private bool FindValue(Annotation a, ColumnName key, out string value)
{
if (nameKeyMap.ContainsKey(key))
{
HashSet<string> keys = nameKeyMap[key];
foreach (var ck in keys)
{
if (a.Annotations.ContainsKey(ck))
{
value = (a.Annotations[ck] as string).Trim();
return true;
}
}
}
value = StatusValue.NA;
return false;
}
public override IEnumerable<string> Process()
{
var format = new AnnotationFormat();
var items = format.ReadFromFile(_options.ClinicalFile);
format.Format.Headers = sampleBarcodeKey + "\t" + format.Format.Headers;
var itemMap = items.ToDictionary(m => m.BarCode());
using (StreamReader sr = new StreamReader(_options.DataFile))
{
var barcodes = sr.ReadLine().Split('\t').Where(m => m.StartsWith("TCGA")).ToList();
List<Annotation> found = new List<Annotation>();
foreach (var barcode in barcodes)
{
var patient = barcode.Substring(0, 12);
Annotation ann;
if (!itemMap.TryGetValue(patient, out ann))
{
if (_options.ThrowException)
{
throw new Exception("Cannot find patient information for " + patient);
}
Console.Error.WriteLine("Cannot find patient information for " + patient);
ann = new Annotation();
}
var curann = new Annotation();
curann.Annotations[sampleBarcodeKey] = barcode;
curann.Annotations[TCGAClinicalInformation.BcrPatientBarcode] = patient;
foreach (var e in ann.Annotations)
{
curann.Annotations[e.Key] = e.Value;
}
found.Add(curann);
}
format.WriteToFile(_options.OutputFile, found);
}
return new[] { _options.OutputFile };
}
private string FindValue(Annotation a, Dictionary<string, HashSet<string>> namekeys, string p)
{
var keys = namekeys[p];
foreach (var ann in a.Annotations)
{
if (keys.Contains(ann.Key))
{
return (ann.Value as string).Trim();
}
}
return "NA";
}
private string FindValue(Annotation a, ColumnName key)
{
string result;
FindValue(a, key, out result);
return result;
}
