/// <summary>
/// Build cel count and chip type summary file
/// </summary>
public void BuildChipTypeTable(string tableFileName, string summaryFileName)
{
if (!FileUtils.IsAbsolutePath(tableFileName))
{
tableFileName = Path.Combine(DataDir, tableFileName);
}
if (!FileUtils.IsAbsolutePath(summaryFileName))
{
summaryFileName = Path.Combine(DataDir, summaryFileName);
}
var dic = CelFile.GetChipTypes(this.rExecute, DataDir, true, tableFileName);
using (StreamWriter sw = new StreamWriter(summaryFileName))
{
sw.WriteLine("Dataset\tChiptype\tSample");
var dsMap = dic.ToGroupDictionary(m => Path.GetFileName(Path.GetDirectoryName(m.Key)));
var subdirs = GetDatasetDirectories();
foreach (var subdir in subdirs)
{
var dsName = Path.GetFileName(subdir);
if (dsMap.ContainsKey(dsName))
{
var grp = dsMap[dsName].GroupBy(m => m.Value);
var bFirst = true;
foreach (var g in grp)
{
var name = bFirst ? new DirectoryInfo(subdir).Name : string.Empty;
bFirst = false;
sw.WriteLine("{0}\t{1}\t{2}", name, g.Key, g.Count());
}
}
}
}
}
/// <summary>
/// Normalization cel files and return the file contains all cel file names
/// </summary>
/// <param name="root"></param>
/// <param name="outputFile"></param>
/// <returns></returns>
public string Normalization(string root, string outputFile)
{
var cels = CelFile.GetCelFiles(root);
if (cels.Count == 0)
{
Progress.SetMessage("No cel file found in directory " + DataDir);
return(string.Empty);
}
var inputFile = Path.Combine(root, "celfiles.tsv");
using (var sw = new StreamWriter(inputFile))
{
foreach (var cel in cels)
{
sw.WriteLine(FileUtils.ToLinuxFormat(cel));
}
}
var roptions = new RTemplateProcessorOptions();
roptions.RExecute = rExecute;
roptions.InputFile = inputFile;
roptions.OutputFile = inputFile;
roptions.NoResultFile = true;
roptions.RTemplate = FileUtils.GetTemplateDir() + "\\frma.r";
roptions.CreateNoWindow = true;
new RTemplateProcessor(roptions)
{
Progress = this.Progress
}.Process();
CelFile.GetChipTypes(this.rExecute, root, true, outputFile);
return(outputFile);
}