/// <summary>
/// Read the clinical patient file and store the data into directory. The key is tumor type plus bar code.
/// Also read the
/// </summary>
/// <param name="clinicalData"></param>
/// <param name="tumorType"></param>
/// <param name="queryHeaders"></param>
private void ReadClinData(IDictionary <string, IAnnotation> clinicalData, string tumorType,
ICollection <string> queryHeaders)
{
var clinfile = TCGAUtils.GetClinicPatientFile(_options.TCGADirectory, tumorType);
if (!File.Exists(clinfile))
{
return;
}
var data = new TCGAClinicalInformationFormat().ReadFromFile(clinfile);
foreach (var entry in data)
{
clinicalData[GetSampleKey(tumorType, entry.BarCode())] = entry;
}
var configheader = TemplateDirectory + "/" + Path.GetFileNameWithoutExtension(clinfile) + ".header.xml";
if (!File.Exists(configheader))
{
configheader = TemplateDirectory + "/clinical_patient_tcga.header.xml";
}
var fd = HeaderDefinition.LoadFromFile(configheader);
foreach (var line in fd.Properties)
{
if (!queryHeaders.Contains(line))
{
queryHeaders.Add(line);
}
}
}
/// <summary>
/// Read the clinical patient file and store the data into directory. The key is tumor type plus bar code.
/// Also read the
/// </summary>
/// <param name="clinicalData"></param>
/// <param name="tumorType"></param>
/// <param name="queryHeaders"></param>
private void ReadClinData(IDictionary<string, IAnnotation> clinicalData, string tumorType,
ICollection<string> queryHeaders)
{
var clinfile = TCGAUtils.GetClinicPatientFile(_options.TCGADirectory, tumorType);
if (!File.Exists(clinfile))
{
return;
}
var data = new TCGAClinicalInformationFormat().ReadFromFile(clinfile);
foreach (var entry in data)
{
clinicalData[GetSampleKey(tumorType, entry.BarCode())] = entry;
}
var configheader = TemplateDirectory + "/" + Path.GetFileNameWithoutExtension(clinfile) + ".header.xml";
if (!File.Exists(configheader))
{
configheader = TemplateDirectory + "/clinical_patient_tcga.header.xml";
}
var fd = HeaderDefinition.LoadFromFile(configheader);
foreach (var line in fd.Properties)
{
if (!queryHeaders.Contains(line))
{
queryHeaders.Add(line);
}
}
}
