//
// 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);
}
/// <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>
/// 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).TestDir();
Assert.IsFalse(string.IsNullOrEmpty(filePath));
ApplicationLog.WriteLine($"Bed Parser BVT: Reading the File from location '{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;
}
// Gets all the expected values from xml.
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 BVT: Successfully validated the ID, Start and End Ranges");
}
/// <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>
static void ParserGeneralTestCases(string nodeName,
AdditionalParameters addParam)
{
// Gets the Filename
string filePath = Utility._xmlUtil.GetTextValue(
nodeName, Constants.FilePathNode);
Assert.IsNotEmpty(filePath);
ApplicationLog.WriteLine(string.Format(
"Bed Parser BVT: Reading the File from location '{0}'", filePath));
// Get the rangelist after parsing.
BedParser 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:
rangeList = parserObj.ParseRange(new StreamReader(filePath));
break;
case AdditionalParameters.RangeGroupFileName:
rangeGroup = parserObj.ParseRangeGrouping(filePath);
break;
case AdditionalParameters.RangeGroupTextReader:
rangeGroup = parserObj.ParseRangeGrouping(
new StreamReader(filePath));
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;
}
// Gets all the expected values from xml.
string expectedIDs = Utility._xmlUtil.GetTextValue(
nodeName, Constants.IDNode);
string expectedStarts = Utility._xmlUtil.GetTextValue(
nodeName, Constants.StartNode);
string expectedEnds = Utility._xmlUtil.GetTextValue(
nodeName, Constants.EndNode);
string actualStarts = string.Empty;
string actualEnds = string.Empty;
string actualIDs = string.Empty;
// Reads all the ranges with comma seperated for validation
foreach (ISequenceRange range in rangeList)
{
actualStarts = string.Concat(
actualStarts, range.Start.ToString(), ",");
actualEnds = string.Concat(
actualEnds, range.End.ToString(), ",");
actualIDs = string.Concat(
actualIDs, range.ID.ToString(), ",");
}
Assert.AreEqual(expectedIDs,
actualIDs.Substring(0, actualIDs.Length - 1));
Assert.AreEqual(expectedStarts,
actualStarts.Substring(0, actualStarts.Length - 1));
Assert.AreEqual(expectedEnds,
actualEnds.Substring(0, actualEnds.Length - 1));
ApplicationLog.WriteLine(
"Bed Parser BVT: Successfully validated the ID, Start and End Ranges");
Console.WriteLine(
"Bed Parser BVT: 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>
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);
}
}