/// <summary>
/// Fill reference allele from genome fasta file.
/// </summary>
/// <param name="snpItems"></param>
/// <param name="fastaFile"></param>
/// <param name="progress"></param>
public static void FillReferenceAlleleFromFasta(this IEnumerable<SNPItem> snpItems, string fastaFile, IProgressCallback progress = null)
{
if (progress == null)
{
progress = new ConsoleProgressCallback();
}
var dic = snpItems.ToGroupDictionary(m => m.Chrom);
progress.SetMessage("Filling reference allele from {0} file ...", fastaFile);
using (var sw = new StreamReader(fastaFile))
{
var ff = new FastaFormat();
Sequence seq;
while ((seq = ff.ReadSequence(sw)) != null)
{
progress.SetMessage("chromosome " + seq.Name + " ...");
var chr = HumanChromosomeToInt(seq.Name);
if (dic.ContainsKey(chr))
{
var snps = dic[chr];
foreach (var snp in snps)
{
snp.RefChar = char.ToUpper(seq.SeqString[snp.Position - 1]);
}
}
}
}
progress.SetMessage("Filling reference allele finished.");
}
private static void DoFillAllele2FrequencyFrom1000Gome(this IEnumerable<SNPItem> snpItems, string g1000VcfFile, Func<SNPItem, string> keyFunc, IProgressCallback progress = null)
{
if (progress == null)
{
progress = new ConsoleProgressCallback();
}
var dic = snpItems.ToDictionary(m => keyFunc(m));
progress.SetMessage("Filling MAF from {0} ...", g1000VcfFile);
using (var sr = new StreamReader(g1000VcfFile))
{
progress.SetRange(0, sr.BaseStream.Length);
string line;
while ((line = sr.ReadLine()) != null)
{
if (!line.StartsWith("##"))
{
break;
}
}
int linecount = 0;
while ((line = sr.ReadLine()) != null)
{
linecount++;
if (linecount % 10000 == 0)
{
progress.SetPosition(sr.GetCharpos());
}
var parts = line.Split('\t');
var snp = new SNPItem()
{
Chrom = HumanChromosomeToInt(parts[0]),
Position = int.Parse(parts[1]),
Name = parts[2]
};
SNPItem loc;
if (!dic.TryGetValue(keyFunc(snp), out loc))
{
continue;
}
loc.G1000Allele1 = parts[3][0];
var allele2 = parts[4].Split(',');
var frequencies = parts[7].StringAfter("AF=").StringBefore(";").Split(',');
bool bFound = false;
for (int i = 0; i < allele2.Length; i++)
{
if (allele2[i].Length != 1)
{
continue;
}
loc.G1000Allele2 = allele2[i][0];
if (loc.IsSourceAllelesMatchedWithG1000())
{
loc.G1000Allele2Frequency = double.Parse(frequencies[i]);
bFound = true;
break;
}
}
if (!bFound)
{
loc.G1000Allele1 = ' ';
loc.G1000Allele2 = ' ';
loc.G1000Allele2Frequency = 0.0;
}
}
}
progress.SetMessage("Filling MAF finished.");
}
