/** 
 * Get set up for a run of reporting probesets. Often used to open file
 * streams and print headers to files etc.
 * 
 * @param qMethod - Quantification method to be used.
 * @param layout - Where the probesets, probes, etc are on the chip.
 * 
 * @return true if success, false otherwise.
 */
bool QuantMethodExprCCCHPReport::prepare(QuantMethod &qMethod, const IntensityMart &iMart) 
{
    QuantExprMethod *eMethod = dynamic_cast<QuantExprMethod *>(&qMethod);
    if (eMethod == NULL) { Err::errAbort("Can only use a QuantMethodExprReport with a QuantExprMethod."); }
    
    setupFileNames(iMart);
    int nfiles = m_CHPFileNames.size();
    
    // Make sure our output directory exists.
    if (!Fs::isWriteableDir(m_Prefix.c_str()) &&
        (Fs::mkdirPath(m_Prefix, false) != APT_OK)) {
        APT_ERR_ABORT("Can't make or write to directory: " + m_Prefix);
    }
    
    removeAllChps();
    
    // Get CEL file GUIDs
    ///@todo This be computed by the engine and passed in via AnalysisInfo
    m_celGuids.resize(nfiles);
    std::string tmp_unc_name;
    for (int chip=0; chip<nfiles; chip++) {
        FusionCELData cel;
        try {
            tmp_unc_name=Fs::convertToUncPath(m_CELFileNames[chip]);
            cel.SetFileName(tmp_unc_name.c_str());
            if (!cel.ReadHeader()) {
                Err::errAbort("Unable to read CEL file: "+FS_QUOTE_PATH(tmp_unc_name));
            }
            GenericData *gdata = cel.GetGenericData();
            if (gdata != NULL) {
                m_celGuids[chip] = gdata->Header().GetGenericDataHdr()->GetFileId();
            }
            cel.Close();
        }
        catch (...) {
            Err::errAbort("Unable to read CEL file " + tmp_unc_name);
        }
    }

    int maxProbeSetNameLength = 0;
    for (int i=0; i<m_Info.m_ProbesetNames.size(); i++) {
        int len = (int)strlen(m_Info.m_ProbesetNames.at(i));
        if (m_Info.m_ProbesetDisplayNames.size() > 0 && m_Info.m_ProbesetDisplayNames.at(i) != NULL)
            len = (int)strlen(m_Info.m_ProbesetDisplayNames.at(i));
        maxProbeSetNameLength = Max(maxProbeSetNameLength, len);
    }

    // Prepare headers for all CHP files.
    wstring algName = StringUtils::ConvertMBSToWCS(m_Info.m_AlgName);
    wstring algVersion = StringUtils::ConvertMBSToWCS(m_Info.m_AlgVersion);
    wstring chipType = StringUtils::ConvertMBSToWCS(m_Info.m_ChipType);

    // For each chip, precreate all probeset signal entries (default to 0.0).
    Verbose::out(1,"QuantMethodExprCCCHPReport: Creating temporary files for CHP output");
    for (int chip=0; chip<nfiles; chip++) {
        try {
            ParameterNameValueType param;

            // Create tmp chp file
            std::string tmp_chp_name=m_CHPFileNames[chip] + ".tmp";
            CHPQuantificationData *data = new CHPQuantificationData(tmp_chp_name);
            m_TmpChpFiles.push_back(tmp_chp_name);

            // set parent header
            FusionCELData cel;
            try {
                tmp_unc_name=Fs::convertToUncPath(m_CELFileNames[chip]);
                cel.SetFileName(tmp_unc_name.c_str());
                if (!cel.ReadHeader()) {
                  Err::errAbort("Unable to read CEL file: "+FS_QUOTE_PATH(tmp_unc_name));
                }
                GenericData *gdata = cel.GetGenericData();
                if (gdata != NULL) {
                    data->GetFileHeader()->GetGenericDataHdr()->AddParent(*gdata->Header().GetGenericDataHdr());
                }
                cel.Close();
            }
            catch (...) {
              Err::errAbort("Unable to read CEL file: "+FS_QUOTE_PATH(tmp_unc_name));
            }

