public void TestWrite()
{
var file = "../../../data/1_17716_G.wsm";
var item = new PileupItemFile().ReadFromFile(file);
var filename = "../../../data/1_17716_G.wsm.tmp";
new PileupItemFile().WriteToFile(filename, item);
FileAssert.AreEqual(file, filename, "check file " + Path.GetFullPath(filename) + ", it should be identical to file " + Path.GetFullPath(file));
File.Delete(filename);
}
public void Test()
{
var item = new PileupItemFile().ReadFromFile("../../../data/1_17716_G.wsm");
Assert.AreEqual(8.20E-05, item.InitializeTable().CalculateTwoTailPValue(), 0.0000001);
var cloneItem = item.CloneByFilter(m => m.Score >= 20);
var res = cloneItem.InitializeTable();
Assert.AreEqual(0.000228, res.CalculateTwoTailPValue(), 0.000001);
Assert.AreEqual("G", res.SucceedName);
Assert.AreEqual("A", res.FailedName);
Assert.AreEqual("S1", res.Sample1.Name);
Assert.AreEqual("S2", res.Sample2.Name);
}
public void TestRead()
{
var file = "../../../data/1_17716_G.wsm";
var item = new PileupItemFile().ReadFromFile(file);
Assert.AreEqual("1", item.SequenceIdentifier);
Assert.AreEqual(17716, item.Position);
Assert.AreEqual('G', item.Nucleotide);
Assert.AreEqual(2, item.Samples.Count);
Assert.AreEqual(187, item.Samples[0].Count);
Assert.AreEqual(103, item.Samples[1].Count);
Assert.AreEqual("S1", item.Samples[0].SampleName);
Assert.AreEqual("G", item.Samples[0][0].Event);
Assert.AreEqual(20, item.Samples[0][0].Score);
Assert.AreEqual(StrandType.FORWARD, item.Samples[0][0].Strand);
Assert.AreEqual(PositionType.END, item.Samples[0][0].Position);
Assert.AreEqual("25", item.Samples[0][0].PositionInRead);
}
public MpileupFisherResult Parse(string line, bool writeCandidateFile = true)
{
MpileupFisherResult result = new MpileupFisherResult();
var item = _parser.GetValue(line);
item.Samples[0].SampleName = "NORMAL";
item.Samples[1].SampleName = "TUMOR";
var events = item.GetPairedEvent();
var fisherresult = item.InitializeTable(events);
result.Item = item;
result.Group = fisherresult;
if (!_rdFilter.Accept(item))
{
result.FailedReason = _rdFilter.RejectReason;
_result.MinimumReadDepthFailed++;
return result;
}
//If the bases from all samples are same, ignore the entry.
if (item.OnlyOneEvent())
{
result.FailedReason = "Only one allele detected";
_result.OneEventFailed++;
return result;
}
if (fisherresult.Sample1.FailedPercentage > fisherresult.Sample2.FailedPercentage)
{
result.FailedReason = "MAF decreased in tumor";
_result.MinorAlleleDecreasedFailed++;
return result;
}
if (!_normalTest.Accept(fisherresult))
{
result.FailedReason = _normalTest.RejectReason;
_result.MinorAlleleFailedInNormalSample++;
return result;
}
if (!_tumorTest.Accept(fisherresult))
{
result.FailedReason = _tumorTest.RejectReason;
_result.MinorAlleleFailedInTumorSample++;
return result;
}
//group fisher exact test
fisherresult.CalculateTwoTailPValue();
if (fisherresult.PValue > _options.FisherPvalue)
{
result.FailedReason = string.Format("Fisher pvalue > {0}", _options.FisherPvalue);
_result.GroupFisherFailed++;
return result;
}
if (writeCandidateFile)
{
//get major and second alleles
var bases = new HashSet<string>(new[] { events.MajorEvent, events.MinorEvent });
//save to file
var piFile = new PileupItemFile(bases);
result.CandidateFile = string.Format("{0}/{1}.wsm", _options.CandidatesDirectory, MpileupFisherResultFileFormat.GetString(result, '_', false));
piFile.WriteToFile(result.CandidateFile, item);
}
Progress.SetMessage("{0}\t{1}\t{2}", item.SequenceIdentifier, item.Position, fisherresult);
return result;
}
public MpileupFisherResult Parse(string line, bool writeCandidateFile = true)
{
MpileupFisherResult result = new MpileupFisherResult();
var item = _parser.GetValue(line);
item.Samples[0].SampleName = "NORMAL";
item.Samples[1].SampleName = "TUMOR";
var events = item.GetPairedEvent();
var fisherresult = item.InitializeTable(events);
result.Item = item;
result.Group = fisherresult;
if (!_rdFilter.Accept(item))
{
result.FailedReason = _rdFilter.RejectReason;
_result.MinimumReadDepthFailed++;
return(result);
}
//If the bases from all samples are same, ignore the entry.
