public IAnalysisResult AnalyzeData(IMatrixData mdata, Parameters param, ProcessInfo processInfo)
{
var remoteExe = param.GetParam <string>(InterpreterLabel).Value;
var inFile = Path.GetTempFileName();
PerseusUtils.WriteMatrixToFile(mdata, inFile);
var paramFile = Path.GetTempFileName();
param.ToFile(paramFile);
var outFile = Path.GetTempFileName();
if (!TryGetCodeFile(param, out string codeFile))
{
processInfo.ErrString = $"Code file '{codeFile}' was not found";
return(null);
}
var args = $"{codeFile} {paramFile} {inFile} {outFile}";
if (Utils.RunProcess(remoteExe, args, processInfo.Status, out string errorString) != 0)
{
processInfo.ErrString = errorString;
return(null);
}
return(GenerateResult(outFile, mdata, processInfo));
}
public void ProcessData(IMatrixData inData, INetworkData outData, Parameters param, ref IData[] supplData, ProcessInfo processInfo)
{
var remoteExe = param.GetParam <string>(InterpreterLabel).Value;
var inFile = Path.GetTempFileName();
PerseusUtils.WriteMatrixToFile(inData, inFile, false);
var paramFile = Path.GetTempFileName();
param.ToFile(paramFile);
var outFolder = Path.Combine(Path.GetTempPath(), Path.GetRandomFileName());
if (!TryGetCodeFile(param, out string codeFile))
{
processInfo.ErrString = $"Code file '{codeFile}' was not found";
return;
}
var suppFiles = SupplDataTypes.Select(Utils.CreateTemporaryPath).ToArray();
var args = $"{codeFile} {paramFile} {inFile} {outFolder} {string.Join(" ", suppFiles)}";
Debug.WriteLine($"executing > {remoteExe} {args}");
if (Utils.RunProcess(remoteExe, args, processInfo.Status, out string processInfoErrString) != 0)
{
processInfo.ErrString = processInfoErrString;
return;
}
;
FolderFormat.Read(outData, outFolder, processInfo);
supplData = Utils.ReadSupplementaryData(suppFiles, SupplDataTypes, processInfo);
}
public IAnalysisResult AnalyzeData(IMatrixData mdata, Parameters param, ProcessInfo processInfo)
{
var remoteExe = param.GetParam <string>(InterpreterLabel).Value;
if (string.IsNullOrWhiteSpace(remoteExe))
{
processInfo.ErrString = Resources.RemoteExeNotSpecified;
return(null);
}
var inFile = Path.GetTempFileName();
PerseusUtils.WriteMatrixToFile(mdata, inFile);
var outFiles = new[] { Path.GetTempFileName() }
.Concat(SupplDataTypes.Select(dataType => Path.GetTempFileName()))
.ToArray();
if (!TryGetCodeFile(param, out string codeFile))
{
processInfo.ErrString = $"Code file '{codeFile}' was not found";
return(null);
}
var commandLineArguments = GetCommandLineArguments(param);
var args = $"{codeFile} {commandLineArguments} {inFile} {string.Join(" ", outFiles)}";
if (Utils.RunProcess(remoteExe, args, processInfo.Status, out string errorString) != 0)
{
processInfo.ErrString = errorString;
return(null);
}
return(GenerateResult(outFiles, mdata, processInfo));
}
public static int WriteRNAFiles(IMatrixData mdata, Parameters param, Parameters dataParam, string workingDirectory, out string errString, string RNAexp)
{
//need to write a general version
//accepts text only data for now
string fileTempY = System.IO.Path.Combine(workingDirectory, @".\tempY.txt");
string fileY = System.IO.Path.Combine(workingDirectory, @".\fileY.txt");
IMatrixData mCopyY = (IMatrixData)mdata.Clone();
int[] nameInd = new[] { param.GetParam <int>("Gene Name Column").Value };
