public virtual void ProcessData(IMatrixData mdata, global::BaseLibS.Param.Parameters param, ref IMatrixData[] supplTables, ref IDocumentData[] documents, ProcessInfo processInfo)
{
}
//might need to change this in the future public virtual int GetMaxThreads(global::BaseLibS.Param.Parameters parameters) => 1;
public override void ProcessData(IMatrixData mdata, global::BaseLibS.Param.Parameters param, ref IMatrixData[] supplTables, ref IDocumentData[] documents, ProcessInfo processInfo)
{
// test
//processInfo.ErrString = string.Format("stringcolumn count is: {0}, numerical column count is: {1}, general count is {2}", mdata.StringColumnCount, mdata.NumericColumnCount, mdata.Column);
string geneNameColumn = mdata.StringColumnNames[param.GetParam <int>("Gene Name Column").Value];
string defaultPECAPath = System.IO.Path.Combine(Directory.GetCurrentDirectory(), @".\bin\PECAInstallations\peca_core_N.exe");
string workingDirectory = param.GetParam <string>("Working Directory").Value;
string pythonFDR = System.IO.Path.Combine(Directory.GetCurrentDirectory(), @".\bin\PECAInstallations\fdr.exe");
string outputFile = System.IO.Path.Combine(workingDirectory, @".\data_R_CPS.txt");
string errString;
ParameterWithSubParams <bool> getRNAInf = param.GetParamWithSubParams <bool>(PECAParameters.RNAInference);
string paramInfo = null;
if (getRNAInf.Value)
{
//RNAinf checking
paramInfo = Utils.CheckParameters(mdata, param, getRNAInf.GetSubParameters(), PECAParameters.RNAexp, null, PECAParameters.dataFormGeneric, null);
}
else
{
paramInfo = Utils.CheckParameters(mdata, param, getRNAInf.GetSubParameters());
}
if (paramInfo != null)
{
processInfo.ErrString = paramInfo;
return;
}
if (Utils.WriteInputFiles(mdata, param, getRNAInf.GetSubParameters(), getRNAInf.Value, workingDirectory, processInfo, out errString) != 0)
{
processInfo.ErrString = errString;
return;
}
if (Utils.WriteInputParam(param, getRNAInf.GetSubParameters(), getRNAInf.Value, workingDirectory) != 0)
{
processInfo.ErrString = "Unable To Process the Given Parameters";
return;
}
string inputLocation = "\"" + System.IO.Path.Combine(@workingDirectory, @".\input") + "\"";
//0 is PECA task
//int totPECA = Utils.getMCMCParam(param.GetParamWithSubParams<int>("MCMC Burn-In"), 0) + Utils.getMCMCParam(param.GetParamWithSubParams<int>("MCMC Thinning"), 1) * Utils.getMCMCParam(param.GetParamWithSubParams<int>("MCMC Samples"), 2);
int totPECA = param.GetParam <int>("MCMC Burn-In").Value + param.GetParam <int>("MCMC Thinning").Value *param.GetParam <int>("MCMC Samples").Value;
if (ExternalProcess.RunExe(defaultPECAPath, inputLocation, workingDirectory, processInfo.Status, processInfo.Progress, 0, totPECA, out string processInfoErrString) != 0)
{
processInfo.ErrString = processInfoErrString;
return;
}
int totFDR = mdata.RowCount;
//breaks when user path contains space?
