public void GenerateSpecCount()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string resultFileDir = @"D:\Research\Data\EDRN\DDA\NTT1_NoMod\";
var resultFiles = Directory.GetFiles(resultFileDir, "*.tsv");
var fractionToIds = new Dictionary <int, List <MsGfMatch> >();
foreach (var resultFile in resultFiles)
{
var fraction = Convert.ToInt32(resultFile.Substring(resultFile.IndexOf("_Serum", StringComparison.Ordinal) + 7, 2));
var msgfResults = new MsGfResults(resultFile);
fractionToIds.Add(fraction, msgfResults.GetMatchesAtPsmFdr(0.01));
}
const string spikedInPeptideFile = @"D:\Research\Data\EDRN\SpikedPeptides.txt";
var spikedInPeptides = File.ReadAllLines(spikedInPeptideFile);
Console.WriteLine("Peptide\t{0}", string.Join("\t", Enumerable.Range(1, 12)));
foreach (var spikedInPeptide in spikedInPeptides)
{
Console.Write(spikedInPeptide);
for (var fraction = 1; fraction <= 12; fraction++)
{
var matches = fractionToIds[fraction];
var count = matches.Count(m => m.Peptide.Replace("C+57.021", "C").Replace("K+8.014", "K").Replace("R+10.008", "R").Equals(spikedInPeptide));
Console.Write("\t{0}", count);
}
Console.WriteLine();
}
}
public void GenerateSpecCount()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string resultFileDir = @"D:\Research\Data\EDRN\DDA\NTT1_NoMod\";
var resultFiles = Directory.GetFiles(resultFileDir, "*.tsv");
var fractionToIds = new Dictionary<int, List<MsGfMatch>>();
foreach (var resultFile in resultFiles)
{
var fraction = Convert.ToInt32(resultFile.Substring(resultFile.IndexOf("_Serum", StringComparison.Ordinal) + 7, 2));
var msgfResults = new MsGfResults(resultFile);
fractionToIds.Add(fraction, msgfResults.GetMatchesAtPsmFdr(0.01));
}
const string spikedInPeptideFile = @"D:\Research\Data\EDRN\SpikedPeptides.txt";
var spikedInPeptides = File.ReadAllLines(spikedInPeptideFile);
Console.WriteLine("Peptide\t{0}", string.Join("\t", Enumerable.Range(1, 12)));
foreach (var spikedInPeptide in spikedInPeptides)
{
Console.Write(spikedInPeptide);
for (var fraction = 1; fraction <= 12; fraction++)
{
var matches = fractionToIds[fraction];
var count = matches.Count(m => m.Peptide.Replace("C+57.021", "C").Replace("K+8.014", "K").Replace("R+10.008", "R").Equals(spikedInPeptide));
Console.Write("\t{0}", count);
}
Console.WriteLine();
}
}
public void TestInitialScoring()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string icResultPath = @"C:\cygwin\home\kims336\Data\QCShewQE\Ic_NTT2_03_NoMod_NoRescoring\QC_Shew_13_04_A_17Feb14_Samwise_13-07-28_IcTarget.tsv";
if (!File.Exists(icResultPath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, icResultPath);
}
var icParser = new TsvFileParser(icResultPath);
var icScans = icParser.GetData("Scan").Select(s => Convert.ToInt32(s)).ToArray();
var icPeptides = icParser.GetData("Sequence");
var icScore = icParser.GetData("Score").Select(s => Convert.ToInt32(s)).ToArray();
var map = new Dictionary <string, int>();
for (var i = 0; i < icParser.NumData; i++)
{
map.Add(icScans[i] + ":" + icPeptides[i], icScore[i]);
}
const string msgfPlusResultPath = @"C:\cygwin\home\kims336\Data\QCShewQE\NoMod.tsv";
if (!File.Exists(msgfPlusResultPath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, msgfPlusResultPath);
}
var msgfPlusResults = new MsGfResults(msgfPlusResultPath);
var matches = msgfPlusResults.GetMatchesAtPsmFdr(0.01);
//Console.WriteLine("NumMatches: {0}", matches.Count);
Console.WriteLine("ScanNum\tPeptide\tSpecEValue\tIcScore");
foreach (var match in matches)
{
var scanNum = match.ScanNum;
var peptide = match.Peptide;
var specEValue = match.SpecEValue;
int score;
if (!map.TryGetValue(scanNum + ":" + peptide, out score))
{
score = -1;
}
Console.WriteLine("{0}\t{1}\t{2}\t{3}", scanNum, peptide, specEValue, score);
}
}
public void TestMs1Filter()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string msgfPlusResultPath = @"C:\cygwin\home\kims336\Data\QCShewQE\NoMod.tsv";
if (!File.Exists(msgfPlusResultPath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, msgfPlusResultPath);
