public void FeatureFind(List <ProteinSpectrumMatch> prsms, LcMsRun run, string outTsvFilePath)
{
var featureFinder = new LcMsPeakMatrix(run, new LcMsFeatureLikelihood());
// write result files
var tsvWriter = new StreamWriter(outTsvFilePath);
tsvWriter.WriteLine(LcMsFeatureFinderLauncher.GetHeaderString(false));
var featureId = 1;
foreach (var match in prsms)
{
var minScan = run.GetPrevScanNum(match.ScanNum, 1);
var maxScan = run.GetNextScanNum(match.ScanNum, 1);
var feature = featureFinder.GetLcMsPeakCluster(match.Mass, match.Charge, minScan, maxScan);
if (feature == null)
{
continue;
}
tsvWriter.WriteLine("{0}\t{1}", featureId, LcMsFeatureFinderLauncher.GetString(feature, false));
featureId++;
}
tsvWriter.Close();
}
public void TestGeneratingMs1FeatureFile()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string specFilePath = @"\\proto-11\MSXML_Cache\PBF_Gen_1_193\2015_2\QC_ShewIntact_1_19Jun15_Bane_14-09-01RZ.pbf";
if (!File.Exists(specFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, specFilePath);
}
const string outFolderPath = @"\\proto-2\UnitTest_Files\InformedProteomics_TestFiles\Output";
if (!Directory.Exists(outFolderPath))
{
Assert.Ignore(@"Skipping test {0} since folder not found: {1}", methodName, outFolderPath);
}
//const string specFilePath = @"D:\MassSpecFiles\test\QC_Shew_Intact_4_01Jan15_Bane_C2-14-08-02RZ.raw";
const int minScanCharge = 2;
const int maxScanCharge = 60;
const double minScanMass = 3000;
const double maxScanMass = 5000;
const int maxThreads = 10;
var param = new LcMsFeatureFinderInputParameter()
{
InputPath = specFilePath,
OutputPath = outFolderPath,
MinSearchMass = minScanMass,
MaxSearchMass = maxScanMass,
MinSearchCharge = minScanCharge,
MaxSearchCharge = maxScanCharge,
CsvOutput = true,
ScoreReport = false,
MaxThreads = maxThreads
};
var featureFinder = new LcMsFeatureFinderLauncher(param);
featureFinder.Run();
}
public void TestQuantifyIdedProteoforms()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
const string rawFolder = @"\\proto-11\MSXML_Cache\PBF_Gen_1_193\2015_2";
const string promexOutFolder = @"D:\MassSpecFiles\UTEX\MSAlign";
const string msAlignResultFolder = @"D:\MassSpecFiles\UTEX\MSAlign";
if (!Directory.Exists(rawFolder))
{
Assert.Ignore(@"Skipping test {0} since folder not found: {1}", methodName, rawFolder);
}
var nDataset = 32;
var dataset = new string[nDataset];
for (var i = 0; i < nDataset; i++)
{
dataset[i] = string.Format("Syn_utex2973_Top_{0,2:D2}_TopDown_7May15_Bane_14-09-01RZ", i + 1);
//var rawFile = string.Format(@"{0}\{1}.pbf", rawFolder, dataset[i]);
}
var prsmReader = new ProteinSpectrumMatchReader(0.01);
var filesProcessed = 0;
var tolerance = new Tolerance(10);
for (var i = 0; i < dataset.Length; i++)
{
var rawFile = string.Format(@"{0}\{1}.pbf", rawFolder, dataset[i]);
if (!File.Exists(rawFile))
{
Console.WriteLine(@"Warning: Skipping file not found: {0}", rawFile);
continue;
}
var run = PbfLcMsRun.GetLcMsRun(rawFile);
var path = string.Format(@"{0}\{1}_MSAlign_ResultTable.txt", msAlignResultFolder, dataset[i]);
if (!File.Exists(path))
{
Console.WriteLine(@"Warning: Skipping file not found: {0}", path);
continue;
}
var prsmList = prsmReader.LoadIdentificationResult(path, ProteinSpectrumMatch.SearchTool.MsAlign);
filesProcessed++;
for (var j = 0; j < prsmList.Count; j++)
{
var match = prsmList[j];
match.ProteinId = match.ProteinName.Substring(match.ProteinName.IndexOf(ProteinNamePrefix) + ProteinNamePrefix.Length, 5);
