/// <summary>
/// NCBI Reference nuc
/// </summary>
/// <param name="referenceName">NCBI Reference Accession </param>
/// <param name="nucName">consensus name</param>
/// <param name="nucs">consensus nucreotides</param>
/// <param name="outAlignPath">output agliment file path</param>
public static void OutAgliment(string referenceName, string nucName, string nucs, string outAlignPath, ref string message)
{
var mes = string.Empty;
var reference = SeveralUtils.GetCoronaReference(referenceName, ref mes);
if (!string.IsNullOrEmpty(mes) ||
string.IsNullOrEmpty(reference.Key) ||
string.IsNullOrEmpty(reference.Value))
{
message += mes + Environment.NewLine;
message += "alignment process error...";
return;
}
var tmpFasta = outAlignPath.EndsWith(".fasta") ?
Path.ChangeExtension(outAlignPath, ".fna") :
Path.ChangeExtension(outAlignPath, ".fasta");
var fastaLines = new string[]
{
">" + reference.Key,
reference.Value,
">" + nucName,
nucs
};
// 一時Fasta
WfComponent.Utils.FileUtils.WriteFile(tmpFasta, fastaLines, ref message);
if (!string.IsNullOrEmpty(message))
{
return;
}
var alignProc = new WfComponent.External.Kalign(
new WfComponent.External.KalignOptions()
{
fastaPath = tmpFasta,
outAlign = outAlignPath,
isFastaOut = true
});
// ほぼ一瞬で終わるはずなのでCancel 考えない。
try
{
alignProc.StartProcess();
message = alignProc.Message;
if (File.Exists(outAlignPath))
{
message = AliView.AliViewStart(outAlignPath);
}
}
catch (Exception e)
{
message += e.Message;
message += "execute agliment program error, " + alignProc.Message;
}
return;
}
public static void OutTree(string outTreePath, int sampleId, int topNo, ref string message)
{
// 当該サンプル情報
var mes = string.Empty;
var sample = Dao.SampleDao.GetSample(sampleId, ref mes);
if (!string.IsNullOrEmpty(mes) || sample == null || sample.ID <= 0)
{
message += mes;
return;
}
var nucName = sample.ViewName;
var nucs = GetDbValue(sample.Cns_Nucs, topNo);
var referenceName = GetDbValue(sample.Accession, topNo);
var reference = SeveralUtils.GetCoronaReference(referenceName, ref mes);
if (!string.IsNullOrEmpty(mes) ||
string.IsNullOrEmpty(reference.Key) ||
string.IsNullOrEmpty(reference.Value))
{
message += mes + Environment.NewLine;
message += "create tree process error...";
return;
}
// for tree base fasta, to add reference , add consensus
var baseTreeFasta = FileUtils.FindFile(
Path.Combine(
AppDomain.CurrentDomain.BaseDirectory.TrimEnd('\\'),
referencesDir,
TreeReferenceDir),
CommonFlow.covBaseName,
FnaFooter);
var coronaRefseq = baseTreeFasta.Any() ?
baseTreeFasta.First():
Path.Combine( // mapping reference
FluGASv25.Proc.Flow.CommonFlow.GetMappingReferenceDir,
CommonFlow.covBaseName + FnaFooter);
var coronaRefseqLines = FileUtils.ReadFile(coronaRefseq, ref mes);
var coronaReference = new List <string>(coronaRefseqLines);
coronaReference.Add(">" + reference.Key);
coronaReference.Add(reference.Value);
coronaReference.Add(">" + nucName);
coronaReference.Add(nucs);
var tmpFasta = outTreePath.EndsWith(".fasta") ?
Path.ChangeExtension(outTreePath, ".fna") :
Path.ChangeExtension(outTreePath, ".fasta");
if (File.Exists(tmpFasta))
{
File.Delete(tmpFasta);
}
// 一時Fasta
FileUtils.WriteFile(tmpFasta, coronaReference, ref message);
if (!string.IsNullOrEmpty(message))
{
return;
}
var clustalO = new ClustalOmega(
new ClustalOmegaOptions()
{
targetFile = tmpFasta,
outGuidTreeFile = outTreePath
});
try {
var s = clustalO.StartProcess();
if (!string.IsNullOrEmpty(s))
{
message += s;
}
if (string.IsNullOrEmpty(clustalO.Message))
{
message += clustalO.Message;
}
}
catch (Exception e)
{
message += e.Message;
}
return;
}
