public void TestPromexClustering()
{
var provider = new ScanSummaryProviderCache();
var reader1 = provider.GetScanSummaryProvider(pbf1, 0) as InformedProteomicsReader;
var reader2 = provider.GetScanSummaryProvider(pbf2, 1) as InformedProteomicsReader;
var reader3 = provider.GetScanSummaryProvider(pbf3, 2) as InformedProteomicsReader;
var promexFileReader1 = new PromexFileReader(reader1, 0);
var features1 =
promexFileReader1.ReadFile(ms1ft1);
var promexFileReader2 = new PromexFileReader(reader2, 1);
var features2 =
promexFileReader2.ReadFile(ms1ft2);
var promexFileReader3 = new PromexFileReader(reader3, 2);
var features3 =
promexFileReader3.ReadFile(ms1ft3);
var features = new List <UMCLight>();
features.AddRange(features1);
features.AddRange(features2);
features.AddRange(features3);
var clusterer = new PromexClusterer
{
Readers = provider,
};
var clusters = clusterer.Cluster(features);
Console.WriteLine(clusters.Count(c => c.Features.Count > 1));
}
public void TestPromexFileReading()
{
const int datasetId = 0;
var reader = new InformedProteomicsReader(datasetId, pbf1);
var promexFileReader = new PromexFileReader(reader, datasetId);
var features =
promexFileReader.ReadFile(ms1ft1);
Console.WriteLine(features.Count());
}
/// <summary>
/// Loads feature data from the files provided.
/// </summary>
/// <returns></returns>
public static IList <UMCLight> LoadUmcFeatureData(DatasetInformation dataset, IUmcDAO featureCache, IScanSummaryProvider provider = null)
{
var features = new List <UMCLight>();
var extension = Path.GetExtension(dataset.Features.Path);
if (extension == null)
{
return(features);
}
extension = extension.ToUpper();
switch (extension)
{
case ".TXT":
if (dataset.Features.Path.EndsWith("_LCMSFeatures.txt"))
{
var reader = new LcImsFeatureFileReader(provider, dataset.DatasetId);
features = reader.ReadFile(dataset.Features.Path).ToList();
}
else
{
var umcReader = new LCMSFeatureFileReader(dataset.Features.Path);
features = umcReader.GetUmcList();
}
break;
case ".DB3":
features = featureCache.FindByDatasetId(dataset.DatasetId);
break;
case ".MS1FT":
if (provider != null && provider is InformedProteomicsReader)
{
var promexReader = new PromexFileReader(provider as InformedProteomicsReader, dataset.DatasetId);
features = promexReader.ReadFile(dataset.Features.Path).ToList();
}
break;
default: //Was reconstructing features from scratch even when they were already cached because the file extention was ".csv" not ".db3"
features = featureCache.FindByDatasetId(dataset.DatasetId);
break;
}
if (features != null && provider is ISpectraProvider)
{
var spectraProvider = provider as ISpectraProvider;
LoadMsMs(features, spectraProvider);
}
return(features);
}
public void CompareClustering()
{
// Cluster using MultiAlign to Promex adapters
var provider = new ScanSummaryProviderCache();
var reader1 = provider.GetScanSummaryProvider(pbf1, 0) as InformedProteomicsReader;
var reader2 = provider.GetScanSummaryProvider(pbf2, 1) as InformedProteomicsReader;
var promexFileReader1 = new PromexFileReader(reader1, 0);
var features1 = promexFileReader1.ReadFile(ms1ft1);
var promexFileReader2 = new PromexFileReader(reader2, 1);
var features2 =
promexFileReader2.ReadFile(ms1ft2);
var features = new List <UMCLight>();
features.AddRange(features1);
features.AddRange(features2);
var clusterer = new PromexClusterer
{
Readers = provider,
};
var clusters = clusterer.Cluster(features);
var clusterCount = clusters.Count(c => c.UmcList.Count > 1);
// Cluster using only ProMex
var lcmsRun1 = PbfLcMsRun.GetLcMsRun(pbf1);
var lcmsRun2 = PbfLcMsRun.GetLcMsRun(pbf2);
var aligner = new LcMsFeatureAlignment(new LcMsFeatureAlignComparer(new Tolerance(10, ToleranceUnit.Ppm)));
var promexFeatures1 = LcMsFeatureAlignment.LoadProMexResult(0, ms1ft1, lcmsRun1);
aligner.AddDataSet(0, promexFeatures1, lcmsRun1);
var promexFeatures2 = LcMsFeatureAlignment.LoadProMexResult(1, ms1ft2, lcmsRun2);
aligner.AddDataSet(1, promexFeatures2, lcmsRun2);
aligner.AlignFeatures();
var promexClusters = aligner.GetAlignedFeatures();
var promexClusterCount = promexClusters.Count(c => c.Count(f => f != null) > 1);
Assert.AreEqual(clusters.Count, promexClusters.Count);
Assert.AreEqual(clusterCount, promexClusterCount);
}
public void CompareFileReading()
{
// Read using MultiAlign to Promex adapters
var provider = new ScanSummaryProviderCache();
var reader1 = provider.GetScanSummaryProvider(pbf1, 0) as InformedProteomicsReader;
var promexFileReader = new PromexFileReader(reader1, 0);
var features = promexFileReader.ReadFile(ms1ft1).ToList();
var lcmsRun = PbfLcMsRun.GetLcMsRun(pbf1);
var promexFeatures = LcMsFeatureAlignment.LoadProMexResult(0, ms1ft1, lcmsRun).ToList();
Assert.AreEqual(features.Count, promexFeatures.Count);
for (int i = 0; i < features.Count; i++)
{
Assert.AreEqual(features[i].MassMonoisotopic, promexFeatures[i].Mass);
////Assert.AreEqual(features[i].Mz, promexFeatures[i].RepresentativeMz);
Assert.AreEqual(features[i].Net, promexFeatures[i].Net);
Assert.AreEqual(features[i].ScanStart, promexFeatures[i].MinScanNum);
Assert.AreEqual(features[i].ScanEnd, promexFeatures[i].MaxScanNum);
Assert.AreEqual(features[i].Abundance, promexFeatures[i].Abundance);
}
}
