public static Plink readPlinkS3(string bucketRegion,
string bucketName,
string keyFAM,
string keyBED,
string keyBIM = null,
string bucketRegionBIM = null,
string bucketNameBIM = null,
string keyBIMFile = null)
{
if (keyBIM == null)
{
using (var sr = new StreamReader(readStreamFromS3ToMemory(bucketRegion: bucketRegion,
bucketName: bucketName,
keyName: keyBIMFile).Result))
{
keyBIM = sr.ReadToEnd();
}
}
Console.WriteLine("KeyBIM: " + keyBIM);
if (bucketRegionBIM == null)
{
bucketRegionBIM = bucketRegion;
}
if (bucketNameBIM == null)
{
bucketNameBIM = bucketName;
}
return(Plink.readPlinkFromStream(sr_fam: new StreamReader(readStreamFromS3ToMemory(bucketRegion: bucketRegion,
bucketName: bucketName,
keyName: keyFAM).Result),
sr_bim: new StreamReader(readStreamFromS3ToMemory(bucketRegion: bucketRegionBIM,
bucketName: bucketNameBIM,
keyName: keyBIM).Result),
br_bed: new BinaryReader(readStreamFromS3ToMemory(bucketRegion: bucketRegion,
bucketName: bucketName,
keyName: keyBED).Result)));
}
public static CalcResult calcGenotype(string code,
string sn,
string tableRegion = null,
string tableName = null,
string bucketRegion = null,
string bucketName = null,
string bucketRegionBIM = null,
string bucketNameBIM = null,
Plink.Plink plink = null)
{
var preference = new Preference().preference;
JArray metas = new JArray();
string stage = String.Format("{0}-{1}-{2}", code, "genotype", "calculation");
ProgressWriter.writer(sn: sn, stage: stage, status: "start").Wait();
foreach (var meta in readDynamoTable(tableRegion: tableRegion ?? preference["Dynamo"]["MetaGenotype"]["Region"].ToString(),
tableName: tableName ?? preference["Dynamo"]["MetaGenotype"]["Name"].ToString(),
hashKey: code,
queryFilter: new QueryFilter()).Select(x => JObject.Parse(x.ToJson())))
{
metas.Add(meta);
}
List <string> snpnames = metas.Select(meta => meta["var"].ToString()).ToList();
plink = plink ?? readPlinkS3(bucketRegion: bucketRegion ?? preference["S3"]["Plink"]["Region"].ToString(),
bucketName: bucketName ?? preference["S3"]["Plink"]["Name"].ToString(),
keyFAM: sn + ".fam",
keyBED: sn + ".bed",
keyBIMFile: sn + "_bim.txt",
bucketRegionBIM: bucketRegionBIM ?? preference["S3"]["BPM"]["Region"].ToString(),
bucketNameBIM: bucketNameBIM ?? preference["S3"]["BPM"]["Name"].ToString());
var genotype = plink.checkRepeat(snpnames: snpnames).AsParallel().Select(x => x[0]).ToArray();
var alleles = plink.getAlleles(snpnames: snpnames);
float result = 0;
for (int metaIdx = 0; metaIdx < metas.Count; ++metaIdx)
{
var meta = metas[metaIdx];
if (genotype[metaIdx] != 0)
{
if (meta["meta"]["Eff"].ToString() == alleles[metaIdx][1])
{
result += (genotype[metaIdx] - 1) * Convert.ToSingle(meta["meta"]["beta"].ToString());
}
else if (meta["meta"]["Eff"].ToString() == alleles[metaIdx][0])
{
result += (3 - genotype[metaIdx]) * Convert.ToSingle(meta["meta"]["beta"].ToString());
}
}
}
metas = new JArray(metas.Where((meta, metaIdx) => genotype[metaIdx] != 0));
metas = new JArray(metas.Concat(metas));
ProgressWriter.writer(sn: sn, stage: stage, status: "end").Wait();
return(new CalcResult(result, metas));
}
