/// <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);
                }
            }
        }
Example #2
0
    /// <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);
        }
      }
    }