public void TestGetChrom()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string rafFilePath = @"\\proto-2\UnitTest_Files\InformedProteomics_TestFiles\TopDown\ProductionQCShew\QC_Shew_13_04_A_17Feb14_Samwise_13-07-28.pbf";
if (!File.Exists(rafFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, rafFilePath);
}
var pbfRun = new PbfLcMsRun(rafFilePath);
Console.WriteLine(@"Chromatogram");
// chromatogram comparison
const double targetMz = 655.01;
var tolerance = new Tolerance(10);
var xic = pbfRun.GetFullPrecursorIonExtractedIonChromatogram(targetMz, tolerance);
const int MAX_POINTS = 50;
xic.Display(MAX_POINTS);
Console.WriteLine(@"Done");
}
public void TestGetChrom()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
var pbfFilePath = Path.Combine(Utils.DEFAULT_TEST_FILE_FOLDER, @"TopDown\ProductionQCShew\QC_Shew_13_04_A_17Feb14_Samwise_13-07-28.pbf");
if (!File.Exists(pbfFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, pbfFilePath);
}
var pbfRun = new PbfLcMsRun(pbfFilePath);
Console.WriteLine(@"Chromatogram");
// chromatogram comparison
const double targetMz = 655.01;
var tolerance = new Tolerance(10);
var xic = pbfRun.GetFullPrecursorIonExtractedIonChromatogram(targetMz, tolerance);
const int MAX_POINTS = 50;
xic.Display(MAX_POINTS);
Console.WriteLine(@"Done");
}
public void TestReadingPbfFile()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string pbfFilePath = @"\\proto-2\UnitTest_Files\InformedProteomics_TestFiles\TopDown\ProductionQCShew\QC_Shew_13_04_A_17Feb14_Samwise_13-07-28.pbf";
if (!File.Exists(pbfFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, pbfFilePath);
}
var pbfRun = new PbfLcMsRun(pbfFilePath);
var specFilePath = Path.ChangeExtension(pbfFilePath, "raw");
if (!File.Exists(specFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, specFilePath);
}
Console.WriteLine(@"Loading .pbf into memory");
var run = InMemoryLcMsRun.GetLcMsRun(specFilePath);
Console.WriteLine(@"Comparing spectra between .pbf and in-memory spectra");
// spectrum comparison
for (var scanNum = run.MinLcScan; scanNum <= run.MaxLcScan; scanNum++)
{
var spec1 = run.GetSpectrum(scanNum);
var spec2 = pbfRun.GetSpectrum(scanNum);
Assert.IsTrue(spec1.Peaks.Length == spec2.Peaks.Length);
for (var i = 0; i < spec1.Peaks.Length; i++)
{
var p1 = spec1.Peaks[i];
var p2 = spec2.Peaks[i];
Assert.True(p1.Equals(p2));
Assert.True(Math.Abs(p1.Mz - p2.Mz) < 1e-8);
Assert.True(Math.Abs(p1.Intensity - p2.Intensity) < 0.001);
}
}
Console.WriteLine(@"Comparing XICs");
// chromatogram comparison
const double targetMz = 655.01;
var tolerance = new Tolerance(10);
var xic1 = run.GetFullPrecursorIonExtractedIonChromatogram(targetMz, tolerance);
var xic2 = pbfRun.GetFullPrecursorIonExtractedIonChromatogram(targetMz, tolerance);
Assert.True(xic1.Count == xic2.Count);
for (var i = 0; i < xic1.Count; i++)
{
if (!xic1[i].Equals(xic2[i]))
{
Console.WriteLine(@"{0} {1} {2}", i, xic1[i], xic2[i]);
}
Assert.True(xic1[i].Equals(xic2[i]));
}
Console.WriteLine(@"Done");
}
public void TestRunningTimeChromGen()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string rafFilePath = @"C:\cygwin\home\kims336\Data\QCShewQE\QC_Shew_13_04_A_17Feb14_Samwise_13-07-28.raf";
if (!File.Exists(rafFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, rafFilePath);
}
var rafRun = new PbfLcMsRun(rafFilePath);
var tolerance = new Tolerance(10);
const string dbFile = @"D:\Research\Data\CommonContaminants\H_sapiens_Uniprot_SPROT_2013-05-01_withContam.fasta";
if (!File.Exists(dbFile))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, dbFile);
}
var db = new FastaDatabase(dbFile);
var indexedDb = new IndexedDatabase(db);
var aaSet = new AminoAcidSet(Modification.Carbamidomethylation);
var sw = new System.Diagnostics.Stopwatch();
sw.Start();
var numPeptides = 0;
foreach (var peptide in indexedDb.AnnotationsAndOffsets(6, 30, 2, 2, Enzyme.Trypsin))
{
++numPeptides;
var comp = new Sequence(peptide.Annotation.Substring(2, peptide.Annotation.Length - 4), aaSet).Composition + Composition.H2O;
var mz = new Ion(comp, 2).GetMonoIsotopicMz();
//Console.WriteLine(peptide.Annotation + " " + mz);
rafRun.GetFullPrecursorIonExtractedIonChromatogram(mz, tolerance);
//run.GetFullPrecursorIonExtractedIonChromatogram(mz, tolerance);
//var xic1 = run.GetFullPrecursorIonExtractedIonChromatogram(mz, tolerance);
//var xic2 = rafRun.GetFullPrecursorIonExtractedIonChromatogram(mz, tolerance);