            data->SetEntryCount(m_Info.m_NumProbeSets, maxProbeSetNameLength); 
            data->SetAlgName(algName);
            data->SetAlgVersion(algVersion);
            data->SetArrayType(chipType);

            param.SetName(L"program-name");
            param.SetValueText(StringUtils::ConvertMBSToWCS(m_Info.m_ProgramName));
            data->GetGenericData().Header().GetGenericDataHdr()->AddNameValParam(param);
            param.SetName(L"program-version");
            param.SetValueText(StringUtils::ConvertMBSToWCS(m_Info.m_ProgramVersion));
            data->GetGenericData().Header().GetGenericDataHdr()->AddNameValParam(param);
            param.SetName(L"program-company");
            param.SetValueText(StringUtils::ConvertMBSToWCS(m_Info.m_ProgramCompany));
            data->GetGenericData().Header().GetGenericDataHdr()->AddNameValParam(param);

            // Add algorithm parameters to list.
            ParameterNameValueTypeList paramList;
            assert(m_Info.m_ParamNames.size() == m_Info.m_ParamValues.size());
            for (int i=0; i<m_Info.m_ParamNames.size(); i++) {
                if (m_Info.m_ParamValues[i].length() > 0) {
                    param.SetName(StringUtils::ConvertMBSToWCS(m_Info.m_ParamNames[i]));
                    param.SetValueText(StringUtils::ConvertMBSToWCS(m_Info.m_ParamValues[i]));
                    paramList.push_back(param);
                }
            }

            // Add list of all CEL GUIDs in batch
            ///@todo should this be computed by the engine and passed in via AnalysisInfo?
            string prefix = "apt-opt-";
            for (int chip=0; chip<m_CHPFileNames.size(); chip++) {
                if (m_celGuids[chip].empty() == false) {
                    string paramName = prefix + "cel-guid-" + ToStr(chip+1);
                    param.SetName(StringUtils::ConvertMBSToWCS(paramName));
                    param.SetValueText(StringUtils::ConvertMBSToWCS(m_celGuids[chip]));
                    paramList.push_back(param);
                }
            }
            data->AddAlgParams(paramList);

            // Add the run report parameters to the list
            ParameterNameValueTypeList summaryParamList;
            std::string blankStr(256, ' ');
            for (int source=0; source<m_ChipSummaries.size(); source++) {
                ChipSummary::metricDefVec_t metricDefs = m_ChipSummaries[source]->getMetricDefs();
                for (int i = 0; i < metricDefs.size(); i++) {
                    param.SetName(StringUtils::ConvertMBSToWCS(metricDefs[i].m_name));
                    if (metricDefs[i].m_type == ChipSummary::Metric::Double) {
                        param.SetValueFloat(-1.0);
                    } 
                    else if (metricDefs[i].m_type == ChipSummary::Metric::Integer) {
                        param.SetValueInt32(-1);
                    } 
                    else if (metricDefs[i].m_type == ChipSummary::Metric::String) {
                        param.SetValueAscii(blankStr);
                    } 
                    else {
                        Err::errAbort("QuantMethodExprCCCHPReport: Unable to handle unknown type: " + 
                                      ToStr(metricDefs[i].m_type) );
                    }
                    summaryParamList.push_back(param);
                }
            }
            data->AddSummaryParams(summaryParamList);
			
            ProbeSetQuantificationData entry;
            CHPQuantificationFileWriter writer(*data);
            writer.SeekToDataSet();        // seek to data table location
            for (int index=0; index<m_Info.m_ProbesetNames.size(); index++) {
                if (m_Info.m_ProbesetDisplayNames.size() > 0 && m_Info.m_ProbesetDisplayNames[index] != NULL)
                    entry.name = m_Info.m_ProbesetDisplayNames[index];
                else
                    entry.name = m_Info.m_ProbesetNames[index];
                entry.quantification = 0.0f;
                writer.WriteEntry(entry);
            }
            
            delete data;
        }
        catch (...) {
            Err::errAbort("QuantMethodExprCHPReport::prepare() - Unable to write header and/or precreate signal entries to file: " + m_CHPFileNames[chip] + ".tmp");
        }
    }
    