}
// PrSM To Feature
var prsmToFeatureIdMap = new int[prsmList.Count];
for (var k = 0; k < prsmToFeatureIdMap.Length; k++)
{
prsmToFeatureIdMap[k] = -1;
}
// Feature To PrSM
var featureToPrsm = new List <ProteinSpectrumMatchSet>();
var featureFinder = new LcMsPeakMatrix(run, new LcMsFeatureLikelihood());
var featureList = new List <LcMsPeakCluster>();
var featureId = 0;
for (var j = 0; j < prsmList.Count; j++)
{
if (prsmToFeatureIdMap[j] >= 0)
{
continue;
}
var match = prsmList[j];
var minScanNum = match.ScanNum;
var maxScanNum = match.ScanNum;
var mass = match.Mass;
var charge = match.Charge;
var massTh = tolerance.GetToleranceAsMz(mass);
var id1 = match.ProteinId;
var feature = featureFinder.GetLcMsPeakCluster(mass, charge, minScanNum, maxScanNum);
var prsmSet = new ProteinSpectrumMatchSet(i)
{
match
};
if (feature == null)
{
feature = featureFinder.GetLcMsPeaksFromNoisePeaks(mass, charge, minScanNum, maxScanNum, charge, charge);
prsmToFeatureIdMap[j] = featureId;
}
else
{
prsmToFeatureIdMap[j] = featureId;
var etTol = Math.Max(run.GetElutionTime(run.MaxLcScan) * 0.005, feature.ElutionLength * 0.2);
for (var k = j + 1; k < prsmList.Count; k++)
{
var otherMatch = prsmList[k];
var id2 = otherMatch.ProteinId;
var et2 = run.GetElutionTime(otherMatch.ScanNum);
if (id1.Equals(id2) &&
feature.MinElutionTime - etTol < et2 && et2 < feature.MaxElutionTime - etTol &&
Math.Abs(otherMatch.Mass - mass) < massTh)
{
prsmToFeatureIdMap[k] = featureId;
prsmSet.Add(otherMatch);
}
}
}
featureId++;
feature.Flag = 1;
featureList.Add(feature);
featureToPrsm.Add(prsmSet);
}
// Overlap between features???
for (var j = 0; j < featureList.Count; j++)
{
var f1 = featureList[j];
if (f1.Flag < 1)
{
continue;
}
var prsm1 = featureToPrsm[j];
for (var k = j + 1; k < featureList.Count; k++)
{
var f2 = featureList[k];
if (f2.Flag < 1)
{
continue;
}
var prsm2 = featureToPrsm[k];
if (Math.Abs(f1.Mass - f2.Mass) > tolerance.GetToleranceAsMz(f1.Mass))
{
continue;
}
if (!f1.CoElutedByNet(f2, 0.005))
{
continue;
}
if (!prsm1.ShareProteinId(prsm2))
{
continue;
}
// let us merge!!
if (f1.ScanLength > f2.ScanLength)
{
prsm1.AddRange(prsm2);
prsm2.Clear();
f2.Flag = 0;
}
else
{
prsm2.AddRange(prsm1);
prsm1.Clear();
f1.Flag = 0;
}
}
}
// now output results!!
var ms1ftFilePath = string.Format(@"{0}\{1}.ms1ft", promexOutFolder, dataset[i]);
var writer = new StreamWriter(ms1ftFilePath);
writer.WriteLine(LcMsFeatureFinderLauncher.GetHeaderString());
for (var j = 0; j < featureList.Count; j++)
{
var f1 = featureList[j];
if (f1.Flag < 1)
{
continue;
}
var prsm1 = featureToPrsm[j];
var minScanNum = run.GetPrevScanNum(prsm1.MinScanNum, 1);
var maxScanNum = run.GetNextScanNum(prsm1.MaxScanNum, 1);
f1.ExpandScanRange(minScanNum, maxScanNum);
writer.Write("{0}\t", j + 1);
writer.WriteLine(LcMsFeatureFinderLauncher.GetString(f1));
}
writer.Close();
Console.WriteLine(ms1ftFilePath);
}
if (filesProcessed == 0)
{
Assert.Ignore("Skipped since data files not found");
}
}
public void TestAlignFeatures()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
const string rawFolder = @"\\proto-11\MSXML_Cache\PBF_Gen_1_193\2015_2";
const string promexOutFolder = @"D:\MassSpecFiles\UTEX\MSAlign";
const string msAlignResultFolder = @"D:\MassSpecFiles\UTEX\MSAlign";
if (!Directory.Exists(rawFolder))
{
Assert.Ignore(@"Skipping test {0} since folder not found: {1}", methodName, rawFolder);
}
var nDataset = 32;
