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;
}