if (ExternalProcess.RunExe(pythonFDR, null, workingDirectory, processInfo.Status, processInfo.Progress, 1, totFDR, out string processInfoErrString3) != 0)
{
processInfo.ErrString = processInfoErrString3;
return;
}
if (getRNAInf.Value)
{
PluginPECA.Utils.GetOutput(mdata, param, getRNAInf.GetSubParameters(), outputFile, geneNameColumn, PECAParameters.RNAexp, 2);
}
else
{
PluginPECA.Utils.GetOutput(mdata, param, getRNAInf.GetSubParameters(), outputFile, geneNameColumn);
}
////need to include the GSA part
//new version no longer need this
//if (Utils.WriteCPSInputParam(param, workingDirectory) != 0)
//{
// processInfo.ErrString = "Unable To Process the Enrichment Analysis Parameters";
// return;
//}
//string exeCPS = System.IO.Path.Combine(Directory.GetCurrentDirectory(), @".\bin\PECAInstallations\cps.exe");
//string inputCPSLocation = "\"" + System.IO.Path.Combine(@workingDirectory, @".\cps_input") + "\"";
//if (ExternalProcess.RunExe(exeCPS, inputCPSLocation, workingDirectory, processInfo.Status, processInfo.Progress, -1, -1, out string processInfoErrString4) != 0)
//{
// processInfo.ErrString = processInfoErrString4;
// return;
//}
IMatrixData supplData = PluginPECA.Utils.getGSA(param, mdata, workingDirectory, -2, processInfo, out string gsaErrString);
if (gsaErrString != null)
{
processInfo.ErrString = gsaErrString;
return;
}
//processInfo.ErrString = processInfoErrString5;
supplTables = new IMatrixData[] { supplData };
processInfo.Progress(0);
}
public override void ProcessData(IMatrixData mdata, global::BaseLibS.Param.Parameters param, ref IMatrixData[] supplTables, ref IDocumentData[] documents, ProcessInfo processInfo)
{
string geneNameColumn = mdata.StringColumnNames[param.GetParam <int>("Gene Name Column").Value];
string defaultPECAPath = System.IO.Path.Combine(Directory.GetCurrentDirectory(), @".\bin\PECAInstallations\peca_core_N.exe");
string workingDirectory = param.GetParam <string>("Working Directory").Value;
string pythonFDR = System.IO.Path.Combine(Directory.GetCurrentDirectory(), @".\bin\PECAInstallations\fdr.exe");
string outputFile = System.IO.Path.Combine(workingDirectory, @".\data_R_CPS.txt");
string errString;
ParameterWithSubParams <bool> getRNAInf = param.GetParamWithSubParams <bool>(PECAParameters.RNAInference);
string paramInfo = null;
if (getRNAInf.Value)
{
//RNAinf checking
paramInfo = Utils.CheckCoreParameters(mdata, param, getRNAInf.GetSubParameters(), PECAParameters.RNAexp, null, PECAParameters.dataFormGeneric, null);
}
else
{
paramInfo = Utils.CheckCoreParameters(mdata, param, getRNAInf.GetSubParameters());
}
if (paramInfo != null)
{
processInfo.ErrString = paramInfo;
return;
}
//prepares the input files needed
if (Utils.WriteInputFilesCond(mdata, param, getRNAInf.GetSubParameters(), getRNAInf.Value, workingDirectory, out errString) != 0)
{
processInfo.ErrString = errString;
return;
}
//prepares the input parameters
if (Utils.WriteInputParam(param, getRNAInf.GetSubParameters(), workingDirectory, getRNAInf.Value) != 0)
{
processInfo.ErrString = "Unable To Process the Given Parameters";
return;
}
string inputLocation = "\"" + System.IO.Path.Combine(@workingDirectory, @".\input") + "\"";
//0 is PECA task
//int totPECA = Utils.getMCMCParam(param.GetParamWithSubParams<int>("MCMC Burn-In"), 0) + Utils.getMCMCParam(param.GetParamWithSubParams<int>("MCMC Thinning"), 1) * Utils.getMCMCParam(param.GetParamWithSubParams<int>("MCMC Samples"), 2);
int totPECA = param.GetParam <int>("MCMC Burn-In").Value + param.GetParam <int>("MCMC Thinning").Value *param.GetParam <int>("MCMC Samples").Value;
if (ExternalProcess.RunExe(defaultPECAPath, inputLocation, workingDirectory, processInfo.Status, processInfo.Progress, 0, totPECA, out string processInfoErrString) != 0)
{