var dataset = new string[nDataset];
for (var i = 0; i < nDataset; i++)
{
dataset[i] = string.Format("Syn_utex2973_Top_{0,2:D2}_TopDown_7May15_Bane_14-09-01RZ", i + 1);
//var rawFile = string.Format(@"{0}\{1}.pbf", rawFolder, dataset[i]);
}
var tolerance = new Tolerance(10);
var ftComparer = new UtexFeatureComparer(tolerance);
var align = new LcMsFeatureAlignment(ftComparer);
var prsmReader = new ProteinSpectrumMatchReader(0.01);
var filesProcessed = 0;
for (var i = 0; i < dataset.Length; i++)
{
var rawFile = string.Format(@"{0}\{1}.pbf", rawFolder, dataset[i]);
if (!File.Exists(rawFile))
{
Console.WriteLine(@"Warning: Skipping file not found: {0}", rawFile);
continue;
}
var run = PbfLcMsRun.GetLcMsRun(rawFile);
var path = string.Format(@"{0}\{1}_MSAlign_ResultTable.txt", msAlignResultFolder, dataset[i]);
if (!File.Exists(path))
{
Console.WriteLine(@"Warning: Skipping file not found: {0}", path);
continue;
}
var ms1ftPath = string.Format(@"{0}\{1}.ms1ft", promexOutFolder, dataset[i]);
if (!File.Exists(ms1ftPath))
{
Console.WriteLine(@"Warning: Skipping file not found: {0}", ms1ftPath);
continue;
}
filesProcessed++;
//var map = new ProteinSpectrumMathMap(run, i, dataset[i]);
//map.LoadIdentificationResult(path, ProteinSpectrumMatch.SearchTool.MsAlign);
var prsmList = prsmReader.LoadIdentificationResult(path, ProteinSpectrumMatch.SearchTool.MsAlign);
for (var j = 0; j < prsmList.Count; j++)
{
var match = prsmList[j];
match.ProteinId =
match.ProteinName.Substring(
match.ProteinName.IndexOf(ProteinNamePrefix) + ProteinNamePrefix.Length, 5);
}
var features = LcMsFeatureAlignment.LoadProMexResult(i, ms1ftPath, run);
// tag features by PrSMs
for (var j = 0; j < features.Count; j++)
{
//features[j].ProteinSpectrumMatches = new ProteinSpectrumMatchSet(i);
var massTol = tolerance.GetToleranceAsMz(features[j].Mass);
foreach (var match in prsmList)
{
if (features[j].MinScanNum < match.ScanNum && match.ScanNum < features[j].MaxScanNum && Math.Abs(features[j].Mass - match.Mass) < massTol)
{
features[j].ProteinSpectrumMatches.Add(match);
}
}
}
align.AddDataSet(i, features, run);
}
if (filesProcessed == 0)
{
Assert.Ignore("Skipped since input files not found");
}
align.AlignFeatures();
Console.WriteLine("{0} alignments ", align.CountAlignedFeatures);
align.RefineAbundance();
var alignedFeatureList = align.GetAlignedFeatures();
for (var i = 0; i < nDataset; i++)
{
var ms1ftPath = string.Format(@"{0}\{1}_aligned.ms1ft", promexOutFolder, dataset[i]);
var writer = new StreamWriter(ms1ftPath);
writer.Write(LcMsFeatureFinderLauncher.GetHeaderString());
writer.WriteLine("\tIdedMs2ScanNums");
for (var j = 0; j < alignedFeatureList.Count; j++)
{
writer.Write(j + 1);
writer.Write("\t");
if (alignedFeatureList[j][i] == null)
{
for (var k = 0; k < 14; k++)
{
writer.Write("0\t");
}
writer.Write("0\n");
}
else
{
writer.Write(LcMsFeatureFinderLauncher.GetString(alignedFeatureList[j][i]));
writer.Write("\t");
if (alignedFeatureList[j][i].ProteinSpectrumMatches == null)
{
writer.Write("");
}
else
{
var scanNums = string.Join(";", alignedFeatureList[j][i].ProteinSpectrumMatches.Select(prsm => prsm.ScanNum));
writer.Write(scanNums);
}
writer.Write("\n");
}
}
writer.Close();
}
}
private void OutputAlignmentResult(LcMsFeatureAlignment align, string outFilePath, IReadOnlyList <string> rawFiles, bool isTemp = true)
{
var alignedFeatureList = align.GetAlignedFeatures();
var writer = new StreamWriter(outFilePath);
