private static string FormatSampleGenotype(SnpResult snp, List<string> alleles, string reference)
{
string[] variants = snp.Genotype.ToArray().Select(x => x.ToString()).ToArray();
List<string> map = new List<string>();
foreach (var variant in variants)
{
if (snp.RSID == "rs397515963")
{
if (variant == "-")
{
map.Add("0");
}
else
{
map.Add("1");
}
}
else
{
if (variant == reference)
{
map.Add("0");
}
else
{
map.Add((alleles.IndexOf(variant) + 1).ToString());
}
}
}
return string.Join("|", map);
}
public override void LoadData(string filePath)
{
string[] data = File.ReadAllLines(filePath);
foreach (var dataLine in data.Skip(1))
{
var patientRepo = new PatientRepository();
var sourceRepo = new SourceRepository();
var entityRepo = new EntityRepository();
var fields = dataLine.Split(Delimiter);
var patient = patientRepo.AddPatient(fields[0], fields[1], fields[2], fields[3], DateTime.Parse(fields[4]));
var resultedOn = DateTime.Parse(fields[5]);
var lab = fields[6];
var snps = new List<SnpResult>();
for (int fieldIndex = 7; fieldIndex < 135; fieldIndex += 4)
{
var snp = new SnpResult()
{
RSID = fields[fieldIndex],
Chromosome = fields[fieldIndex + 1],
Position = int.Parse(fields[fieldIndex + 2]),
Genotype = fields[fieldIndex + 3],
ReferenceBase = referenceBases[fields[fieldIndex]]
};
snps.Add(snp);
}
var source = sourceRepo.AddSource(lab, string.Empty);
var file = AddResultFile(filePath, source);
entityRepo.AddSnps(file, patient, resultedOn, snps);
}
}
static string GetVariant(SnpResult snp)
{
char[] variant = snp.Genotype.ToCharArray();
if (variant[0] != variant[1])
{
return string.Format("Variant_seq={0},{1};Variant_reads=10,10;Genotype=heterozygous", variant[0], variant[1]);
}
else
{
return string.Format("Variant_seq={0};Variant_reads=10;Genotype=homozygous", variant[0]);
}
}
static void Main(string[] args)
{
// Read in our list of patients and their corresponding randomization variables
var data = File.ReadAllLines(ConfigurationManager.AppSettings["GVFList"]);
foreach (var dataLine in data.Skip(1))
{
var fields = dataLine.Split(Delimiter);
var dataRow = new DataRow()
{
MRN = fields[0],
MRNSource = fields[1],
FirstName = fields[2],
LastName = fields[3],
DOB = DateTime.Parse(fields[4]),
ResultedOn = DateTime.Parse(fields[5]),
Lab = fields[6],
SNPs = new List<SnpResult>()
};
for (int fieldIndex = 7; fieldIndex < 135; fieldIndex += 4)
{
var snp = new SnpResult()
{
RSID = fields[fieldIndex],
Chromosome = fields[fieldIndex + 1],
Position = int.Parse(fields[fieldIndex + 2]),
Genotype = fields[fieldIndex + 3]
};
dataRow.SNPs.Add(snp);
}
GenerateGVF(dataRow);
}
}
static List<string> GetVariants(SnpResult snp, string reference)
{
string[] variants = snp.Genotype.ToArray().Select(x => x.ToString()).ToArray();
List<string> results = new List<string>();
foreach (var variant in variants)
{
// Special handling for the insertion SNP
if (snp.RSID == "rs397515963")
{
if (variant != "-" && !results.Contains("GG"))
{
results.Add("GG");
}
}
else if (variant != reference && !results.Contains(variant))
{
results.Add(variant);
}
}
return results;
}
