public ExpressionData ReadFromFile(string fileName) { ExpressionData result = reader.ReadFromFile(fileName); using (StreamReader sr = new StreamReader(fileName)) { string line = sr.ReadLine(); line = sr.ReadLine(); result.IsLog2Value = line.Contains("log2"); } return(result); }
public override IEnumerable <string> Process(string targetfile) { var dirs = Directory.GetDirectories(dataDir, "*.Level_3*"); Progress.SetMessage("Total {0} directories", dirs.Length); var reader = new ExpressionDataRawReader(2, 1, 2); var finder = TCGATechnology.Microarray.GetFinder(null, dataDir); var datas = new List <ExpressionData>(); int dircount = 0; foreach (var dir in dirs) { dircount++; Progress.SetMessage("{0}/{1} : {2}", dircount, dirs.Length, dir); var files = Directory.GetFiles(dir, "*level3.data.txt"); Progress.SetRange(1, files.Length); foreach (var file in files) { Progress.Increment(1); var data = reader.ReadFromFile(file); data.SampleBarcode = finder.FindParticipant(Path.GetFileName(file)); datas.Add(data); } } Progress.SetMessage("Sorting barcodes ..."); datas.SortBarcode(); Progress.SetMessage("Filling and sorting genes ..."); datas.FillAndSortGenes(); Progress.SetMessage("Saving result ..."); new ExpressionDataFastFormat <ExpressionData>().WriteToFile(targetfile, datas); Progress.SetMessage("Finished!"); return(new string[] { targetfile }); }
public override IEnumerable<string> Process(string targetfile) { var dirs = Directory.GetDirectories(dataDir, "*.Level_3*"); Progress.SetMessage("Total {0} directories", dirs.Length); var reader = new ExpressionDataRawReader(2, 1, 2); var finder = TCGATechnology.Microarray.GetFinder(null, dataDir); var datas = new List<ExpressionData>(); int dircount = 0; foreach (var dir in dirs) { dircount++; Progress.SetMessage("{0}/{1} : {2}", dircount, dirs.Length, dir); var files = Directory.GetFiles(dir, "*level3.data.txt"); Progress.SetRange(1, files.Length); foreach (var file in files) { Progress.Increment(1); var data = reader.ReadFromFile(file); data.SampleBarcode = finder.FindParticipant(Path.GetFileName(file)); datas.Add(data); } } Progress.SetMessage("Sorting barcodes ..."); datas.SortBarcode(); Progress.SetMessage("Filling and sorting genes ..."); datas.FillAndSortGenes(); Progress.SetMessage("Saving result ..."); new ExpressionDataFastFormat<ExpressionData>().WriteToFile(targetfile, datas); Progress.SetMessage("Finished!"); return new string[] { targetfile }; }