writer.Write("MonoMass\tMinElutionTime\tMaxElutionTime");
for (var i = 0; i < align.CountDatasets; i++)
{
var dataSetName = Path.GetFileNameWithoutExtension(rawFiles[i]);
writer.Write("\t{0}", dataSetName);
}
for (var i = 0; i < align.CountDatasets; i++)
{
//var dataSetName = Path.GetFileNameWithoutExtension(align.RawFileList[i]);
writer.Write("\t{0}_Score", i);
}
/*
* for (var i = 0; i < align.CountDatasets; i++)
* {
* //var dataSetName = Path.GetFileNameWithoutExtension(align.RawFileList[i]);
* writer.Write("\t{0}_Net", i);
* }*/
writer.Write("\n");
for (var i = 0; i < align.CountAlignedFeatures; i++)
{
var features = alignedFeatureList[i];
var minMaxNet = GetMinMaxNet(features);
writer.Write(@"{0}\t{1:0.00000}\t{2:0.00000}", minMaxNet.Item1, minMaxNet.Item3, minMaxNet.Item4);
for (var j = 0; j < align.CountDatasets; j++)
{
var feature = features[j];
writer.Write("\t");
writer.Write(feature?.Abundance ?? 0d);
}
for (var j = 0; j < align.CountDatasets; j++)
{
var feature = features[j];
writer.Write("\t");
writer.Write(feature?.Score ?? 0d);
}
/*
* for (var j = 0; j < align.CountDatasets; j++)
* {
* var feature = features[j];
* writer.Write("\t");
* if (feature != null) writer.Write("{0:0.00000}", feature.MinNet);
* else writer.Write(0);
* }
*
* for (var j = 0; j < align.CountDatasets; j++)
* {
* var feature = features[j];
* writer.Write("\t");
* if (feature != null) writer.Write("{0:0.00000}", feature.MaxNet);
* else writer.Write(0);
* }*/
writer.Write("\n");
}
writer.Close();
if (isTemp)
{
return;
}
var outDirectory = Path.GetDirectoryName(Path.GetFullPath(outFilePath));
for (var i = 0; i < align.CountDatasets; i++)
{
var dataSetName = Path.GetFileNameWithoutExtension(rawFiles[i]);
//writer.Write("\t{0}", dataSetName);
// now output results!!
var ms1ftFilePath = string.Format(@"{0}\{1}.aligned.ms1ft", outDirectory, dataSetName);
var writer2 = new StreamWriter(ms1ftFilePath);
writer2.WriteLine(LcMsFeatureFinderLauncher.GetHeaderString());
for (var j = 0; j < align.CountAlignedFeatures; j++)
{
var f1 = alignedFeatureList[j][i];
writer2.Write("{0}\t", j + 1);
writer2.WriteLine(LcMsFeatureFinderLauncher.GetString(f1));
}
writer2.Close();
}
}
static int Main(string[] args)
{
LcMsFeatureFinderInputParameters parameters;
try
{
var osVersionInfo = new clsOSVersionInfo();
if (osVersionInfo.GetOSVersion().ToLower().Contains("windows"))
{
var handle = Process.GetCurrentProcess().MainWindowHandle;
SetConsoleMode(handle, EnableExtendedFlags);
}
//args = new string[] {"-i", @"D:\MassSpecFiles\training\raw\QC_Shew_Intact_26Sep14_Bane_C2Column3.pbf", "-minMass", "3000", "-maxMass", "30000"};
var parser = new CommandLineParser <ProMexInputParameters>(Name, Version);
parser.UsageExamples.Add("To create a PNG of the features in an existing ms1ft file " +
"(requires both a .pbf file and a .ms1ft file):\n\tProMex.exe -i dataset.pbf -ms1ft dataset.ms1ft -featureMap");
var results = parser.ParseArgs(args);
if (!results.Success)
{
// Wait for 1.5 seconds
System.Threading.Thread.Sleep(1500);
return(-1);
}
if (!results.ParsedResults.Validate())
{
parser.PrintHelp();
// Wait for 1.5 seconds
System.Threading.Thread.Sleep(1500);
return(-1);
}
parameters = results.ParsedResults;
}
catch (Exception ex)
{
Console.WriteLine("Exception while parsing the command line parameters: " + ex.Message);
return(-5);
}
#if (!DEBUG)
try
{
#endif
// Example text: ProMex version 1.0.6527 (November 14, 2017)
