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 };
}
public Level3MicroarrayDataTxtReader()
{
this.reader = new ExpressionDataRawReader(2, 1, 2);
}
