public void TestReadFromFileWithoutFilter() { var data = new MpileupFisherResultFileFormat().ReadFromFile(@"../../../data/TCGA-BH-A0E0-DNA-TP-NB.candidates"); Assert.AreEqual(850, data.Count); var res = data[0]; Assert.AreEqual("1", res.Item.SequenceIdentifier); Assert.AreEqual(5732744, res.Item.Position); Assert.AreEqual('G', res.Item.Nucleotide); Assert.AreEqual("G", res.Group.SucceedName); Assert.AreEqual("T", res.Group.FailedName); Assert.AreEqual(44, res.Group.Sample1.Succeed); Assert.AreEqual(1, res.Group.Sample1.Failed); Assert.AreEqual(11, res.Group.Sample2.Succeed); Assert.AreEqual(3, res.Group.Sample2.Failed); Assert.AreEqual(3.8E-02, res.Group.PValue, 0.01); }
public void TestReadFromFileWithFilter() { var data = new MpileupFisherResultFileFormat().ReadFromFile(@"../../../data/glmvc.candidates"); Assert.AreEqual(24, data.Count); var res = data[3]; Assert.AreEqual("2", res.Item.SequenceIdentifier); Assert.AreEqual(110301779, res.Item.Position); Assert.AreEqual('A', res.Item.Nucleotide); Assert.AreEqual("A", res.Group.SucceedName); Assert.AreEqual("", res.Group.FailedName); Assert.AreEqual(23, res.Group.Sample1.Succeed); Assert.AreEqual(0, res.Group.Sample1.Failed); Assert.AreEqual(9, res.Group.Sample2.Succeed); Assert.AreEqual(0, res.Group.Sample2.Failed); Assert.AreEqual(1.0E00, res.Group.PValue, 0.01); Assert.AreEqual("Read depth < 10", res.FailedReason); }
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" }; }