int[] yInd = dataParam.GetParam <int[]>(RNAexp).Value;
double baseVal = GetBase(dataParam.GetParamWithSubParams <int>(PECAParameters.dataFormGeneric));
SetupMDataForInput(mCopyY, yInd, nameInd, baseVal);
try
{
//hacky way of removing comments
PerseusUtils.WriteMatrixToFile(mCopyY, fileTempY, false);
RemoveCommentsFromFile(fileTempY, fileY);
}
catch (Exception e)
{
//need to reorganize this
errString = e.ToString();
return(-1);
}
errString = null;
return(0);
}
public void Export(Parameters parameters, IMatrixData data, ProcessInfo processInfo)
{
string filename = parameters.GetParam <string>("File name").Value;
bool addtlMatrices = parameters.GetParam <bool>("Write quality and imputed matrices").Value;
addtlMatrices = addtlMatrices && data.IsImputed != null && data.Quality != null && data.IsImputed.IsInitialized() &&
data.Quality.IsInitialized();
PerseusUtils.WriteMatrixToFile(data, filename, addtlMatrices);
}
public static ButtonParamWf DataPreviewButton(IMatrixData mdata)
{
return(new ButtonParamWf("Download data for preview", "save", (o, args) =>
{
var dialog = new SaveFileDialog
{
FileName = $"{mdata.Name}.txt",
Filter = "tab-separated data, *.txt|*.txt"
};
if (dialog.ShowDialog() == DialogResult.OK)
{
PerseusUtils.WriteMatrixToFile(mdata, dialog.FileName, false);
}
}));
}
public void ProcessData(IMatrixData mdata, Parameters param, ref IMatrixData[] supplTables, ref IDocumentData[] documents,
ProcessInfo processInfo)
{
var remoteExe = param.GetParam <string>(InterpreterLabel).Value;
if (string.IsNullOrWhiteSpace(remoteExe))
{
processInfo.ErrString = Resources.RemoteExeNotSpecified;
return;
}
var inFile = Path.GetTempFileName();
PerseusUtils.WriteMatrixToFile(mdata, inFile, AdditionalMatrices);
var outFile = Path.GetTempFileName();
if (!TryGetCodeFile(param, out string codeFile))
{
processInfo.ErrString = $"Code file '{codeFile}' was not found";
return;
}
;
if (supplTables == null)
{
supplTables = Enumerable.Range(0, NumSupplTables).Select(i => PerseusFactory.CreateMatrixData()).ToArray();
}
var suppFiles = supplTables.Select(i => Path.GetTempFileName()).ToArray();
var commandLineArguments = GetCommandLineArguments(param);
var args = $"{codeFile} {commandLineArguments} {inFile} {outFile} {string.Join(" ", suppFiles)}";
Debug.WriteLine($"executing > {remoteExe} {args}");
if (Utils.RunProcess(remoteExe, args, processInfo.Status, out string processInfoErrString) != 0)
{
processInfo.ErrString = processInfoErrString;
return;
}
;
mdata.Clear();
PerseusUtils.ReadMatrixFromFile(mdata, processInfo, outFile, '\t');
for (int i = 0; i < NumSupplTables; i++)
{
PerseusUtils.ReadMatrixFromFile(supplTables[i], processInfo, suppFiles[i], '\t');
}
}
public void ProcessData(IMatrixData mdata, Parameters param, ref IMatrixData[] supplTables, ref IDocumentData[] documents,
ProcessInfo processInfo)
{
var remoteExe = param.GetParam <string>(InterpreterLabel).Value;
var inFile = Path.GetTempFileName();
PerseusUtils.WriteMatrixToFile(mdata, inFile, false);
var paramFile = Path.GetTempFileName();
param.ToFile(paramFile);
var outFile = Path.GetTempFileName();
var codeFile = GetCodeFile(param);
var args = $"{codeFile} {paramFile} {inFile} {outFile}";
Debug.WriteLine($"executing > {remoteExe} {args}");