    // initialize expression signal buffer writer
    m_ExpressionQuantificationBufferWriter.Initialize(&m_TmpChpFiles);

    return true;
}
Exemplo n.º 2
0
void CopyNumberResultWriterTest::testWrite()
{
	CopyNumberResultWriter writer;
    const char *fileNames[] = {"test1.cn", "test2.cn"};

    list<ParameterNameValueType> algParams;
    list<ParameterNameValueType> sumParams;
    vector<ColumnInfo> cols;

    writer.MaximumProbeSetNameLength(12);
    writer.MaximumCytoRegionNameLength(12);
	writer.MaximumGenotypeProbeSetNameLength(12);
    writer.AlgName() = "MYALG";
    writer.AlgVersion() = "1.0";
    writer.NumberProbeSets() = 10;
    writer.NumberCytoRegions() = 10;
	writer.NumberGenotypeProbeSets() = 10;
    writer.Columns() = cols;
    writer.AlgParams() = algParams;
    writer.SetChromosomeProbeSetIndexInformation(X_CHR, 0, writer.NumberProbeSets());
    for (int i=0; i<2; i++)
    {
        FusionCELData cel;
        cel.SetFileName("../data/small_cel_file");
        cel.Read(false);

        writer.SummaryParams() = sumParams;
        writer.CreateResultFile(cel, fileNames[i]);
        cel.Close();

        ProbeSetMultiDataCopyNumberData entry;
        char buf[64];
        for (int j=0; j<writer.NumberProbeSets(); j++)
        {
            entry.chr = X_CHR;
            entry.position = j+i;
            snprintf(buf, 64, "%d", j+i);
            entry.name = buf;
            writer.WriteProbeSetResult(entry);
        }
        ProbeSetMultiDataCytoRegionData cy;
        for (int j=0; j<writer.NumberCytoRegions(); j++)
        {
            cy.call = 1;
            cy.confidenceScore = (float)(j+i);
            snprintf(buf, 64, "%d", j+i);
            cy.name = buf;
            writer.WriteCytoRegionResult(cy);
        }
        ProbeSetMultiDataGenotypeData gt;
        for (int j=0; j<writer.NumberGenotypeProbeSets(); j++)
        {
            gt.call = 1;
			gt.confidence = (float)(j+i);
            snprintf(buf, 64, "%d", j+i);
            gt.name = buf;
			writer.WriteGenotypeProbeSetResult(gt);
        }
        writer.CloseResultsFile();
    }

    for (int i=0; i<2; i++)
    {
        FusionCHPData *chp = FusionCHPDataReg::Read(fileNames[i]);
	    CPPUNIT_ASSERT(chp != NULL);
	    FusionCHPMultiDataData *genoChp = FusionCHPMultiDataData::FromBase(chp); 
	    CPPUNIT_ASSERT(genoChp != NULL);

	    CPPUNIT_ASSERT(genoChp->GetAlgName() == L"MYALG");
	    CPPUNIT_ASSERT(genoChp->GetAlgVersion() == L"1.0");
	    CPPUNIT_ASSERT(genoChp->GetArrayType() == L"Hg-small");
	    CPPUNIT_ASSERT(genoChp->GetEntryCount(ExpressionMultiDataType) == 0);
	    CPPUNIT_ASSERT(genoChp->GetEntryCount(GenotypeMultiDataType) == 10);
	    CPPUNIT_ASSERT(genoChp->GetEntryCount(CopyNumberMultiDataType) == 10);
	    CPPUNIT_ASSERT(genoChp->GetEntryCount(CytoMultiDataType) == 10);

        DataSetHeader *dsh = genoChp->GetDataSetHeader(CopyNumberMultiDataType);
        CPPUNIT_ASSERT(dsh->GetNameValParamCnt() == 3);
        ParameterNameValueTypeConstIt begin;
        ParameterNameValueTypeConstIt end;
        ParameterNameValueTypeConstIt it;
        dsh->GetNameValIterators(begin, end);
        it = begin;
        CPPUNIT_ASSERT(it->GetValueInt32() == 0);
        ++it;
        CPPUNIT_ASSERT(it->GetValueInt32() == 10);
        ++it;
        CPPUNIT_ASSERT(it->GetValueAscii() == "X");
        
