private void RunFeatureAlignment(IList <string> ms1FtFiles, IReadOnlyList <string> rawFiles, string outFilePath)
{
var runList = new List <LcMsRun>();
foreach (var rawFile in rawFiles)
{
runList.Add(new PbfLcMsRun(rawFile));
}
var align = new LcMsFeatureAlignment(ms1FtFiles, runList, new LcMsFeatureAlignComparer(new Tolerance(10)));
align.AlignFeatures();
Console.WriteLine("# of aligned features = {0}", align.CountAlignedFeatures);
var tempOutPath = outFilePath + ".tmp";
OutputAlignmentResult(align, tempOutPath, rawFiles, true);
align.RefineAbundance();
OutputAlignmentResult(align, outFilePath, rawFiles, false);
}
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();
}
}
public List <UMCClusterLight> Cluster(List <UMCLight> data, IProgress <ProgressData> progress = null)
{
progress = progress ?? new Progress <ProgressData>();
if (data.Count == 0)
{
return(new List <UMCClusterLight>());
}
this.maxFeatureId = data.Select(d => d.Id).Max();
this.featureMap = new Dictionary <Tuple <int, int>, UMCLight>();
foreach (var feature in data)
{
var key = new Tuple <int, int>(feature.GroupId, feature.Id);
this.featureMap.Add(key, feature);
}
var lcmsFeatureAligner =
new LcMsFeatureAlignment(new LcMsFeatureAlignComparer(new Tolerance(10, ToleranceUnit.Ppm)));
// Group features by dataset
var idToFeatures = new Dictionary <int, List <UMCLight> >();
foreach (var umcLight in data)
{
if (!idToFeatures.ContainsKey(umcLight.GroupId))
{
idToFeatures.Add(umcLight.GroupId, new List <UMCLight>());
}
idToFeatures[umcLight.GroupId].Add(umcLight);
}
// Convert UMCLights to InformedProteomics LcMsFeatures
foreach (var ds in idToFeatures)
{
var lcmsFeatures = new List <LcMsFeature>(ds.Value.Select(this.GetLcMsFeature));
lcmsFeatureAligner.AddDataSet(ds.Key, lcmsFeatures, this.GetLcMsRun(ds.Key));
}
// Perform clustering
lcmsFeatureAligner.AlignFeatures();
// Fill in mising features using noise.
lcmsFeatureAligner.RefineAbundance(-30, progress);
var clusteredFeatures = lcmsFeatureAligner.GetAlignedFeatures();
// Convert InformedProteomics clusters to UMCClusterLight
int clustId = 0;
var clusters = new List <UMCClusterLight>();
foreach (var cluster in clusteredFeatures)
{
var firstFeature = cluster.FirstOrDefault(f => f != null);
if (firstFeature == null)
{
continue;
}
var umcCluster = new UMCClusterLight
{
Id = clustId++,
};
int datasetId = 0; // Promex doesn't keep track of which dataset noise features belong to, so we need to.
foreach (var feature in cluster)
{
if (feature == null)
{
continue;
}
feature.DataSetId = datasetId++;
var umc = this.GetUMC(feature);
umcCluster.AddChildFeature(umc);
umc.SetParentFeature(umcCluster);
}
umcCluster.CalculateStatistics(ClusterCentroidRepresentation.Median);
clusters.Add(umcCluster);
}
return(clusters);
}
private void RunFeatureAlignment(List<string> ms1FtFiles, List<string> rawFiles, string outFilePath)
{
var runList = new List<LcMsRun>();
foreach(var rawFile in rawFiles)
runList.Add(new PbfLcMsRun(rawFile));
var align = new LcMsFeatureAlignment(ms1FtFiles, runList, new LcMsFeatureAlignComparer(new Tolerance(10)));
align.AlignFeatures();
Console.WriteLine("# of aligned features = {0}", align.CountAlignedFeatures);
var tempOutPath = outFilePath + ".tmp";
OutputAlignmentResult(align, tempOutPath, rawFiles, true);
align.RefineAbundance();
OutputAlignmentResult(align, outFilePath, rawFiles, false);
}