//Assert.True(xic1.Count == xic2.Count);
//for (var i = 0; i < xic1.Count; i++)
//{
// if (!xic1[i].Equals(xic2[i]))
// {
// Console.WriteLine("{0} {1} {2}", i, xic1[i], xic2[i]);
// }
// Assert.True(xic1[i].Equals(xic2[i]));
//}
if (numPeptides == 100000)
{
break;
}
}
sw.Stop();
Console.WriteLine(@"{0:f4} sec", sw.Elapsed.TotalSeconds);
}
public void TestReadingPbfFile()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string pbfFilePath = @"\\proto-2\UnitTest_Files\InformedProteomics_TestFiles\TopDown\ProductionQCShew\QC_Shew_13_04_A_17Feb14_Samwise_13-07-28.pbf";
if (!File.Exists(pbfFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, pbfFilePath);
}
var pbfRun = new PbfLcMsRun(pbfFilePath);
var specFilePath = Path.ChangeExtension(pbfFilePath, "raw");
if (!File.Exists(specFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, specFilePath);
}
Console.WriteLine(@"Loading .pbf into memory");
var run = InMemoryLcMsRun.GetLcMsRun(specFilePath);
Console.WriteLine(@"Comparing spectra between .pbf and in-memory spectra");
// spectrum comparison
for (var scanNum = run.MinLcScan; scanNum <= run.MaxLcScan; scanNum++)
{
var spec1 = run.GetSpectrum(scanNum);
var spec2 = pbfRun.GetSpectrum(scanNum);
Assert.IsTrue(spec1.Peaks.Length == spec2.Peaks.Length);
for (var i = 0; i < spec1.Peaks.Length; i++)
{
var p1 = spec1.Peaks[i];
var p2 = spec2.Peaks[i];
Assert.True(p1.Equals(p2));
Assert.True(Math.Abs(p1.Mz - p2.Mz) < 1e-8);
Assert.True(Math.Abs(p1.Intensity - p2.Intensity) < 0.001);
}
}
Console.WriteLine(@"Comparing XICs");
// chromatogram comparison
const double targetMz = 655.01;
var tolerance = new Tolerance(10);
var xic1 = run.GetFullPrecursorIonExtractedIonChromatogram(targetMz, tolerance);
var xic2 = pbfRun.GetFullPrecursorIonExtractedIonChromatogram(targetMz, tolerance);
Assert.True(xic1.Count == xic2.Count);
for (var i = 0; i < xic1.Count; i++)
{
if (!xic1[i].Equals(xic2[i]))
{
Console.WriteLine(@"{0} {1} {2}", i, xic1[i], xic2[i]);
}
Assert.True(xic1[i].Equals(xic2[i]));
}
Console.WriteLine(@"Done");
}
public void TestRunningTimeChromGen()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string rafFilePath = @"C:\cygwin\home\kims336\Data\QCShewQE\QC_Shew_13_04_A_17Feb14_Samwise_13-07-28.raf";
if (!File.Exists(rafFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, rafFilePath);
}
var rafRun = new PbfLcMsRun(rafFilePath);
var tolerance = new Tolerance(10);
const string dbFile = @"D:\Research\Data\CommonContaminants\H_sapiens_Uniprot_SPROT_2013-05-01_withContam.fasta";
if (!File.Exists(dbFile))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, dbFile);
}
var db = new FastaDatabase(dbFile);
var indexedDb = new IndexedDatabase(db);
var aaSet = new AminoAcidSet(Modification.Carbamidomethylation);
var sw = new System.Diagnostics.Stopwatch();
sw.Start();
var numPeptides = 0;
foreach (var peptide in indexedDb.AnnotationsAndOffsets(6, 30, 2, 2, Enzyme.Trypsin))
{
++numPeptides;
var comp = new Sequence(peptide.Annotation.Substring(2, peptide.Annotation.Length-4), aaSet).Composition + Composition.H2O;
var mz = new Ion(comp, 2).GetMonoIsotopicMz();
//Console.WriteLine(peptide.Annotation + " " + mz);
rafRun.GetFullPrecursorIonExtractedIonChromatogram(mz, tolerance);
//run.GetFullPrecursorIonExtractedIonChromatogram(mz, tolerance);
//var xic1 = run.GetFullPrecursorIonExtractedIonChromatogram(mz, tolerance);
//var xic2 = rafRun.GetFullPrecursorIonExtractedIonChromatogram(mz, tolerance);
//Assert.True(xic1.Count == xic2.Count);
//for (var i = 0; i < xic1.Count; i++)
//{
// if (!xic1[i].Equals(xic2[i]))
// {
// Console.WriteLine("{0} {1} {2}", i, xic1[i], xic2[i]);
// }
// Assert.True(xic1[i].Equals(xic2[i]));
//}
if (numPeptides == 100000) break;
}
sw.Stop();
Console.WriteLine(@"{0:f4} sec", sw.Elapsed.TotalSeconds);
}
public void TestGetChrom()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string rafFilePath = @"\\proto-2\UnitTest_Files\InformedProteomics_TestFiles\TopDown\ProductionQCShew\QC_Shew_13_04_A_17Feb14_Samwise_13-07-28.pbf";
if (!File.Exists(rafFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, rafFilePath);
}
var pbfRun = new PbfLcMsRun(rafFilePath);
Console.WriteLine(@"Chromatogram");
// chromatogram comparison
const double targetMz = 655.01;
var tolerance = new Tolerance(10);
var xic = pbfRun.GetFullPrecursorIonExtractedIonChromatogram(targetMz, tolerance);
const int MAX_POINTS = 50;
xic.Display(MAX_POINTS);
Console.WriteLine(@"Done");
}
