/// <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);
}
}
}
public override IEnumerable <string> Process()
{
var result = new List <string>();
Dictionary <string, BarInfo> barMap;
barMap = new Dictionary <string, BarInfo>();
foreach (var tumor in _options.TumorTypes)
{
var curMap = TCGAUtils.GetBarcodeFileMap(_options.TCGADirectory,
_options.GetTechnology(), tumor, _options.Platforms, _options.GetTCGASampleCodes().ToArray());
foreach (var v in curMap)
{
barMap[GetSampleKey(tumor, v.Key)] = v.Value;
}
}
var headers = new List <string>();
var clindata = new Dictionary <string, IAnnotation>();
foreach (var tumor in _options.TumorTypes)
{
ReadClinData(clindata, tumor, headers);
}
Console.WriteLine("{0} patient clinical information readed", clindata.Count);
List <string> noclinical = new List <string>();
var keyvalues = barMap.ToList();
foreach (var bm in keyvalues)
{
if (!clindata.ContainsKey(GetSampleKey(GetTumorType(bm.Key), bm.Value.Paticipant)))
{
noclinical.Add(bm.Key);
Console.Error.WriteLine(string.Format("Cannot find clinical data for patient {0}", bm.Value.Paticipant));
if (_options.WithClinicalInformationOnly)
{
barMap.Remove(bm.Key);
}
}
}
Progress.SetMessage("Reading data ...");
Func <double, double> getValue;
var valueMap = GetData(barMap, out getValue);
var genes = GetCommonGenes(valueMap);
var samples = valueMap.Keys.OrderBy(m => m).ToList();
Progress.SetMessage("Saving data ...");
result.Add(_options.OutputFile);
result.Add(_options.DesignFile);
if (_options.TumorTypes.Count > 1)
{
using (var sw = new StreamWriter(_options.OutputFile))
{
sw.WriteLine("Gene\t{0}", samples.Merge("\t"));
foreach (var gene in genes)
{
sw.Write(gene);
foreach (var sample in samples)
{
sw.Write("\t{0}", getValue(valueMap[sample][gene]));
}
sw.WriteLine();
}
}
using (var sw = new StreamWriter(_options.DesignFile))
{
sw.Write("Sample\tBarcode\tPatient\tTumorType\tPlatform\tSampleType\tSampleTypeDescription");
if (headers.Count > 0)
{
sw.WriteLine("\t{0}", headers.Merge("\t"));
}
else
{
sw.WriteLine();
}
foreach (var entry in barMap)
{
var tumor = GetTumorType(entry.Key);
var type = TCGASampleCode.Find(entry.Value.Sample);
sw.Write("{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}", entry.Key, entry.Value.BarCode, entry.Value.Paticipant, tumor, entry.Value.Platform, type.ShortLetterCode,
type.Definition);
var key = GetSampleKey(tumor, entry.Value.Paticipant);
var vdata = clindata.ContainsKey(key) ? clindata[key] : new Annotation();
foreach (var header in headers)
{
if (vdata.Annotations.ContainsKey(header))
{
sw.Write("\t{0}", vdata.Annotations[header]);
}
else
{
sw.Write("\t");
}
}
sw.WriteLine();
}
}
}
else
{
using (var sw = new StreamWriter(_options.OutputFile))
{
sw.WriteLine("Gene\t{0}", (from s in samples select s.StringAfter("_")).Merge("\t"));
foreach (var gene in genes)
{
sw.Write(gene);
foreach (var sample in samples)
{
sw.Write("\t{0}", getValue(valueMap[sample][gene]));
}
sw.WriteLine();
}
}
using (var sw = new StreamWriter(_options.DesignFile))
{
sw.Write("Sample\tBarcode\tPatient\tTumorType\tPlatform\tSampleType\tSampleTypeDescription");
if (headers.Count > 0)
{
sw.WriteLine("\t{0}", headers.Merge("\t"));
}
else
{
sw.WriteLine();
}
foreach (var entry in barMap)
{
var tumor = _options.TumorTypes.First();
var type = TCGASampleCode.Find(entry.Value.Sample);
sw.Write("{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}", entry.Key.StringAfter("_"), entry.Value.BarCode, entry.Value.Paticipant, tumor, entry.Value.Platform, type.ShortLetterCode,
type.Definition);
var key = GetSampleKey(tumor, entry.Value.Paticipant);
var vdata = clindata.ContainsKey(key) ? clindata[key] : new Annotation();
foreach (var header in headers)
{
if (vdata.Annotations.ContainsKey(header))
{
sw.Write("\t{0}", vdata.Annotations[header]);
}
else
{
sw.Write("\t");
}
}
sw.WriteLine();
}
}
var clinicalOptions = new TCGAClinicalInformationBuilderOptions()
{
ClinicalFile = TCGAUtils.GetClinicPatientFile(_options.TCGADirectory, _options.TumorTypes.First()),
DataFile = _options.OutputFile,
ThrowException = false,
};
result.AddRange(new TCGAClinicalInformationBuilder(clinicalOptions)
{
Progress = this.Progress
}.Process());
}
Progress.End();
if (noclinical.Count == 0)
{
return(result.ToArray());
}
else
{
return(new[] { string.Format("There are {0} samples without patient information:\n {1}\n\nResult have been saved to:\n {2}", noclinical.Count, noclinical.Merge("\n "), result.Merge("\n ")) });
}
}
