/// <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;
}
/// <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 OutAglimentNcbi(string referenceName, string nucName, string nucs, string outAlignPath, ref string message)
{
SequenceProperties ncbidat = null;
try {
ncbidat = WfComponent.Utils.Genbank.GetSequenceProperties(referenceName, ref message);
if (!string.IsNullOrEmpty(message) ||
ncbidat == null ||
string.IsNullOrEmpty(ncbidat.accession))
{
message += "get genbank sequence data error. ";
return; // genbank error
}
}
catch (Exception e)
{
message += e.Message;
return;
}
var tmpFasta = outAlignPath.EndsWith(".fasta") ?
Path.ChangeExtension(outAlignPath, ".fna") :
Path.ChangeExtension(outAlignPath, ".fasta");
var fastaLines = new string[]
{
">" + ncbidat.accession,
ncbidat.sequence,
">" + 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;
}
