISequenceRange> rangeList = null;
SequenceRangeGrouping rangeGroup = null;
// Gets the Range list/Range Group based on the parameters.
switch (addParam)
{
case AdditionalParameters.RangeFileName:
rangeList = parserObj.ParseRange(filePath);
break;
case AdditionalParameters.RangeTextReader:
using (var strObj = File.OpenRead(filePath))
{
rangeList = parserObj.ParseRange(strObj);
}
break;
case AdditionalParameters.RangeGroupFileName:
rangeGroup = parserObj.ParseRangeGrouping(filePath);
break;
case AdditionalParameters.RangeGroupTextReader:
using (var strObj = File.OpenRead(filePath))
{
rangeGroup = parserObj.ParseRangeGrouping(strObj);
}
break;
default:
break;
}
// Gets the Range list from Group
switch (addParam)
{
case AdditionalParameters.RangeGroupTextReader:
case AdditionalParameters.RangeGroupFileName:
IEnumerable<string> grpIDsObj = rangeGroup.GroupIDs;
string rangeID = string.Empty;
foreach (string grpID in grpIDsObj)
{
rangeID = grpID;
}
rangeList = rangeGroup.GetGroup(rangeID);
break;
default:
break;
}
string[] expectedIDs = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.IDNode).Split(',');
string[] expectedStarts = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.StartNode).Split(',');
string[] expectedEnds = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.EndNode).Split(',');
int i = 0;
// Reads all the ranges with comma seperated for validation
foreach (ISequenceRange range in rangeList)
{
Assert.AreEqual(expectedStarts[i], range.Start.ToString((IFormatProvider) null));
Assert.AreEqual(expectedEnds[i], range.End.ToString((IFormatProvider) null));
Assert.AreEqual(expectedIDs[i], range.ID.ToString(null));
i++;
}
ApplicationLog.WriteLine(
"Bed Parser P1: Successfully validated the ID, Start and End Ranges");
}
/// <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);
}
//
// Read a Bed file into memory
//
public static SequenceRangeGrouping ReadBedFile(string filename)
{
var parser = new BedParser();
IList<ISequenceRange> listSequenceRange = parser.ParseRange(filename);
if (verbose)
{
//listSequenceRange.ToString();
Console.Error.WriteLine("Processed File: {0}", filename);
ListSequenceRangeToString(listSequenceRange);
}
var srg = new SequenceRangeGrouping(listSequenceRange);
if (arguments.normalizeInputs)
{
srg.MergeOverlaps(); // could be called Normalize() or Cannonicalize()
}
return srg;
}