        ProbeSetMultiDataCopyNumberData entry;
        char buf[64];
        for (int j=0; j<10; j++)
        {
            genoChp->GetCopyNumberEntry(CopyNumberMultiDataType, j, entry);
            CPPUNIT_ASSERT(entry.chr == X_CHR);
            CPPUNIT_ASSERT(entry.position == j+i);
            snprintf(buf, 64, "%d", j+i);
            CPPUNIT_ASSERT(entry.name.compare(buf) == 0);
        }

        ProbeSetMultiDataCytoRegionData cy;
        for (int j=0; j<10; j++)
        {
            genoChp->GetCytoRegionEntry(CytoMultiDataType, j, cy);
            CPPUNIT_ASSERT(cy.call == 1);
            CPPUNIT_ASSERT_DOUBLES_EQUAL(cy.confidenceScore, j+i, 0.0001f);
            snprintf(buf, 64, "%d", j+i);
            CPPUNIT_ASSERT(cy.name.compare(buf) == 0);
        }

        ProbeSetMultiDataGenotypeData gt;
        for (int j=0; j<10; j++)
        {
            genoChp->GetGenotypeEntry(GenotypeMultiDataType, j, gt);
            CPPUNIT_ASSERT(gt.call == 1);
            CPPUNIT_ASSERT_DOUBLES_EQUAL(gt.confidence, j+i, 0.0001f);
            snprintf(buf, 64, "%d", j+i);
            CPPUNIT_ASSERT(gt.name.compare(buf) == 0);
        }

        delete chp;
    }
}
Exemplo n.º 3
0
/*! Create a "quantification" CHP file with just the header information. The remainder of the file
 * will be created at a later time using the buffer writer technique.
 * The CHP file will contain only "quantification" results from an expression analysis.
 * @param execId The execution identifier. This identifier is used to identify the batch run that created the CHP files.
 * @param celFile The full path to the parent CEL file. The header of the CEL file is copied to the CHP file.
 * @param outFile The name of the output CHP file.
 * @param probeSetNames The probe set names.
 * @param algName The name of the algorithm used to create the results.
 * @param algVersion The algorithm version.
 * @param chipType the chip type, also known as the probe array type.
 * @param programName The name of the program used to create the CHP file.
 * @param programVersion The version of the program.
 * @param programCompany The company or institution who developed the CHP creating software.
 * @param paramNames A list of parameter names to store in the CHP file header.
 * @param paramValues A list of parameter values to store in the CHP file header.
 * @param sumNames A list of summary statistic names to store in the CHP file header.
 * @param sumValues A list of summary statistic values to store in the CHP file header.
*/
static void CreateFileWithHeader
(
	const string &execId,
	const string &celFile,
	const string &outFile,
	const list<string> &probeSetNames,
	const string &algName,
	const string &algVersion,
	const string &chipType,
	const string &programName,
	const string &programVersion,
	const string &programCompany,
	const vector<string>& paramNames,
	const vector<string>& paramValues,
	const vector<string>& sumNames,
	const vector<string>& sumValues
)
{
	// Determine the max probe set name.
	int numEntries = (int) probeSetNames.size();
	int maxProbeSetNameLength = 0;
	for (list<string>::const_iterator it=probeSetNames.begin(); it!=probeSetNames.end(); it++)
	{
		maxProbeSetNameLength = max(maxProbeSetNameLength, (int) it->length());
	}

	// Create the data object
	CHPQuantificationData *data = new CHPQuantificationData(outFile);
    data->SetEntryCount(numEntries, maxProbeSetNameLength);
	data->SetAlgName(StringUtils::ConvertMBSToWCS(algName));
	data->SetAlgVersion(StringUtils::ConvertMBSToWCS(algVersion));
	data->SetArrayType(StringUtils::ConvertMBSToWCS(chipType));

	// Store the CEL header
	if (celFile.length() > 0 && FileUtils::Exists(celFile.c_str()) == true)
	{
		FusionCELData cel;
		cel.SetFileName(celFile.c_str());
        cel.ReadHeader();
	    GenericData *gdata = cel.GetGenericData();
	    if (gdata != NULL)
			data->GetFileHeader()->GetGenericDataHdr()->AddParent(*gdata->Header().GetGenericDataHdr()); 
	    cel.Close();
	}