if (item.OnlyOneEvent())
{
result.FailedReason = "Only one allele detected";
_result.OneEventFailed++;
return(result);
}
if (fisherresult.Sample1.FailedPercentage > fisherresult.Sample2.FailedPercentage)
{
result.FailedReason = "MAF decreased in tumor";
_result.MinorAlleleDecreasedFailed++;
return(result);
}
if (!_normalTest.Accept(fisherresult))
{
result.FailedReason = _normalTest.RejectReason;
_result.MinorAlleleFailedInNormalSample++;
return(result);
}
if (!_tumorTest.Accept(fisherresult))
{
result.FailedReason = _tumorTest.RejectReason;
_result.MinorAlleleFailedInTumorSample++;
return(result);
}
//group fisher exact test
fisherresult.CalculateTwoTailPValue();
if (fisherresult.PValue > _options.FisherPvalue)
{
result.FailedReason = string.Format("Fisher pvalue > {0}", _options.FisherPvalue);
_result.GroupFisherFailed++;
return(result);
}
if (writeCandidateFile)
{
//get major and second alleles
var bases = new HashSet <string>(new[] { events.MajorEvent, events.MinorEvent });
//save to file
var piFile = new PileupItemFile(bases);
result.CandidateFile = string.Format("{0}/{1}.wsm", _options.CandidatesDirectory, MpileupFisherResultFileFormat.GetString(result, '_', false));
piFile.WriteToFile(result.CandidateFile, item);
}
Progress.SetMessage("{0}\t{1}\t{2}", item.SequenceIdentifier, item.Position, fisherresult);
return(result);
}
public MpileupFisherResult Parse(string line, bool writeCandidateFile = true)
{
var parts = line.Split('\t');
if (bedMap.Count > 0)
{
var sp = _parser.GetSequenceIdentifierAndPosition(parts);
if (IsIgnored(sp.SequenceIdentifier, sp.Position))
{
_result.Ignored++;
return(null);
}
}
//for debug
//var sptemp = _parser.GetSequenceIdentifierAndPosition(parts);
//if (sptemp.SequenceIdentifier == "2" && sptemp.Position == 89161431)
//{
// var debugFile = string.Format("{0}/debug.txt", _options.CandidatesDirectory);
// File.WriteAllLines(debugFile, new[] { line });
// Console.WriteLine("Catched the line");
// System.Windows.Forms.Application.Exit();
//}
//didn't consider minimum score requirement
if (!_parser.HasEnoughReads(parts))
{
_result.MinimumReadDepthFailed++;
return(null);
}
//didn't consider minimum score requirement
if (!_parser.HasMinorAllele(parts))
{
_result.OneEventFailed++;
return(null);
}
//parsing full result considering score limitation
var item = _parser.GetValue(parts);
if (item == null)
{
_result.MinimumReadDepthFailed++;
return(null);
}
//If the bases from all samples are same, ignore the entry.
if (item.OnlyOneEvent())
{
_result.OneEventFailed++;
return(null);
}
item.Samples[0].SampleName = "NORMAL";
item.Samples[1].SampleName = "TUMOR";
var events = item.GetPairedEvent();
var fisherresult = item.InitializeTable(events);
if (fisherresult.Sample1.FailedPercentage > fisherresult.Sample2.FailedPercentage)
{
_result.MinorAlleleDecreasedFailed++;
return(null);
}
if (!_tumorTest.Accept(fisherresult))
{
_result.MinorAlleleFailedInTumorSample++;
return(null);
}
if (!_normalTest.Accept(fisherresult))
{
_result.MinorAlleleFailedInNormalSample++;
return(null);
}
//group fisher exact test
fisherresult.CalculateTwoTailPValue();
if (_options.UseZeroMinorAlleleStrategy && fisherresult.Sample1.Failed == 0)
{
//Console.WriteLine("UseZeroMinorAlleleStrategy : {0}", fisherresult);
if (fisherresult.PValue > _options.ZeroMinorAlleleStrategyFisherPvalue)
{
_result.GroupFisherFailed++;
return(null);
}
}
else if (fisherresult.PValue > _options.FisherPvalue)
{
_result.GroupFisherFailed++;
return(null);
}
//passed all criteria
_result.CandidateCount++;
var result = new MpileupFisherResult
{
Item = item,
Group = fisherresult,
};
//save to file
if (writeCandidateFile)
{
//get major and second alleles
var bases = new HashSet <string>(new[] { events.MajorEvent, events.MinorEvent });
var piFile = new PileupItemFile(bases);
result.CandidateFile = string.Format("{0}/{1}.wsm", _options.CandidatesDirectory, MpileupFisherResultFileFormat.GetString(result, '_', false));
piFile.WriteToFile(result.CandidateFile, item);
}
Progress.SetMessage("{0}\t{1}\t{2}", item.SequenceIdentifier, item.Position, fisherresult);
return(result);
}
