public static void PeptideFDRTest()
{
string myFile = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\PrunedDbSpectra.mzml");
string myFile2 = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\PrunedDbSpectra2.mzml");
if (!File.Exists(myFile2))
{
File.Copy(myFile, myFile2);
}
string myDatabase = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\DbForPrunedDb.fasta");
string folderPath = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestPeptideFDR");
DbForTask db = new DbForTask(myDatabase, true);
Directory.CreateDirectory(folderPath);
// search something with multiple hits of the same peptide to see if peptide FDR is calculated at the end
new SearchTask().RunTask(folderPath, new List <DbForTask> {
db
}, new List <string> {
myFile, myFile2
}, "normal");
List <string> columns = null;
int cumDecoys = 0;
int cumTargets = 0;
double finalQValue = 0;
foreach (string line in File.ReadAllLines(Path.Combine(folderPath, @"AllPeptides.psmtsv")))
{
string[] lineline = line.Split('\t');
if (line.StartsWith("File Name")) // header
{
columns = lineline.ToList();
}
// since each PSM has a duplicate, these counts will be 1,3,5,7, etc. if peptide FDR isn't calculated
// if peptide FDR is calculated, they will be 1,2,3,4, etc. as expected
else if (lineline[columns.IndexOf("Decoy/Contaminant/Target")] == "D")
{
Assert.AreEqual(++cumDecoys, int.Parse(lineline[columns.IndexOf("Cumulative Decoy")]));
finalQValue = double.Parse(lineline[columns.IndexOf("QValue")], CultureInfo.InvariantCulture);
}
else
{
Assert.AreEqual(++cumTargets, int.Parse(lineline[columns.IndexOf("Cumulative Target")]));
finalQValue = double.Parse(lineline[columns.IndexOf("QValue")], CultureInfo.InvariantCulture);
}
}
// test that the final q-value follows the (target / decoy) formula
// intermediate q-values no longer always follow this formula, so I'm not testing them here
Assert.AreEqual(cumDecoys / (double)cumTargets, finalQValue, 0.0001);
Directory.Delete(folderPath, true);
}
public static void GlyTest_RunTask()
{
GlycoSearchTask task = new GlycoSearchTask();
task._glycoSearchParameters.GlycoSearchType = GlycoSearchType.NGlycanSearch;
Directory.CreateDirectory(Path.Combine(Environment.CurrentDirectory, @"TESTGlycoData"));
DbForTask db = new DbForTask(Path.Combine(TestContext.CurrentContext.TestDirectory, @"GlycoTestData/Q9C0Y4.fasta"), false);
string raw = Path.Combine(TestContext.CurrentContext.TestDirectory, @"GlycoTestData/yeast_glycan_25170.mgf");
new EverythingRunnerEngine(new List <(string, MetaMorpheusTask)> {
("Task", task)
}, new List <string> {
public static void TestLibraryGeneration()
{
string thisTaskOutputFolder = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\SpectralLibrarySearch\FileOutput");
SearchTask task = Toml.ReadFile <SearchTask>(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\SpectralLibrarySearch\SpectralSearchTask.toml"), MetaMorpheusTask.tomlConfig);
task.SearchParameters.WriteMzId = true;
task.SearchParameters.WriteSpectralLibrary = true;
DbForTask db = new DbForTask(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\SpectralLibrarySearch\uniprot-yeast-filtered-reviewed_yes.fasta.gz"), false);
string raw = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\SpectralLibrarySearch\slicedYeast.raw");
EverythingRunnerEngine MassSpectraFile = new EverythingRunnerEngine(new List <(string, MetaMorpheusTask)> {
("SpectraFileOutput", task)
}, new List <string> {
public static void PostSearchNormalizeTest()
{
SearchTask searchTask = new SearchTask()
{
SearchParameters = new SearchParameters
{
Normalize = true
},
};
string myFile = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\PrunedDbSpectra.mzml");
string myDatabase = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\DbForPrunedDb.fasta");
string folderPath = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestNormalizationExperDesign");
string experimentalDesignFile = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\ExperimentalDesign.tsv");
using (StreamWriter output = new StreamWriter(experimentalDesignFile))
{
output.WriteLine("FileName\tCondition\tBiorep\tFraction\tTechrep");
