/* * Store the start index and count of probe sets for the given chromosome. */ void CopyNumberResultWriter::SetChromosomeProbeSetIndexInformation(u_int8_t chr, int startIndex, int count) { ostringstream str; str << (int) chr; wstring schr = StringUtils::ConvertMBSToWCS(str.str()); ParameterNameValueType param; param.SetName(schr + L":start"); param.SetValueInt32(startIndex); chrStartStop.push_back(param); param.SetName(schr + L":count"); param.SetValueInt32(count); chrStartStop.push_back(param); param.SetName(schr + L":display"); param.SetValueAscii(ChromosomeToString(chr)); chrStartStop.push_back(param); }
void CHPData::SetInt32ToGenericHdr(const std::wstring& name, int32_t value) { ParameterNameValueType paramType; paramType.SetName(name); paramType.SetValueInt32(value); GenericDataHeader* hdr = genericData.Header().GetGenericDataHdr(); hdr->AddNameValParam(paramType); }
void TestFileGenerator::WriteSmallDatFileWithGridAndSubgridsAndParameters() { std::string filename = "small_DAT_file_with_subgrids_and_parameters"; WriteDatFile(filename, L"Hg-small", 4, 5, true); DATData data(filename); AddGridAndSubgrids(data, 2.5, 10); ParameterNameValueType nvt; nvt.SetName(L"Zip Code"); nvt.SetValueInt32(95051); data.AddGridAlignmentAlgorithmParameter(nvt); nvt.SetName(L"County"); nvt.SetValueText(L"Santa Clara"); data.AddGridAlignmentAlgorithmParameter(nvt); DATFileUpdater update(data); update.Update(); }
/** * No more probesets will be processed, this is a chance to finish outputting * results and clean up. * @param qMethod - Quantification method that was used. * @return true if success, false otherwise. */ bool QuantMethodExprCCCHPReport::finish(QuantMethod &qMethod) { // Sanity to check we saw all the probe sets we were expecting. if (m_CurrentProbeSetCount != m_Info.m_NumProbeSets) { Err::errAbort("QuantMethodExprCCCHPReport::finish() - Expecting: " + ToStr(m_Info.m_NumProbeSets) + " but got: " + ToStr(m_CurrentProbeSetCount) + ". Command Console CHP file will be corrupt."); } // Flush remaining signal entries in the buffer. m_ExpressionQuantificationBufferWriter.FlushBuffer(); // Rewrite CHP files to get chip summary entires Verbose::out(1,"Creating final files for CHP output"); Verbose::progressBegin(1, ToStr("Finalizing Expression CHP Files"), m_CHPFileNames.size(), 1, m_CHPFileNames.size()); try { for (unsigned int chip = 0; chip < m_CHPFileNames.size(); chip++) { // open up tmp chp file to pull results from GenericData data; GenericFileReader reader; std::string filename = m_CHPFileNames[chip]+".tmp"; reader.SetFilename(filename); reader.ReadHeader(data); GenericDataHeader* hdr = data.Header().GetGenericDataHdr(); GenericDataHeader updateHdr; 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++) { ChipSummary::Metric metric; if (!m_ChipSummaries[source]->getMetric(chip, metricDefs[i].m_name, metric)) { Err::errAbort("QuantMethodExprCCCHPReport: metric '" + metricDefs[i].m_name + "' was not found"); } std::wstring mName(CHIP_SUMMARY_PARAMETER_NAME_PREFIX); mName += StringUtils::ConvertMBSToWCS(metric.m_Name); ParameterNameValueType param; if (hdr->FindNameValParam(mName, param) == false) { Err::errAbort("QuantMethodExprCCCHPReport: metric name '" + StringUtils::ConvertWCSToMBS(mName) + "' could not be found in the header of " + filename); } switch (param.GetParameterType()) { case ParameterNameValueType::Int8Type: param.SetValueInt8((int8_t)metric.m_Integer); break; case ParameterNameValueType::UInt8Type: param.SetValueUInt8((u_int8_t)metric.m_Integer); break; case ParameterNameValueType::Int16Type: param.SetValueInt16((int16_t)metric.m_Integer); break; case ParameterNameValueType::UInt16Type: