public static List <SNPItem> ReadFromFile(string fileName)
{
var result = new List <SNPItem>();
using (var sr = new StreamReader(fileName))
{
var line = sr.ReadLine();
var hasFlip = line.Contains("_AlleleNeedFlip");
var platforms = line.Split('\t').ToList().ConvertAll(m => m.StringBefore("_Allele"));
var step = hasFlip ? 3 : 2;
while ((line = sr.ReadLine()) != null)
{
var parts = line.Split('\t');
//sw.WriteLine("Dbsnp_ID\tCHROM\tPOS\tDbsnp_RefAllele\tDbsnp_AltAllele\tDbsnp_IsReversed\t1000G_REF\t1000G_ALT\t1000G_MAF\tDataset\t{0}",
var item = new SNPItem()
{
Name = parts[0],
Chrom = int.Parse(parts[1]),
Position = int.Parse(parts[2]),
Allele1 = parts[3][0],
Allele2 = parts[4],
DbsnpIsReversed = bool.Parse(parts[5]),
G1000Allele1 = parts[6][0],
G1000Allele2 = parts[7][0],
G1000Allele2Frequency = double.Parse(parts[8]),
Dataset = parts[9]
};
for (int i = 10; i < parts.Length; i += step)
{
if (string.IsNullOrEmpty(parts[i]))
{
continue;
}
var alleles = parts[i].Split(':');
var aitem = new Alleles()
{
Allele1 = alleles[0],
Allele2 = alleles[1]
};
aitem.Allele2Frequency = double.Parse(parts[i + 1]);
if (hasFlip)
{
aitem.NeedFlip = bool.Parse(parts[i + 2]);
}
item.Platforms[platforms[i]] = aitem;
}
result.Add(item);
}
}
return(result);
}
public static List<SNPItem> ReadFromFile(string fileName)
{
var result = new List<SNPItem>();
using (var sr = new StreamReader(fileName))
{
var line = sr.ReadLine();
var hasFlip = line.Contains("_AlleleNeedFlip");
var platforms = line.Split('\t').ToList().ConvertAll(m => m.StringBefore("_Allele"));
var step = hasFlip ? 3 : 2;
while ((line = sr.ReadLine()) != null)
{
var parts = line.Split('\t');
//sw.WriteLine("Dbsnp_ID\tCHROM\tPOS\tDbsnp_RefAllele\tDbsnp_AltAllele\tDbsnp_IsReversed\t1000G_REF\t1000G_ALT\t1000G_MAF\tDataset\t{0}",
var item = new SNPItem()
{
Name = parts[0],
Chrom = int.Parse(parts[1]),
Position = int.Parse(parts[2]),
Allele1 = parts[3][0],
Allele2 = parts[4],
DbsnpIsReversed = bool.Parse(parts[5]),
G1000Allele1 = parts[6][0],
G1000Allele2 = parts[7][0],
G1000Allele2Frequency = double.Parse(parts[8]),
Dataset = parts[9]
};
for (int i = 10; i < parts.Length; i += step)
{
if (string.IsNullOrEmpty(parts[i]))
{
continue;
}
var alleles = parts[i].Split(':');
var aitem = new Alleles()
{
Allele1 = alleles[0],
Allele2 = alleles[1]
};
aitem.Allele2Frequency = double.Parse(parts[i + 1]);
if (hasFlip)
{
aitem.NeedFlip = bool.Parse(parts[i + 2]);
}
item.Platforms[platforms[i]] = aitem;
}
result.Add(item);
}
}
return result;
}