processInfo.ErrString = processInfoErrString;
return;
}
int totFDR = mdata.RowCount;
if (ExternalProcess.RunExe(pythonFDR, null, workingDirectory, processInfo.Status, processInfo.Progress, 1, totFDR, out string processInfoErrString3) != 0)
{
processInfo.ErrString = processInfoErrString3;
return;
}
//reads in the output as matrix
if (getRNAInf.Value)
{
Utils.GetOutput(mdata, param, getRNAInf.GetSubParameters(), outputFile, geneNameColumn, PECAParameters.RNAexp, 2);
}
else
{
Utils.GetOutput(mdata, param, getRNAInf.GetSubParameters(), outputFile, geneNameColumn);
}
ParameterWithSubParams <bool> getAnalysis = param.GetParamWithSubParams <bool>(PECAParameters.gsa);
if (getAnalysis.Value)
{
IMatrixData supplData = Utils.getGSA(getAnalysis.GetSubParameters(), mdata, workingDirectory, -1, processInfo, out string gsaErrString);
if (gsaErrString != null)
{
processInfo.ErrString = gsaErrString;
return;
}
supplTables = new IMatrixData[] { supplData };
}
processInfo.Progress(0);
}
public override void ProcessData(IMatrixData mdata, global::BaseLibS.Param.Parameters param, ref IMatrixData[] supplTables, ref IDocumentData[] documents, ProcessInfo processInfo)
{
// test
//processInfo.ErrString = string.Format("stringcolumn count is: {0}, numerical column count is: {1}, general count is {2}", mdata.StringColumnCount, mdata.NumericColumnCount, mdata.Column);
string geneNameColumn = mdata.StringColumnNames[param.GetParam <int>("Gene Name Column").Value];
string defaultPECAPath = System.IO.Path.Combine(Directory.GetCurrentDirectory(), @".\bin\PECAInstallations\peca_r_ps.exe");
string workingDirectory = param.GetParam <string>("Working Directory").Value;
string pythonFDR = System.IO.Path.Combine(Directory.GetCurrentDirectory(), @".\bin\PECAInstallations\fdr2.exe");
string outputFile = System.IO.Path.Combine(workingDirectory, @".\data_R_CPS.txt");
string errString;
if (Utils.WriteInputFiles(mdata, param, workingDirectory, out errString, PECAParameters.pecaPSSeries1, PECAParameters.pecaPSSeries2, PECAParameters.pecaPSSeries3) != 0)
{
processInfo.ErrString = errString;
return;
}
if (Utils.WriteInputParam(param, workingDirectory) != 0)
{
processInfo.ErrString = "Unable To Process the Given Parameters";
return;
}
string inputLocation = "\"" + System.IO.Path.Combine(@workingDirectory, @".\input") + "\"";
//0 is PECA task
int totPECA = param.GetParam <int>("MCMC Burn-In").Value + param.GetParam <int>("MCMC Thinning").Value *param.GetParam <int>("MCMC Samples").Value;
if (ExternalProcess.RunExe(defaultPECAPath, inputLocation, workingDirectory, processInfo.Status, processInfo.Progress, 0, totPECA, out string processInfoErrString) != 0)
{
processInfo.ErrString = processInfoErrString;
return;
}
int totFDR = mdata.RowCount;
//breaks when user path contains space?
if (ExternalProcess.RunExe(pythonFDR, null, workingDirectory, processInfo.Status, processInfo.Progress, 1, totFDR, out string processInfoErrString3) != 0)
{
processInfo.ErrString = processInfoErrString3;
return;
}
PluginPECA.Utils.GetOutput(mdata, param, param, outputFile, geneNameColumn, PECAParameters.pecaPSSeries1, 3);
ParameterWithSubParams <bool> getAnalysis = param.GetParamWithSubParams <bool>(PECAParameters.gsa);
if (getAnalysis.Value)
{
IMatrixData supplDataSynth = PluginPECA.Utils.getGSA(getAnalysis.GetSubParameters(), mdata, workingDirectory, 1, processInfo, out string gsaErrString);
if (gsaErrString != null)
{
processInfo.ErrString = gsaErrString;
return;
}
IMatrixData supplDataDeg = PluginPECA.Utils.getGSA(getAnalysis.GetSubParameters(), mdata, workingDirectory, 0, processInfo, out string gsaErrString2);
if (gsaErrString2 != null)
{
processInfo.ErrString = gsaErrString2;
return;
}
supplTables = new IMatrixData[] { supplDataSynth, supplDataDeg };
}
processInfo.Progress(0);
}