param.SetValueUInt16((u_int16_t)metric.m_Integer); break; case ParameterNameValueType::Int32Type: param.SetValueInt32((int32_t)metric.m_Integer); break; case ParameterNameValueType::UInt32Type: param.SetValueUInt32((u_int32_t)metric.m_Integer); break; case ParameterNameValueType::FloatType: param.SetValueFloat((float)metric.m_Double); break; case ParameterNameValueType::TextType: param.SetValueText(StringUtils::ConvertMBSToWCS(metric.m_String), (int) metric.m_String.length()); break; case ParameterNameValueType::AsciiType: if (metric.m_String.size() > 256) { Err::errAbort("QuantMethodExprCCCHPReport: string header parameter too long, name = '" + metric.m_Name + "', value = '" + metric.m_String + "'"); } param.SetValueAscii(metric.m_String, (int) metric.m_String.length()); break; default: Err::errAbort("QuantMethodExprCCCHPReport: unknown header parameter type found in file " + filename); } updateHdr.AddNameValParam(param); } } std::ofstream os; Fs::aptOpen(os, filename, std::ios::out|std::ios::binary|std::ios::in); if (!os) { Err::errAbort("QuantMethodExprCCCHPReport: file " + filename + " could not be opened for writing"); } GenericDataHeaderUpdater updater; updater.Update(os, updateHdr, *hdr); os.close(); Verbose::progressStep(1); } } catch (...) { removeAllChps(); Err::errAbort("Error in creating final CHP output."); } Verbose::progressEnd(1, ToStr("Done.")); // Remove .tmp extension for (unsigned int i = 0; i < m_CHPFileNames.size(); i++) { std::string from = m_CHPFileNames[i] + ".tmp"; std::string to = m_CHPFileNames[i]; if (!Fs::fileRename(from.c_str(),to.c_str())) { removeAllChps(); Err::errAbort("Unable to rename '" + from + "' to '" + to + "'"); } } removeTmpChps(); return true; }
/** * 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; }
void CalvinCHPMultiDataFileUpdaterTest::CreateReferenceFile2() { CHPMultiDataData data(TEST2_FILE); vector<ColumnInfo> cols; ParameterNameValueType nv; ByteColumn bcol(L"byte"); cols.push_back(bcol); UByteColumn ubcol(L"ubyte"); cols.push_back(ubcol); ShortColumn scol(L"short"); cols.push_back(scol); UShortColumn uscol(L"ushort"); cols.push_back(uscol); IntColumn icol(L"int"); cols.push_back(icol); UIntColumn uicol(L"uint"); cols.push_back(uicol); FloatColumn fcol(L"float"); cols.push_back(fcol); ASCIIColumn acol(L"ascii", 7); cols.push_back(acol); UnicodeColumn tcol(L"text", 10); cols.push_back(tcol); ProbeSetMultiDataGenotypeData e; data.SetEntryCount(GenotypeMultiDataType, 4, 10, cols); CHPMultiDataFileWriter *writer = new CHPMultiDataFileWriter(data); nv.SetName(L"byte"); nv.SetValueInt8(8); e.metrics.push_back(nv); nv.SetName(L"ubyte"); nv.SetValueUInt8(8); e.metrics.push_back(nv); nv.SetName(L"short"); nv.SetValueInt16(16); e.metrics.push_back(nv); nv.SetName(L"ushort"); nv.SetValueUInt16(16); e.metrics.push_back(nv); nv.SetName(L"int"); nv.SetValueInt32(32); e.metrics.push_back(nv); nv.SetName(L"uint"); nv.SetValueUInt32(32); e.metrics.push_back(nv); nv.SetName(L"float"); nv.SetValueFloat(44.0f); e.metrics.push_back(nv); nv.SetName(L"ascii"); nv.SetValueAscii("ascii"); e.metrics.push_back(nv); nv.SetName(L"text"); nv.SetValueText(L"text"); e.metrics.push_back(nv); writer->SeekToDataSet(GenotypeMultiDataType); e.name = "1"; e.call = 1; e.confidence = 10.0f; writer->WriteEntry(e); e.name = "2"; e.call = 2; e.confidence = 20.0f; writer->WriteEntry(e); e.name = "3"; e.call = 3; e.confidence = 30.0f; writer->WriteEntry(e); e.name = "4"; e.call = 4; e.confidence = 40.0f; writer->WriteEntry(e); delete writer; }
