示例#1
0
        public void BuildMzqcAndWrite(string path, Run run, Dictionary <string, dynamic> qcParams, string inputFileInclPath)
        {
            List <JsonClasses.QualityParameters> qualityParameters = new List <JsonClasses.QualityParameters>();

            foreach (var metric in qcParams)
            {
                var matchingMetric = QualityParameterLookup.SingleOrDefault(x => x.accession == metric.Key);
                if (matchingMetric != null)
                {
                    matchingMetric.value = metric.Value;
                    qualityParameters.Add(matchingMetric);
                }
                else
                {
                    Logger.Warn("Term \"{0}\" was not found in the MZQC definition when attempting to write output. This term was ignored.", metric.Key);
                }
            }
            //Now for the other stuff
            JsonClasses.FileFormat fileFormat = new JsonClasses.FileFormat()
            {
            };
            List <JsonClasses.FileProperties> fileProperties = new List <JsonClasses.FileProperties>()
            {
            };


            JsonClasses.FileProperties fileProperty   = new JsonClasses.FileProperties("MS", run.FilePropertiesAccession, "SHA-1", run.SourceFileChecksums.First());
            JsonClasses.FileProperties completionTime = new JsonClasses.FileProperties("MS", "MS:1000747", "completion time", run.CompletionTime);
            fileProperties.Add(fileProperty);

            List <JsonClasses.InputFiles> inputFiles = new List <JsonClasses.InputFiles>();

            JsonClasses.InputFiles inputFile = new JsonClasses.InputFiles("file://" + inputFileInclPath, run.SourceFileNames.First(), fileFormat, fileProperties);
            inputFiles.Add(inputFile);

            List <JsonClasses.AnalysisSoftware> analysisSoftwarelist = new List <JsonClasses.AnalysisSoftware>();

            JsonClasses.AnalysisSoftware analysisSoftware = new JsonClasses.AnalysisSoftware()
            {
                cvRef = "MS", accession = "XXXXXXXXXXXXXX", name = "SwaMe", uri = "https://github.com/PaulBrack/Yamato/tree/master/Console", version = "1.0"
            };
            analysisSoftwarelist.Add(analysisSoftware);
            JsonClasses.MetaData metadata = new JsonClasses.MetaData()
            {
                inputFiles = inputFiles, analysisSoftware = analysisSoftwarelist
            };
            JsonClasses.RunQuality runQualitySingle = new JsonClasses.RunQuality()
            {
                metadata = metadata, qualityParameters = qualityParameters.ToArray()
            };
            List <JsonClasses.RunQuality> runQuality = new List <JsonClasses.RunQuality>();

            runQuality.Add(runQualitySingle);
            JsonClasses.NUV qualityControl = new JsonClasses.NUV()
            {
                name = "Proteomics Standards Initiative Quality Control Ontology", uri = "https://raw.githubusercontent.com/HUPO-PSI/mzqc/master/cv/v0_0_11/qc-cv.obo", version = "0.1.0"
            };
            JsonClasses.NUV massSpectrometry = new JsonClasses.NUV()
            {
                name = "Proteomics Standards Initiative Mass Spectrometry Ontology", uri = "https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo", version = "4.1.7"
            };
            JsonClasses.NUV UnitOntology = new JsonClasses.NUV()
            {
                name = "Unit Ontology", uri = "https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo", version = "09:04:2014 13:37"
            };
            JsonClasses.CV cV = new JsonClasses.CV()
            {
                QC = qualityControl, MS = massSpectrometry, UO = UnitOntology
            };
            JsonClasses.MzQC metrics = new JsonClasses.MzQC()
            {
                runQuality = runQuality, cv = cV
            };

            //Then save:
            WriteMzqc(path, metrics);
        }
示例#2
0
        /// <param name="outputFileName">The path to the output file to be opened, or null to send to stdout</param>
        public void BuildMzqcAndWrite(string outputFileName, Run <Scan> run, Dictionary <string, dynamic> qcParams, string inputFileInclPath, object analysisSettings)
        {
            List <JsonClasses.QualityParameters> qualityParameters = new List <JsonClasses.QualityParameters>();

            foreach (var metric in qcParams)
            {
                // Note that this code smashes a value into the given QualityParameters; this will fail if the same one is used more than once, or the initialisation of those parameters is made static.
                if (QualityParametersByAccession.TryGetValue(metric.Key, out var matchingMetric))
                {
                    matchingMetric.value = metric.Value;
                    qualityParameters.Add(matchingMetric);
                }
                else
                {
                    Logger.Warn("Term \"{0}\" was not found in the MZQC definition when attempting to write output. This term was ignored.", metric.Key);
                }
            }
            //Now for the other stuff

            JsonClasses.InputFiles inputFile = new JsonClasses.InputFiles(
                "file://" + inputFileInclPath,
                run.SourceFileNames.First(),
                ToFileFormat(ms, "MS:1000584"),
                new List <JsonClasses.FileProperties>()
            {
                // ToFileProperties("MS", "MS:1000747", run.CompletionTime), // TODO: Include this?
                ToFileProperties(ms, run.FilePropertiesAccession, run.SourceFileChecksums.First())
            }
                );

            Term swaMe = ms.GetById("XXXXXXXXXXXXXX");

            JsonClasses.AnalysisSoftware analysisSoftware = new JsonClasses.AnalysisSoftware()
            {
                cvRef            = ms.PrimaryNamespace,
                accession        = swaMe.Id,
                name             = swaMe.Name,
                uri              = "https://github.com/PaulBrack/Yamato/tree/master/Console",
                version          = typeof(MzqcWriter).Assembly.GetName().Version.ToString(),
                analysisSettings = analysisSettings
            };

            JsonClasses.MzQC metrics = new JsonClasses.MzQC()
            {
                version    = "0.0.11",
                runQuality = new List <JsonClasses.RunQuality>
                {
                    new JsonClasses.RunQuality()
                    {
                        metadata = new JsonClasses.MetaData()
                        {
                            inputFiles = new List <JsonClasses.InputFiles>()
                            {
                                inputFile
                            },
                            analysisSoftware = new List <JsonClasses.AnalysisSoftware>()
                            {
                                analysisSoftware
                            }
                        },
                        qualityParameters = qualityParameters.ToArray()
                    }
                },
                cv = cvLibrary.ControlledVocabularies.ToDictionary(cv => cv.PrimaryNamespace, ToNUV)
            };

            //Then save:
            WriteMzqc(outputFileName, metrics);
        }