public static bool TryParse(string name, out ITCGATechnology value)
{
var lname = name.ToLower();
foreach (var tec in Technoligies)
{
if (tec.ToString().ToLower().Equals(lname))
{
value = tec;
return true;
}
}
value = null;
return false;
}
public static bool TryParse(string name, out ITCGATechnology value)
{
var lname = name.ToLower();
foreach (var tec in Technoligies)
{
if (tec.ToString().ToLower().Equals(lname))
{
value = tec;
return(true);
}
}
value = null;
return(false);
}
private Dictionary <string, Dictionary <string, double> > GetData(Dictionary <string, BarInfo> barMap,
out Func <double, double> getValue)
{
Func <string, string> getFilename;
IFileReader <ExpressionData> reader = null;
ITCGATechnology tec = _options.GetTechnology();
if (_options.IsCount && null != tec.GetCountReader())
{
reader = tec.GetCountReader();
getFilename = tec.GetCountFilename;
getValue = Math.Round;
}
else
{
reader = tec.GetReader();
getFilename = m => m;
getValue = m => m;
}
//tumor=>barcode=>gene=>value
var result = new Dictionary <string, Dictionary <string, double> >();
Progress.SetRange(0, barMap.Count);
long count = 0;
foreach (var bm in barMap)
{
var data = reader.ReadFromFile(getFilename(bm.Value.FileName));
var values = data.Values.ToDictionary(m => m.Name, m => m.Value);
result[bm.Key] = values;
count++;
Progress.SetPosition(count);
}
return(result);
}
public static Dictionary <string, BarInfo> GetBarcodeFileMap(string tcgaRootDir, ITCGATechnology tec, string tumor, IList <string> platforms, TCGASampleCode[] sampleTypes = null, Func <List <BarInfo>, BarInfo> barSelect = null, TCGAVialConflict vc = TCGAVialConflict.KeepLast)
{
Func <string, bool> acceptBarcode = null;
HashSet <int> sampleCodes = null;
if (sampleTypes != null)
{
sampleCodes = new HashSet <int>(sampleTypes.ToList().ConvertAll(m => m.Code));
acceptBarcode = m => sampleCodes.Contains(new BarInfo(m, null).Sample);
}
tumor = tumor.ToLower();
var dir = tcgaRootDir + "/" + tumor;
if (!Directory.Exists(dir))
{
return(new Dictionary <string, BarInfo>());
}
if (!Directory.Exists(tec.GetTechnologyDirectory(dir)))
{
return(new Dictionary <string, BarInfo>());
}
var dataset = tec.GetDataset(dir, platforms, null);
if (acceptBarcode != null)
{
var barcodes = dataset.GetBarCodes();
foreach (var barcode in barcodes)
{
if (!acceptBarcode(barcode))
{
dataset.BarInfoListMap.Remove(barcode);
}
}
}
if (barSelect == null)
{
barSelect = m =>
{
if (m.Count > 1 && m.Any(l => l.Platform.Equals(tec.DefaultPreferPlatform)))
{
return(m.First(l => l.Platform.Equals(tec.DefaultPreferPlatform)));
}
return(m.First());
};
}
//For data from different platforms, barSelect solves the conflict
var result = dataset.BarInfoListMap.Values.ToList().ConvertAll(m => barSelect(m));
if (vc == TCGAVialConflict.KeepAll)
{
return(result.ToDictionary(m => m.BarCode));
}
var lst = result.GroupBy(m => m.BarCode.Substring(0, 15)).ToList();
//For data from same sample but with different vials, keep the last one
if (vc == TCGAVialConflict.KeepLast)
{
return(lst.ConvertAll(n =>
{
if (n.Count() == 1)
{
return n.First();
}
return (from l in n select new { Item = l, Vial = l.BarCode.Last() }).OrderByDescending(l => l.Vial).First().Item;
}).ToDictionary(n => n.BarCode));
}
else
{
return(lst.ConvertAll(n =>
{
if (n.Count() == 1)
{
return n.First();
}
return (from l in n select new { Item = l, Vial = l.BarCode.Last() }).OrderByDescending(l => l.Vial).Last().Item;
}).ToDictionary(n => n.BarCode));
}
}