void CalvinCHPMultiDataFileUpdaterTest::CreateReferenceFile3() { CHPMultiDataData data(TEST3_FILE); vector<ColumnInfo> cols; ParameterNameValueType nv; ByteColumn bcol(L"byte"); cols.push_back(bcol); UByteColumn ubcol(L"ubyte"); cols.push_back(ubcol); ShortColumn scol(L"short"); cols.push_back(scol); UShortColumn uscol(L"ushort"); cols.push_back(uscol); IntColumn icol(L"int"); cols.push_back(icol); UIntColumn uicol(L"uint"); cols.push_back(uicol); FloatColumn fcol(L"float"); cols.push_back(fcol); ASCIIColumn acol(L"ascii", 7); cols.push_back(acol); UnicodeColumn tcol(L"text", 10); cols.push_back(tcol); ProbeSetMultiDataCopyNumberData e; ProbeSetMultiDataCytoRegionData c; data.SetEntryCount(CopyNumberMultiDataType, 4, 10, cols); data.SetEntryCount(CytoMultiDataType, 2, 10); CHPMultiDataFileWriter *writer = new CHPMultiDataFileWriter(data); nv.SetName(L"byte"); nv.SetValueInt8(8); e.metrics.push_back(nv); nv.SetName(L"ubyte"); nv.SetValueUInt8(8); e.metrics.push_back(nv); nv.SetName(L"short"); nv.SetValueInt16(16); e.metrics.push_back(nv); nv.SetName(L"ushort"); nv.SetValueUInt16(16); e.metrics.push_back(nv); nv.SetName(L"int"); nv.SetValueInt32(32); e.metrics.push_back(nv); nv.SetName(L"uint"); nv.SetValueUInt32(32); e.metrics.push_back(nv); nv.SetName(L"float"); nv.SetValueFloat(44.0f); e.metrics.push_back(nv); nv.SetName(L"ascii"); nv.SetValueAscii("ascii"); e.metrics.push_back(nv); nv.SetName(L"text"); nv.SetValueText(L"text"); e.metrics.push_back(nv); writer->SeekToDataSet(CopyNumberMultiDataType); e.name = "1"; e.chr = 1; e.position = 10; writer->WriteEntry(e); e.name = "2"; e.chr = 2; e.position = 20; writer->WriteEntry(e); e.name = "3"; e.chr = 3; e.position = 30; writer->WriteEntry(e); e.name = "4"; e.chr = 4; e.position = 40; writer->WriteEntry(e); writer->SeekToDataSet(CytoMultiDataType); c.name = "1"; c.chr= 1; c.startPosition = 1; c.stopPosition = 2; c.call = 1; c.confidenceScore = 10.0f; writer->WriteEntry(c); c.name = "2"; c.chr= 2; c.startPosition = 2; c.stopPosition = 3; c.call = 2; c.confidenceScore = 20.0f; writer->WriteEntry(c); delete writer; }
void TestFileGenerator::WriteRemaingSmallCelFileWithGridParameters(CelFileData& data) { data.SetIntensityCount(25); data.SetStdDevCount(25); data.SetPixelCount(25); data.SetOutlierCount(2); data.SetMaskCount(3); data.SetRows(5); data.SetCols(5); data.SetArrayType(L"Hg-small"); data.SetLibraryPackageName(L"Hg-small-lib-package"); data.SetMasterFileName(L"Hg-small-master-file"); data.SetAlgorithmName(L"Feature Extraction"); ParameterNameValueType nvt; nvt.SetName(L"percentile"); nvt.SetValueFloat(0.75f); data.AddAlgorithmParameter(nvt); nvt.SetName(L"outlierlow"); nvt.SetValueFloat(1.004f); data.AddAlgorithmParameter(nvt); nvt.SetName(L"CellMargin"); nvt.SetValueInt32(2); data.AddAlgorithmParameter(nvt); // Add grid wchar_t* gridParams[] = {L"GridULX", L"GridULY", L"GridURX", L"GridURY", L"GridLRX", L"GridLRY", L"GridLLX", L"GridLLY" }; for (int32_t i = 0; i < 8; ++i) { nvt.SetName(gridParams[i]); nvt.SetValueFloat(2.0f + (float)i); data.AddAlgorithmParameter(nvt); } CelFileWriter* writer = new CelFileWriter(data); FloatVector vInten; FloatVector vStdev; Int16Vector vPixels; for (int i=0; i<25; ++i) { vInten.push_back(100.0f*i); vStdev.push_back(.5*i); vPixels.push_back(25); } // Do some writing writer->WriteIntensities(vInten); writer->WriteStdDevs(vStdev); writer->WritePixels(vPixels); // XYCoordVector XYCoordVector outlier; XYCoord xy(0,0); outlier.push_back(xy); xy.xCoord = 1; xy.yCoord = 2; outlier.push_back(xy); writer->WriteOutlierCoords(outlier); XYCoordVector masked; xy.xCoord = 1; xy.yCoord = 0; masked.push_back(xy); xy.xCoord = 2; xy.yCoord = 1; masked.push_back(xy); xy.xCoord = 3; xy.yCoord = 2; masked.push_back(xy); writer->WriteMaskCoords(masked); delete writer; }