output.WriteLine("PrunedDbSpectra.mzml" + "\t" + "condition" + "\t" + "1" + "\t" + "1" + "\t" + "1");
}
DbForTask db = new DbForTask(myDatabase, false);
// run the task
Directory.CreateDirectory(folderPath);
searchTask.RunTask(folderPath, new List <DbForTask> {
db
}, new List <string> {
myFile
}, "normal");
Directory.Delete(folderPath, true);
// delete the exper design and try again. this should skip quantification
File.Delete(experimentalDesignFile);
// run the task
Directory.CreateDirectory(folderPath);
searchTask.RunTask(folderPath, new List <DbForTask> {
db
}, new List <string> {
myFile
}, "normal");
// PSMs should be present but no quant output
Assert.That(!File.Exists(Path.Combine(folderPath, "AllQuantifiedPeptides.tsv")));
Assert.That(File.Exists(Path.Combine(folderPath, "AllPSMs.psmtsv")));
Directory.Delete(folderPath, true);
}
public static void SemiSpecificTest()
{
List <FragmentationTerminus> terminiToTest = new List <FragmentationTerminus>
{
FragmentationTerminus.N,
FragmentationTerminus.C
};
string outputFolder = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestSemiSpecific");
string myFile = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\PrunedDbSpectra.mzml");
string myDatabase = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\DbForPrunedDb.fasta");
foreach (FragmentationTerminus fragTerm in terminiToTest)
{
SearchTask searchTask = new SearchTask()
{
SearchParameters = new SearchParameters
{
SearchType = SearchType.NonSpecific,
LocalFdrCategories = new List <FdrCategory>
{
FdrCategory.FullySpecific,
FdrCategory.SemiSpecific
}
},
CommonParameters = new CommonParameters(scoreCutoff: 4, addCompIons: true,
digestionParams: new DigestionParams(searchModeType: CleavageSpecificity.Semi, fragmentationTerminus: fragTerm))
};
DbForTask db = new DbForTask(myDatabase, false);
List <(string, MetaMorpheusTask)> taskList = new List <(string, MetaMorpheusTask)> {
("TestSemiSpecific", searchTask)
};
var engine = new EverythingRunnerEngine(taskList, new List <string> {
myFile
}, new List <DbForTask> {
new DbForTask(myDatabase, false)
}, outputFolder);
engine.Run();
string outputPath = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestSemiSpecific\TestSemiSpecific\AllPSMs.psmtsv");
var output = File.ReadAllLines(outputPath);
Assert.That(output.Length == 13); //if N is only producing 11 lines, then the c is not being searched with it. //If only 12 lines, maybe missed mono issue
}
Directory.Delete(outputFolder, true);
}
public static void SemiSpecificFullAndSmallMatches()
{
SearchTask searchTask = new SearchTask()
{
SearchParameters = new SearchParameters
{
WriteMzId = true,
SearchType = SearchType.NonSpecific,
LocalFdrCategories = new List <FdrCategory>
{
FdrCategory.FullySpecific,
FdrCategory.SemiSpecific
}
},
CommonParameters = new CommonParameters(addCompIons: true, scoreCutoff: 11,
digestionParams: new DigestionParams(minPeptideLength: 7, searchModeType: CleavageSpecificity.Semi, fragmentationTerminus: FragmentationTerminus.N))
};
string myFile = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\tinySemi.mgf");
string myDatabase = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\semiTest.fasta");
DbForTask db = new DbForTask(myDatabase, false);
List <(string, MetaMorpheusTask)> taskList = new List <(string, MetaMorpheusTask)> {
("TestSemiSpecificSmall", searchTask)
};
var engine = new EverythingRunnerEngine(taskList, new List <string> {
myFile
}, new List <DbForTask> {
new DbForTask(myDatabase, false)
}, Environment.CurrentDirectory);
engine.Run();
string outputPath = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestSemiSpecificSmall\AllPSMs.psmtsv");
var output = File.ReadAllLines(outputPath);
Assert.IsTrue(output.Length == 3);
var mzId = File.ReadAllLines(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestSemiSpecificSmall\tinySemi.mzID"));
Assert.That(mzId[115].Equals(" <cvParam name=\"mzML format\" cvRef=\"PSI-MS\" accession=\"MS:1000584\" />"));
Assert.That(mzId[118].Equals(" <cvParam name=\"mzML unique identifier\" cvRef=\"PSI-MS\" accession=\"MS:1001530\" />"));
Assert.That(mzId[97].Equals(" <cvParam name=\"pep:FDR threshold\" value=\"0.01\" cvRef=\"PSI-MS\" accession=\"MS:1001448\" />"));
