// Aa変異をvcf形式で取得する
public static (string vcfString, IEnumerable <VcfAnnotation> aaVariableList) GetAaVariation(IDictionary <string, string> fastaWithAnnotations, ref string message)
{
// var message = string.Empty;
// vcf annotation strings, top3 consensus fasta....
var resAaVcfList = new List <string>();
var aaChangesList = new List <VcfAnnotation>();
foreach (var seqName2annotNuc in fastaWithAnnotations)
{
// mapping reference name. -> Genbank Sequence
var referenceProperty = GetReferenceProperties(seqName2annotNuc.Key, ref message);
if (referenceProperty == null)
{
message += "error, ncbi genbank infomations is not found.";
resAaVcfList.Add(string.Empty); // Top1 取れなかった。エラーはmessageに格納
continue;
}
// amino properties
var aaChangeVcf = new List <string>();
foreach (var aminoProp in referenceProperty.aminoProps)
{
var aaChanges = GetAmminoChanges(
aminoProp.AAseq,
seqName2annotNuc.Value,
aminoProp.SubLocations,
ref message);
if (!aaChanges.Any())
{
continue; // 対象のgene/CDS で変異が無い。
}
aaChanges.ForEach(a => a.referenceName = aminoProp.Name);
// DB格納文字列
aaChangeVcf.Add(aminoProp.Name + "[" +
string.Join(",", aaChanges.Select(s => s.GetVcfString)) +
"[");
// aaChangeVcf.Add( aminoProp.Name + "[" + string.Join(",", aaChanges.g + "]");
// すべてのAa変異をTablerで保存
aaChangesList.AddRange(aaChanges);
}
resAaVcfList.Add(string.Join(",", aaChangeVcf)); // top1 分。
}
// 表形式でファイルへ書き込み対象
return(CommonFlow.DbDefaultTop3(resAaVcfList),
aaChangesList);
}
public Home(IWebDriver _driver) : base(_driver)
{
_homepageLocator = new HomePageLocators();
_commonFlow = new CommonFlow(_driver);
}
