protected override IProcessor GetProcessor() { TCGADatatableBuilderOptions options = new TCGADatatableBuilderOptions(); options.DataType = lbDataTypes.SelectedItem as string; options.TCGADirectory = rootDir.FullName; options.TumorTypes = GetSelectedTumors(); options.Platforms = GetSelectedPlatforms(); options.OutputFile = targetFile.FullName; options.IsCount = cbCount.Checked; options.TCGASampleCodeStrings = GetSampleCodes(); options.WithClinicalInformationOnly = cbClinicalOnly.Checked; return(new TCGADatatableBuilder(options)); }
protected override IProcessor GetProcessor() { TCGADatatableBuilderOptions options = new TCGADatatableBuilderOptions(); options.DataType = lbDataTypes.SelectedItem as string; options.TCGADirectory = rootDir.FullName; options.TumorTypes = GetSelectedTumors(); options.Platforms = GetSelectedPlatforms(); options.OutputFile = targetFile.FullName; options.IsCount = cbCount.Checked; options.TCGASampleCodeStrings = GetSampleCodes(); options.WithClinicalInformationOnly = cbClinicalOnly.Checked; return new TCGADatatableBuilder(options); }
public static void ExtractData(string tcgaDir, string targetDir, string prefix, string[] tumors, string datatype, string[] platforms, TCGASampleCode[] sampleCodes = null, bool outputCountDataOnly = false) { var tec = TCGATechnology.Parse(datatype); var platforms_str = (from p in platforms select p.StringBefore("_")).Merge("_"); var counts = outputCountDataOnly ? new[] { true } : new[] { true, false }; foreach (var count in counts) { string resultFile; if (tec.HasCountData) { resultFile = string.Format(@"{0}\{1}_{2}_{3}_{4}.tsv", targetDir, prefix, datatype, platforms_str, count ? "Count" : tec.ValueName); } else { resultFile = string.Format(@"{0}\{1}_{2}_{3}.tsv", targetDir, prefix, datatype, platforms_str); } var options = new TCGADatatableBuilderOptions(); options.DataType = datatype; options.TCGADirectory = tcgaDir; options.TumorTypes = tumors.ToList(); options.Platforms = platforms; options.IsCount = count; options.OutputFile = resultFile; options.TCGASampleCodeStrings = sampleCodes == null ? new List <string>() : sampleCodes.ToList().ConvertAll(m => m.ShortLetterCode).ToList(); options.WithClinicalInformationOnly = true; if (!options.PrepareOptions()) { throw new Exception("Error:\n" + options.ParsingErrors.Merge("\n")); } new TCGADatatableBuilder(options).Process(); if (!tec.HasCountData) { break; } } }
public TCGADatatableBuilder(TCGADatatableBuilderOptions options) { _options = options; _options.PrepareOptions(); this.TemplateDirectory = FileUtils.GetTemplateDir(); }
public MutationDatatableBuilder(TCGADatatableBuilderOptions options) { this._options = options; }
public TCGADatatableBuilder(TCGADatatableBuilderOptions options) { _options = options; _options.PrepareOptions(); this.TemplateDirectory = FileUtils.GetTemplateDir(); }
public MutationDatatableBuilder(TCGADatatableBuilderOptions options) { this._options = options; }