}
public static void MultipleCustomFragmentations()
{
string outputFolder = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestCustomFragmentations");
string myFile = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\PrunedDbSpectra.mzml");
string myDatabase = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\DbForPrunedDb.fasta");
// create 3 search tasks with different custom fragmentation ions
var task1 = Toml.ReadFile <SearchTask>(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\customBY.toml"), MetaMorpheusTask.tomlConfig);
var task2 = Toml.ReadFile <SearchTask>(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\customCZ.toml"), MetaMorpheusTask.tomlConfig);
var task3 = Toml.ReadFile <SearchTask>(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\customBCZ.toml"), MetaMorpheusTask.tomlConfig);
// run all tasks
DbForTask db = new DbForTask(myDatabase, false);
List <(string, MetaMorpheusTask)> taskList = new List <(string, MetaMorpheusTask)> {
("TestSearchBY", task1), ("TestSearchCZ", task2), ("TestSearchBCZ", task3)
};
var engine = new EverythingRunnerEngine(taskList, new List <string> {
myFile
}, new List <DbForTask> {
new DbForTask(myDatabase, false)
}, outputFolder);
engine.Run();
// read generated toml settings and make sure custom fragmentations match are handled properly for each task
string outputPath = Path.Combine(outputFolder, @"Task Settings");
var task1Settings = Toml.ReadFile <SearchTask>(Path.Combine(outputPath, @"TestSearchBYConfig.toml"), MetaMorpheusTask.tomlConfig);
var task2Settings = Toml.ReadFile <SearchTask>(Path.Combine(outputPath, @"TestSearchCZConfig.toml"), MetaMorpheusTask.tomlConfig);
var task3Settings = Toml.ReadFile <SearchTask>(Path.Combine(outputPath, @"TestSearchBCZConfig.toml"), MetaMorpheusTask.tomlConfig);
var task1CustomIons = task1Settings.CommonParameters.CustomIons;
var task2CustomIons = task2Settings.CommonParameters.CustomIons;
var task3CustomIons = task3Settings.CommonParameters.CustomIons;
Assert.That(task1CustomIons.Contains(ProductType.b) && task1CustomIons.Contains(ProductType.y) && task1CustomIons.Count == 2);
Assert.That(task2CustomIons.Contains(ProductType.c) && task2CustomIons.Contains(ProductType.zDot) && task2CustomIons.Count == 2);
Assert.That(task3CustomIons.Contains(ProductType.c) && task3CustomIons.Contains(ProductType.zDot) && task3CustomIons.Contains(ProductType.b) && task3CustomIons.Count == 3);
Directory.Delete(outputFolder, true);
}
public static void PostSearchNormalizeTest()
{
SearchTask searchTask = new SearchTask()
{
SearchParameters = new SearchParameters
{
Normalize = true
},
};
string myFile = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\PrunedDbSpectra.mzml");
string myDatabase = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\DbForPrunedDb.fasta");
string folderPath = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestNormalization");
string filePath = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\ExperimentalDesign.tsv");
using (StreamWriter output = new StreamWriter(filePath))
{
output.WriteLine("FileName\tCondition\tBiorep\tFraction\tTechrep");
output.WriteLine("PrunedDbSpectra" + "\t" + "condition" + "\t" + "1" + "\t" + "1" + "\t" + "1");
}
DbForTask db = new DbForTask(myDatabase, false);
Directory.CreateDirectory(folderPath);
searchTask.RunTask(folderPath, new List <DbForTask> {
db
}, new List <string> {
myFile
}, "normal");
File.Delete(filePath);
Assert.That(() => searchTask.RunTask(folderPath, new List <DbForTask> {
db
}, new List <string> {
myFile
}, "normal"),
Throws.TypeOf <MetaMorpheusException>());
Directory.Delete(folderPath, true);
}
public static void SemiSpecificFullAndSmallMatches()
{
SearchTask searchTask = new SearchTask()
{
SearchParameters = new SearchParameters
{
SearchType = SearchType.NonSpecific,
LocalFdrCategories = new List <FdrCategory>
{
FdrCategory.FullySpecific,
FdrCategory.SemiSpecific
}
},
CommonParameters = new CommonParameters(addCompIons: true, scoreCutoff: 11,
digestionParams: new DigestionParams(minPeptideLength: 7, searchModeType: CleavageSpecificity.Semi, fragmentationTerminus: FragmentationTerminus.N))