// (the build date is computed automatically)
Console.WriteLine("************ {0} {1} ************", Name, Version);
parameters.Display();
var launcher = new LcMsFeatureFinderLauncher(parameters);
int errorCode;
if (string.IsNullOrWhiteSpace(parameters.ExistingFeaturesFilePath))
{
errorCode = launcher.Run();
}
else
{
errorCode = launcher.CreateFeatureMapImage(parameters.InputPath, parameters.ExistingFeaturesFilePath);
}
return(errorCode);
#if (!DEBUG)
}
catch (Exception ex)
{
// NOTE: The DMS Analysis Manager looks for this text; do not change it
Console.WriteLine("Exception while processing: " + ex.Message);
Console.WriteLine(ex.StackTrace);
var errorCode = -Math.Abs(ex.Message.GetHashCode());
if (errorCode == 0)
{
return(-1);
}
return(errorCode);
}
#endif
}
static int Main(string[] args)
{
try
{
var handle = Process.GetCurrentProcess().MainWindowHandle;
SetConsoleMode(handle, EnableExtendedFlags);
//args = new string[] {"-i", @"D:\MassSpecFiles\training\raw\QC_Shew_Intact_26Sep14_Bane_C2Column3.pbf", "-minMass", "3000", "-maxMass", "30000"};
if (args.Length == 0)
{
PrintUsageInfo();
return(-1);
}
if (args.Length % 2 != 0)
{
PrintUsageInfo("The number of arguments must be even.");
return(-1);
}
// initialize parameters
_paramDic = new Dictionary <string, string>
{
{ LcMsFeatureFinderInputParameter.INPUT_FILE_PATH, null },
{ LcMsFeatureFinderInputParameter.OUTPUT_FOLDER_PATH, null },
{ LcMsFeatureFinderInputParameter.MINIMUM_CHARGE, "1" },
{ LcMsFeatureFinderInputParameter.MAXIMUM_CHARGE, "60" },
{ LcMsFeatureFinderInputParameter.MINIMUM_MASS, "2000.0" },
{ LcMsFeatureFinderInputParameter.MAXIMUM_MASS, "50000.0" },
{ LcMsFeatureFinderInputParameter.INCLUDE_ADDITIONAL_SCORES, "n" },
{ LcMsFeatureFinderInputParameter.SAVE_CSV, "n" },
{ LcMsFeatureFinderInputParameter.SAVE_PNG_FEATURE_MAP, "y" },
{ LcMsFeatureFinderInputParameter.LIKELIHOOD_SCORE_THRESHOLD, "-10" },
{ LcMsFeatureFinderInputParameter.MAXIMUM_THREADS, "0" },
{ LcMsFeatureFinderInputParameter.EXISTING_MS1FT_FILE, "" }
};
for (var i = 0; i < args.Length / 2; i++)
{
var key = args[2 * i];
var value = args[2 * i + 1];
if (!_paramDic.ContainsKey(key))
{
PrintUsageInfo("Invalid parameter: " + key);
return(-1);
}
_paramDic[key] = value;
}
// Parse command line parameters
var inputFilePath = _paramDic["-i"];
if (inputFilePath == null)
{
PrintUsageInfo("Missing required parameter -i!");
return(-1);
}
if (!File.Exists(inputFilePath) && !Directory.Exists(inputFilePath))
{
PrintUsageInfo("File not found: " + inputFilePath);
return(-1);
}
}
catch (Exception ex)
{
Console.WriteLine("Exception while parsing the command line parameters: " + ex.Message);
return(-5);
}
#if (!DEBUG)
try
{
#endif
var param = new LcMsFeatureFinderInputParameter(_paramDic);
Console.WriteLine("************ {0} {1} ************", Name, Version);
param.Display();
var launcher = new LcMsFeatureFinderLauncher(param);
int errorCode;
if (string.IsNullOrWhiteSpace(param.ExistingFeaturesFilePath))
{
errorCode = launcher.Run();
}
else
{
errorCode = launcher.CreateFeatureMapImage(param.InputPath, param.ExistingFeaturesFilePath);
}
return(errorCode);
#if (!DEBUG)
}
catch (Exception ex)
{
// NOTE: The DMS Analysis Manager looks for this text; do not change it
Console.WriteLine("Exception while processing: " + ex.Message);
Console.WriteLine(ex.StackTrace);
var errorCode = -Math.Abs(ex.Message.GetHashCode());
if (errorCode == 0)
{
return(-1);
}
return(errorCode);
}
#endif
}