}
var msgfPlusResults = new MsGfResults(msgfPlusResultPath);
const string specFilePath = @"C:\cygwin\home\kims336\Data\QCShewQE\QC_Shew_13_04_A_17Feb14_Samwise_13-07-28.raw";
if (!File.Exists(specFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, specFilePath);
}
var run = InMemoryLcMsRun.GetLcMsRun(specFilePath, 1.4826, 0);
var ms1Filter = new Ms1IsotopeAndChargeCorrFilter(run, new Tolerance(10), 1, 4,
400, 5000, 0.3, 0, 0);
var matches = msgfPlusResults.GetMatchesAtPsmFdr(0.01);
var aminoAcidSet = new AminoAcidSet();
var numPsms = 0;
var numSurvived = 0;
Console.WriteLine("ScanNum\tPeptide\tSpecEValue\tFilter");
foreach (var match in matches)
{
var scanNum = match.ScanNum;
var peptide = match.Peptide;
var specEValue = match.SpecEValue;
var peptideMass = (new Sequence(peptide, aminoAcidSet).Composition + Composition.H2O).Mass;
var survive = ms1Filter.GetMatchingMs2ScanNums(peptideMass).Contains(scanNum) ? 1 : 0;
++numPsms;
numSurvived += survive;
Console.WriteLine("{0}\t{1}\t{2}\t{3}", scanNum, peptide, specEValue, survive);
}
Console.WriteLine("SuccessRage: {0}, {1}/{2}", numSurvived / (float)numPsms, numSurvived, numPsms);
}
public void TestMs1Filter()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string msgfPlusResultPath = @"C:\cygwin\home\kims336\Data\QCShewQE\NoMod.tsv";
if (!File.Exists(msgfPlusResultPath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, msgfPlusResultPath);
}
var msgfPlusResults = new MsGfResults(msgfPlusResultPath);
const string specFilePath = @"C:\cygwin\home\kims336\Data\QCShewQE\QC_Shew_13_04_A_17Feb14_Samwise_13-07-28.raw";
if (!File.Exists(specFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, specFilePath);
}
var run = InMemoryLcMsRun.GetLcMsRun(specFilePath, 1.4826, 0);
var ms1Filter = new Ms1IsotopeAndChargeCorrFilter(run, new Tolerance(10), 1, 4,
400, 5000, 0.3, 0, 0);
var matches = msgfPlusResults.GetMatchesAtPsmFdr(0.01);
var aminoAcidSet = new AminoAcidSet();
var numPsms = 0;
var numSurvived = 0;
Console.WriteLine("ScanNum\tPeptide\tSpecEValue\tFilter");
foreach (var match in matches)
{
var scanNum = match.ScanNum;
var peptide = match.Peptide;
var specEValue = match.SpecEValue;
var peptideMass = (new Sequence(peptide, aminoAcidSet).Composition + Composition.H2O).Mass;
var survive = ms1Filter.GetMatchingMs2ScanNums(peptideMass).Contains(scanNum) ? 1 : 0;
++numPsms;
numSurvived += survive;
Console.WriteLine("{0}\t{1}\t{2}\t{3}", scanNum, peptide, specEValue, survive);
}
Console.WriteLine("SuccessRage: {0}, {1}/{2}", numSurvived/(float)numPsms, numSurvived, numPsms);
}
public void TestInitialScoring()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string icResultPath = @"C:\cygwin\home\kims336\Data\QCShewQE\Ic_NTT2_03_NoMod_NoRescoring\QC_Shew_13_04_A_17Feb14_Samwise_13-07-28_IcTarget.tsv";
if (!File.Exists(icResultPath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, icResultPath);
}
var icParser = new TsvFileParser(icResultPath);
var icScans = icParser.GetData("Scan").Select(s => Convert.ToInt32(s)).ToArray();
var icPeptides = icParser.GetData("Sequence");
var icScore = icParser.GetData("Score").Select(s => Convert.ToInt32(s)).ToArray();
var map = new Dictionary<string, int>();
for (var i = 0; i < icParser.NumData; i++)
{
map.Add(icScans[i]+":"+icPeptides[i], icScore[i]);
}
const string msgfPlusResultPath = @"C:\cygwin\home\kims336\Data\QCShewQE\NoMod.tsv";
if (!File.Exists(msgfPlusResultPath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, msgfPlusResultPath);
}
var msgfPlusResults = new MsGfResults(msgfPlusResultPath);
var matches = msgfPlusResults.GetMatchesAtPsmFdr(0.01);
//Console.WriteLine("NumMatches: {0}", matches.Count);
Console.WriteLine("ScanNum\tPeptide\tSpecEValue\tIcScore");
foreach (var match in matches)
{
var scanNum = match.ScanNum;
var peptide = match.Peptide;
var specEValue = match.SpecEValue;
int score;
if (!map.TryGetValue(scanNum + ":" + peptide, out score)) score = -1;
Console.WriteLine("{0}\t{1}\t{2}\t{3}", scanNum, peptide, specEValue, score);
}
}