};
string myFile = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\tinySemi.mgf");
string myDatabase = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\semiTest.fasta");
DbForTask db = new DbForTask(myDatabase, false);
List <(string, MetaMorpheusTask)> taskList = new List <(string, MetaMorpheusTask)> {
("TestSemiSpecificSmall", searchTask)
};
var engine = new EverythingRunnerEngine(taskList, new List <string> {
myFile
}, new List <DbForTask> {
new DbForTask(myDatabase, false)
}, Environment.CurrentDirectory);
engine.Run();
string outputPath = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestSemiSpecificSmall\AllPSMs.psmtsv");
var output = File.ReadAllLines(outputPath);
Assert.IsTrue(output.Length == 3);
}
public void VariantSpecificOutputFiles()
{
string thisTaskOutputFolder = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestVariantFileOutput");
SearchTask task = Toml.ReadFile <SearchTask>(Path.Combine(TestContext.CurrentContext.TestDirectory, @"VariantSearchTaskConfig.toml"), MetaMorpheusTask.tomlConfig);
task.SearchParameters.DecoyType = DecoyType.None;
DbForTask noVariantDb = new DbForTask(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestNoVariantDb.xml"), false);
DbForTask frameshiftVariantDb = new DbForTask(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestVariantDB_frameshift.xml"), false);
DbForTask missenseVariantDb = new DbForTask(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestVariantDB_missense.xml"), false);
DbForTask stopGainedVariantDb = new DbForTask(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestVariantDB_stopGained.xml"), false);
DbForTask conservativeInsertionVariantDb = new DbForTask(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestVariantDB_conservativeInsertion.xml"), false);
DbForTask disruptiveInsertionVariantDb = new DbForTask(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestVariantDB_disruptiveInsertion.xml"), false);
DbForTask conservativeDeletionVariantDb = new DbForTask(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestVariantDB_conservativeDeletion.xml"), false);
DbForTask disruptiveDeletionVariantDb = new DbForTask(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestVariantDB_disruptiveDeletion.xml"), false);
DbForTask stopLossVariantDb = new DbForTask(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestVariantDB_stopLoss.xml"), false);
string raw = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestVariantPep.mzML");
EverythingRunnerEngine noVariants = new EverythingRunnerEngine(new List <(string, MetaMorpheusTask)> {
("NoVariantOutput", task)
}, new List <string> {
public static void TestIndividualFileOutput()
{
string subFolder = Path.Combine(TestContext.CurrentContext.TestDirectory, @"IndividualOutputTest");
Directory.CreateDirectory(subFolder);
string outputFolder = Path.Combine(subFolder, "Results");
SearchTask allowFilesTask = new SearchTask();
allowFilesTask.SearchParameters.WriteIndividualFiles = true;
allowFilesTask.SearchParameters.CompressIndividualFiles = false;
SearchTask compressFilesTask = new SearchTask();
compressFilesTask.SearchParameters.WriteIndividualFiles = true;
compressFilesTask.SearchParameters.CompressIndividualFiles = true;
SearchTask noFilesTask = new SearchTask();
noFilesTask.SearchParameters.WriteIndividualFiles = false;
PeptideWithSetModifications pwsm = new PeptideWithSetModifications("AAFNSGK", null);
List <(string, MetaMorpheusTask)> tasks = new List <(string, MetaMorpheusTask)> {
("allowFiles", allowFilesTask), ("compressFiles", compressFilesTask), ("noFiles", noFilesTask)
};
DbForTask db = new DbForTask(Path.Combine(TestContext.CurrentContext.TestDirectory, "TestData", "gapdh.fasta"), false);
TestDataFile datafile = new TestDataFile(pwsm);
string pathOne = Path.Combine(subFolder, "fileOne.mzml");
string pathTwo = Path.Combine(subFolder, "fileTwo.mzml");
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(datafile, pathOne, false);
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(datafile, pathTwo, false);
new EverythingRunnerEngine(tasks, new List <string> {
pathOne, pathTwo