if (Utils.RunProcess(remoteExe, args, processInfo.Status, out string processInfoErrString) != 0)
{
processInfo.ErrString = processInfoErrString;
return;
}
;
mdata.Clear();
PerseusUtils.ReadMatrixFromFile(mdata, processInfo, outFile, '\t');
}
public static int WriteInputFiles(IMatrixData mdata, Parameters param, string workingDirectory, out string errString, string expSeries1 = "Expression Series 1", string expSeries2 = "Expression Series 2", string expSeries3 = "Expression Series 3")
{
//need to write a general version
//accepts text only data for now
//set as global
string fileTempX = System.IO.Path.Combine(workingDirectory, @".\tempX.txt");
string fileX = System.IO.Path.Combine(workingDirectory, @".\fileX.txt");
string fileTempM = System.IO.Path.Combine(workingDirectory, @".\tempM.txt");
string fileM = System.IO.Path.Combine(workingDirectory, @".\fileM.txt");
string fileTempY = System.IO.Path.Combine(workingDirectory, @".\tempY.txt");
string fileY = System.IO.Path.Combine(workingDirectory, @".\fileY.txt");
IMatrixData mCopyX = (IMatrixData)mdata.Clone();
IMatrixData mCopyM = (IMatrixData)mdata.Clone();
IMatrixData mCopyY = (IMatrixData)mdata.Clone();
int[] nameInd = new[] { param.GetParam <int>("Gene Name Column").Value };
int[] xInd = param.GetParam <int[]>(expSeries1).Value;
int[] mInd = param.GetParam <int[]>(expSeries2).Value;
int[] yInd = param.GetParam <int[]>(expSeries3).Value;
//int n_tp = param.GetParam<int>("Number of Time Points").Value;
int n_rep = param.GetParam <int>("Number of Replicates").Value;
if (nameInd.Length == 0)
{
errString = "Please select a gene name column";
return(-1);
}
if (xInd.Length == 0)
{
errString = "Please select some columns for Expression Series";
return(-1);
}
if (xInd.Length != yInd.Length || xInd.Length != mInd.Length)
{
errString = "Expression Series need to have matching number of columns";
return(-1);
}
if ((xInd.Length % n_rep) != 0)
{
errString = "number of columns not multiple of Number of Replicates";
return(-1);
}
//check also timepoints here
//if ((xInd.Length % n_tp)!=0)
//{
// errString = "number of columns not multiple of Number of Time Points";
// return -1;
//}
double baseVal1 = PluginPECA.Utils.GetBase(param.GetParamWithSubParams <int>(PECAParameters.dataForm1));
double baseVal2 = PluginPECA.Utils.GetBase(param.GetParamWithSubParams <int>(PECAParameters.dataForm2));
double baseVal3 = PluginPECA.Utils.GetBase(param.GetParamWithSubParams <int>(PECAParameters.dataForm3));
PluginPECA.Utils.SetupMDataForInput(mCopyX, xInd, nameInd, baseVal1);
PluginPECA.Utils.SetupMDataForInput(mCopyM, mInd, nameInd, baseVal2);
PluginPECA.Utils.SetupMDataForInput(mCopyY, yInd, nameInd, baseVal3);
try
{
//hacky way of removing comments
//better to just ask GS to ignore comments from his code
PerseusUtils.WriteMatrixToFile(mCopyX, fileTempX, false);
PluginPECA.Utils.RemoveCommentsFromFile(fileTempX, fileX);
PerseusUtils.WriteMatrixToFile(mCopyM, fileTempM, false);
PluginPECA.Utils.RemoveCommentsFromFile(fileTempM, fileM);
PerseusUtils.WriteMatrixToFile(mCopyY, fileTempY, false);
PluginPECA.Utils.RemoveCommentsFromFile(fileTempY, fileY);
}
catch (Exception e)
{
//need to reorganize this
errString = e.ToString();
return(-1);
}
errString = null;
return(0);
}