public void TestReadFromFile()
{
var items = new FilterItemTextFormat().ReadFromFile("../../../data/TCGA-A7-A0D9-DNA-TP-NB.tsv");
Assert.AreEqual(117, items.Count);
Assert.AreEqual("1", items[0].Chr);
Assert.AreEqual("37568524", items[0].Start);
Assert.AreEqual("37568524", items[0].End);
Assert.AreEqual("A", items[0].MajorAllele);
Assert.AreEqual("G", items[0].MinorAllele);
Assert.AreEqual("a", items[0].ReferenceAllele);
Assert.AreEqual(14, items[0].NormalMajorCount);
Assert.AreEqual(0, items[0].NormalMinorCount);
Assert.AreEqual(7, items[0].TumorMajorCount);
Assert.AreEqual(5, items[0].TumorMinorCount);
Assert.AreEqual(0.0120401337792642, items[0].FisherGroup);
Assert.AreEqual("1", items[0].FisherNormal);
Assert.AreEqual("TRUE", items[0].BrglmConverged);
Assert.AreEqual(0.0559533239203086, items[0].BrglmGroup);
Assert.AreEqual("", items[0].BrglmScore);
Assert.AreEqual("", items[0].BrglmStrand);
Assert.AreEqual("", items[0].BrglmPosition);
Assert.AreEqual(0.0891174471997679, items[0].BrglmGroupFdr);
Assert.AreEqual("GLM_FDR", items[0].Filter);
Assert.AreEqual("1_37568524_a_A_G_14_0_7_5_1.2E-02", items[0].Identity);
}
public void TestWriteToFile()
{
var items = new FilterItemTextFormat().ReadFromFile("../../../data/TCGA-A7-A0D9-DNA-TP-NB.tsv");
var writer = new FilterItemVcfWriter(new FilterProcessorOptions()
{
GlmPvalue = 0.01
});
var value = writer.GetValue(items[0]);
Assert.AreEqual("1\t37568524\t.\tA\tG\t1.05\tGLM_FDR\tBGP=5.6E-2;BGF=8.9E-2;BC=TRUE\tGT:AD:FA\t0/0:14,0:0\t0/1:7,5:0.417", value);
}
public override IEnumerable<string> Process()
{
Progress.SetMessage("filter process started at {0}", DateTime.Now);
var watch = new Stopwatch();
watch.Start();
var tsvfile = _options.OutputFile + ".rtsv";
var roptions = new RProcessorOptions()
{
RExecute = _options.GetRCommand(),
RFile = _options.TargetRFile,
ExpectResultFile = _options.ROutputFile
};
new RProcessor(roptions).Process();
if (!File.Exists(_options.ROutputFile))
{
throw new Exception(string.Format("R command failed, look at the file {0}!\nMake sure that your R and R packages brglm, stringr have been installed.", roptions.RFile + ".log"));
}
else if (!_options.IsValidation)
{
var items = new FilterItemTextFormat().ReadFromFile(_options.ROutputFile);
var unfilteredfile = Path.ChangeExtension(_options.ROutputFile, ".vcf");
new FilterItemVcfWriter(_options).WriteToFile(unfilteredfile, items);
items.RemoveAll(m => !m.Filter.Equals("PASS"));
var vcfFile = Path.ChangeExtension(_options.OutputFile, ".vcf");
new FilterItemVcfWriter(_options).WriteToFile(vcfFile, items);
new FilterItemTextFormat().WriteToFile(_options.OutputFile, items);
}
watch.Stop();
Progress.SetMessage("filter process ended at {0}, cost {1}", DateTime.Now, watch.Elapsed);
return new[] { _options.OutputFile };
}
public override IEnumerable<string> Process()
{
if (!File.Exists(_options.BaseFilename) || new FileInfo(_options.BaseFilename).Length == 0)
{
base.Process();
}
else
{
Progress.SetMessage("Base file {0} exists, ignore pileup ...", _options.BaseFilename);
}
var filterOptions = options.GetFilterOptions();
if (new FileInfo(_options.BaseFilename).Length > 0)
{
if (!filterOptions.PrepareOptions())
{
throw new Exception("Filter options failed: " + filterOptions.ParsingErrors.Merge("\n"));
}
new FilterProcessor(filterOptions).Process();
var lines = File.ReadAllLines(filterOptions.ROutputFile).Skip(1).ToArray();
var glmfailed = lines.Count(m => m.Contains("GLM_PVALUE"));
var summarylines = File.ReadAllLines(_options.SummaryFilename).ToList();
if (summarylines.Last().StartsWith("glm pvalue"))
{
summarylines.RemoveAt(summarylines.Count - 1);
}
summarylines.Add(string.Format("glm pvalue > {0}\t{1}\t{2}", options.GlmPvalue, glmfailed, lines.Length - glmfailed));
File.WriteAllLines(_options.SummaryFilename, summarylines);
}
var mutationList = GetValidationList();
var candidates = new MpileupFisherResultFileFormat().ReadFromFile(options.CandidatesFilename).ToDictionary(m => GenomeUtils.GetKey(m.Item.SequenceIdentifier, m.Item.Position));
var items = new FilterItemTextFormat().ReadFromFile(filterOptions.ROutputFile).ToDictionary(m => GenomeUtils.GetKey(m.Chr, m.Start));
var result = new List<FilterItem>();
foreach (var mutation in mutationList.Items)
{
var key = GenomeUtils.GetKey(mutation.Chr, mutation.Pos);
if (items.ContainsKey(key))
{
result.Add(items[key]);
}
else
{
var item = new FilterItem();
item.Chr = mutation.Chr;
item.Start = mutation.Pos;
item.End = item.Start;
item.FisherNormal = string.Empty;
item.BrglmConverged = string.Empty;
item.BrglmGroup = 1.0;
item.BrglmGroupFdr = 1.0;
item.BrglmScore = string.Empty;
item.BrglmStrand = string.Empty;
item.BrglmPosition = string.Empty;
item.Identity = string.Empty;
result.Add(item);
if (candidates.ContainsKey(key))
{
var cand = candidates[key];
item.ReferenceAllele = cand.Item.Nucleotide.ToString();
item.MajorAllele = cand.Group.SucceedName;
item.MinorAllele = cand.Group.FailedName;
item.NormalMajorCount = cand.Group.Sample1.Succeed;
item.NormalMinorCount = cand.Group.Sample1.Failed;
item.TumorMajorCount = cand.Group.Sample2.Succeed;
item.TumorMinorCount = cand.Group.Sample2.Failed;
item.FisherGroup = cand.Group.PValue;
item.Filter = cand.FailedReason;
Console.WriteLine("In candidates : " + item.Filter);
}
else
{
item.NormalMajorCount = 0;
item.NormalMinorCount = 0;
item.TumorMajorCount = 0;
item.TumorMinorCount = 0;
item.Filter = "No coverage";
Console.WriteLine("No read : " + item.Filter);
}
}
}
new FilterItemVcfWriter(filterOptions).WriteToFile(_options.OutputSuffix + ".vcf", result);
new FilterItemTextFormat().WriteToFile(_options.OutputSuffix + ".tsv", result);
return new string[] { _options.OutputSuffix + ".tsv", _options.OutputSuffix + ".vcf" };
}