	// Add algorithm parameters to list.
    ParameterNameValueTypeList params;
    ParameterNameValueType param;
    
	if (programName.empty() == false)
	{
		param.SetName(L"program-name");
		param.SetValueText(StringUtils::ConvertMBSToWCS(programName));
		data->GetGenericData().Header().GetGenericDataHdr()->AddNameValParam(param);
	}

	if (programVersion.empty() == false)
	{
		param.SetName(L"program-version");
		param.SetValueText(StringUtils::ConvertMBSToWCS(programVersion));
		data->GetGenericData().Header().GetGenericDataHdr()->AddNameValParam(param);
	}

	if (programCompany.empty() == false)
	{
		param.SetName(L"program-company");
		param.SetValueText(StringUtils::ConvertMBSToWCS(programCompany));
		data->GetGenericData().Header().GetGenericDataHdr()->AddNameValParam(param);
	}

	int nparams = (int) paramNames.size();
	param.SetName(L"exec-guid");
	param.SetValueAscii(execId);
	params.push_back(param);
	for(int iparam=0; iparam<nparams; iparam++)
	{
		param.SetName(StringUtils::ConvertMBSToWCS(paramNames[iparam]));
        param.SetValueAscii(paramValues[iparam]);
        params.push_back(param);
	}
	if (params.empty() == false)
		data->AddAlgParams(params);

	params.clear();
	nparams = (int) sumNames.size();
	for(int iparam=0; iparam<nparams; iparam++)
	{
		param.SetName(StringUtils::ConvertMBSToWCS(sumNames[iparam]));
        param.SetValueAscii(sumValues[iparam]);
        params.push_back(param);
	}
	if (params.empty() == false)
		data->AddSummaryParams(params);

	// Creating the writer object will create the file with the header information.
	CHPQuantificationFileWriter writer(*data);

	// Write the probe set names.
	writer.SeekToDataSet();
	ProbeSetQuantificationData entry;
	for (list<string>::const_iterator it=probeSetNames.begin(); it!=probeSetNames.end(); it++)
	{
        entry.name = *it;
        entry.quantification = 0.0f;
        writer.WriteEntry(entry);
    }
}
Exemplo n.º 4
0
/*! Create a "multi-data" CHP file with just the header information. The remainder of the file
 * will be created at a later time using the buffer writer technique.
 * The CHP file will contain only "genotyping" results.
 * @param execId The execution identifier. This identifier is used to identify the batch run that created the CHP files.
 * @param celFile The full path to the parent CEL file. The header of the CEL file is copied to the CHP file.
 * @param outFile The name of the output CHP file.
 * @param extraColNames The names of the extra data columns. Should not include probe set name, call and confidence columns.
 * @param extraColTypes The types (float, int, ubyte) of the extra columns.
 * @param numEntries The number of rows (entries) of results to store in the CHP file.
 * @param maxProbeSetNameLength The maximum length of the probe set names.
 * @param algName The name of the algorithm used to create the results.
 * @param algVersion The algorithm version.
 * @param chipType the chip type, also known as the probe array type.
 * @param programName The name of the program used to create the CHP file.
 * @param programVersion The version of the program.
 * @param programCompany The company or institution who developed the CHP creating software.
 * @param paramNames A list of parameter names to store in the CHP file header.
 * @param paramValues A list of parameter values to store in the CHP file header.
 * @param sumNames A list of summary statistic names to store in the CHP file header.
 * @param sumValues A list of summary statistic values to store in the CHP file header.
*/
static void CreateFileWithHeader
(
	const string &execId,
	const string &celFile,
	const string &outFile,
	const vector<string>& extraColNames,
	const vector<string>& extraColTypes,
	unsigned long numEntries,
	int maxProbeSetNameLength,
	const string &algName,
	const string &algVersion,
	const string &chipType,
	const string &programName,
	const string &programVersion,
	const string &programCompany,
	const vector<string>& paramNames,
	const vector<string>& paramValues,
	const vector<string>& sumNames,
	const vector<string>& sumValues,
	const vector<string>& extraNames,
	const vector<string>& extraValues
)
{
	// Create the vector of extra columns. The sample code here supports only float, 32 bit integers and 8 bit unsigned integers.
	vector<ColumnInfo> extraColumns;
	int ncols = (int)extraColNames.size();
	for (int icol=0; icol<ncols; icol++)
	{
		if (extraColTypes[icol] == "float")
		{
			FloatColumn fcol(StringUtils::ConvertMBSToWCS(extraColNames[icol]));
			extraColumns.push_back(fcol);
		}
		else if (extraColTypes[icol] == "int")
		{
			IntColumn intcol(StringUtils::ConvertMBSToWCS(extraColNames[icol]));
			extraColumns.push_back(intcol);
		}
		else if (extraColTypes[icol] == "ubyte")
		{
			UByteColumn ubcol(StringUtils::ConvertMBSToWCS(extraColNames[icol]));
			extraColumns.push_back(ubcol);
		}
		else
		{
			throw string("Unsupported column type: ") + extraColTypes[icol];
		}
	}

