//
private static SequenceProperties GetReferenceProperties(string consensusName, ref string message)
{
//
// var consensusSequenceName = ">" + sampleName + "|" + subType + Mpileup2ConsensusFooter + cnsCnt +
// " " + pileupItem.ReferenceName +
// " cover=" + pileupItem.ReferenceMappingCoverageRate +
// " depth=" + pileupItem.ReferenceMappingCoverageAvg;
var seqNames = consensusName.Split(" ");
if (seqNames.Length <= 1)
{
message += "Error, reference name is not found. " + Environment.NewLine + consensusName;
return(null); // FluGAS内ではありえない。
}
var refName = seqNames[1]; // pileupItem.ReferenceName
if (!refName.StartsWith("NC"))
{
message += "caution, reference is no NCBI-refseq. " + refName;
// return null; // mapping reference CovGAS は Refseq を使用しているはず
return(GetGenbankInfo(refName, ref message)); // 救済処置へ
}
var refseqAcc = refName.Split(".").First();
var referenceFiles = FileUtils.FindFile(
FluGASv25.Proc.Flow.CommonFlow.GetMappingReferenceDir,
refseqAcc,
Genbank.genbankFooter);
if (!referenceFiles.Any())
{
message += "caution, not found refseq-genbank file. Please check in Data mapping-reference directory";
// Genbank file ないので取得する
return(GetGenbankInfo(refseqAcc, ref message)); // 救済措置
}
var gbSeqProperties = Genbank.GetInfluenzaProperties(referenceFiles.First(), ref message);
if (!gbSeqProperties.Any())
{
message += "caution, reference sequence info is not found from genbank file." + referenceFiles.First();
// return null; // Genbank file から情報とれなかった。
return(GetGenbankInfo(refseqAcc, ref message)); // 救済措置
}
return(gbSeqProperties.First()); // 中務は一個だけ
}
// GenBank情報が取れない場合の救済処置。
private static SequenceProperties GetGenbankInfo(string accession, ref string message)
{
// accession
var searchAcc = accession.Split(".").First(); // MT259281.1 -> MT259281
try
{
return(Genbank.GetSequenceProperties(searchAcc, ref message));
}
catch (Exception e) // net connection error とか。
{
message += e.StackTrace;
message += e.Message;
}
return(null);
}
