public static Dictionary<string, string> GetChipTypes(string rExecute, string directory, bool includingSubDirectory, string outputFile)
{
var cels = GetCelFiles(directory);
foreach (var dir in Directory.GetDirectories(directory))
{
cels.AddRange(GetCelFiles(dir));
}
if (cels.Count == 0)
{
return new Dictionary<string, string>();
}
var inputfile = Path.Combine(directory, "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 = outputFile;
roptions.RTemplate = FileUtils.GetTemplateDir() + "/getceltypes.r";
new RTemplateProcessor(roptions).Process();
return new MapReader(0, 1).ReadFromFile(roptions.OutputFile);
}
/// <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;
}