	// Create the data object
	CHPMultiDataData *data = new CHPMultiDataData(outFile);
    data->SetEntryCount(GenotypeMultiDataType, numEntries, maxProbeSetNameLength, extraColumns);
	data->SetAlgName(StringUtils::ConvertMBSToWCS(algName));
	data->SetAlgVersion(StringUtils::ConvertMBSToWCS(algVersion));
	data->SetArrayType(StringUtils::ConvertMBSToWCS(chipType));

	// Store the CEL header
	if (celFile.length() > 0 && FileUtils::Exists(celFile.c_str()) == true)
	{
		FusionCELData cel;
		cel.SetFileName(celFile.c_str());
        cel.ReadHeader();
	    GenericData *gdata = cel.GetGenericData();
	    if (gdata != NULL)
			data->GetFileHeader()->GetGenericDataHdr()->AddParent(*gdata->Header().GetGenericDataHdr()); 
	    cel.Close();
	}

	// Add algorithm parameters to list.
    ParameterNameValueTypeList params;
    ParameterNameValueType param;
    
	if (programName.empty() == false)
	{
		param.SetName(L"program-name");
		param.SetValueText(StringUtils::ConvertMBSToWCS(programName));
		data->GetGenericData().Header().GetGenericDataHdr()->AddNameValParam(param);
	}

	if (programVersion.empty() == false)
	{
		param.SetName(L"program-version");
		param.SetValueText(StringUtils::ConvertMBSToWCS(programVersion));
		data->GetGenericData().Header().GetGenericDataHdr()->AddNameValParam(param);
	}

	if (programCompany.empty() == false)
	{
		param.SetName(L"program-company");
		param.SetValueText(StringUtils::ConvertMBSToWCS(programCompany));
		data->GetGenericData().Header().GetGenericDataHdr()->AddNameValParam(param);
	}

	int nparams = (int) extraNames.size();
	for(int iparam=0; iparam<nparams; iparam++)
	{
		param.SetName(StringUtils::ConvertMBSToWCS(extraNames[iparam]));
        param.SetValueAscii(extraValues[iparam]);
        data->GetGenericData().Header().GetGenericDataHdr()->AddNameValParam(param);
	}

	nparams = (int) paramNames.size();
	param.SetName(L"exec-guid");
	param.SetValueAscii(execId);
	params.push_back(param);
	for(int iparam=0; iparam<nparams; iparam++)
	{
		param.SetName(StringUtils::ConvertMBSToWCS(paramNames[iparam]));
        param.SetValueAscii(paramValues[iparam]);
        params.push_back(param);
	}
	if (params.empty() == false)
		data->AddAlgParams(params);

	params.clear();
	nparams = (int) sumNames.size();
	for(int iparam=0; iparam<nparams; iparam++)
	{
		param.SetName(StringUtils::ConvertMBSToWCS(sumNames[iparam]));
        param.SetValueAscii(sumValues[iparam]);
        params.push_back(param);
	}
	if (params.empty() == false)
		data->AddSummaryParams(params);

	// Creating the writer object will create the file with the header information.
	CHPMultiDataFileWriter writer(*data);
}