}, new List <DbForTask> {
db
}, outputFolder).Run();
//check that the first task wrote everything fine
HashSet <string> expectedFiles = new HashSet <string>
{
".mzID",
"_Peptides.psmtsv",
"_ProteinGroups.tsv",
"_PSMs.psmtsv",
"_PSMsFormattedForPercolator.tab",
"_QuantifiedPeaks.tsv"
};
HashSet <string> writtenFiles = new HashSet <string>(Directory.GetFiles(Path.Combine(outputFolder, "allowFiles", "Individual File Results")).Select(v => Path.GetFileName(v).Substring(7)));
//check they're the same
Assert.IsTrue(expectedFiles.Except(writtenFiles).Count() == 0);
//check the second one is compressed and contains all the information
writtenFiles = new HashSet <string>(Directory.GetFiles(Path.Combine(outputFolder, "compressFiles")).Select(v => Path.GetFileName(v)));
//check the zip exists
Assert.IsTrue(writtenFiles.Contains("Individual File Results.zip"));
//check the original folder does not exist
string[] subfolders = Directory.GetDirectories(Path.Combine(outputFolder, "compressFiles"));
Assert.IsTrue(subfolders.Length == 0);
ZipFile.ExtractToDirectory(Path.Combine(outputFolder, "compressFiles", "Individual File Results.zip"), Path.Combine(outputFolder, "compressFiles", "Individual File Results"));
//read the extracted files
writtenFiles = new HashSet <string>(Directory.GetFiles(Path.Combine(outputFolder, "compressFiles", "Individual File Results")).Select(v => Path.GetFileName(v).Substring(7)));
//check they're the same
Assert.IsTrue(expectedFiles.Except(writtenFiles).Count() == 0);
//check the last one to make sure nothing was written except for the mzID files
writtenFiles = new HashSet <string>(Directory.GetFiles(Path.Combine(outputFolder, "noFiles", "Individual File Results")).Select(v => Path.GetFileName(v).Substring(7)));
Assert.IsTrue(writtenFiles.Count == 1);
Assert.IsTrue(writtenFiles.Contains(".mzID"));
Directory.Delete(outputFolder, true);
//Do a check that we don't crash if there's only one file but somebody tries to zip the individual file results
SearchTask weirdTask = new SearchTask();
weirdTask.SearchParameters.CompressIndividualFiles = true;
weirdTask.SearchParameters.WriteMzId = false;
new EverythingRunnerEngine(new List <(string, MetaMorpheusTask)> {
("weird", weirdTask)
}, new List <string> {
public static void TestAutodetectDissocationTypeFromScanHeader()
{
SearchTask searchTask = new SearchTask()
{
SearchParameters = new SearchParameters
{
DoQuantification = false // quant disabled just to save some time
},
// use DissociationType.Autodetect as the dissociation type. this signals to the search that the dissociation type
// should be taken from the scan header on a scan-specific basis
CommonParameters = new CommonParameters(dissociationType: DissociationType.Autodetect)
};
string myFile = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\SmallCalibratible_Yeast.mzML");
string myDatabase = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\smalldb.fasta");
string folderPath = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestAutodetectDissocationTypeFromScanHeader");
DbForTask db = new DbForTask(myDatabase, false);
// run the task
var autoTaskFolder = Path.Combine(folderPath, @"Autodetect");
Directory.CreateDirectory(autoTaskFolder);
searchTask.RunTask(autoTaskFolder, new List <DbForTask> {
db
}, new List <string> {
myFile
}, "");
// run identical task but select the HCD dissociation type instead of autodetect
var hcdTaskFolder = Path.Combine(folderPath, @"HCD");
Directory.CreateDirectory(hcdTaskFolder);
searchTask = new SearchTask()
{
SearchParameters = new SearchParameters
{
DoQuantification = false
},
CommonParameters = new CommonParameters(dissociationType: DissociationType.HCD)
};
searchTask.RunTask(hcdTaskFolder, new List <DbForTask> {
db
}, new List <string> {
myFile
}, "");
// check search results
var psmFileAutodetect = File.ReadAllLines(Path.Combine(autoTaskFolder, "AllPSMs.psmtsv"));
var psmFileHcd = File.ReadAllLines(Path.Combine(hcdTaskFolder, "AllPSMs.psmtsv"));
Assert.That(psmFileAutodetect.Length == psmFileHcd.Length);
for (int i = 0; i < psmFileAutodetect.Length; i++)
{
Assert.That(psmFileAutodetect[i].Equals(psmFileHcd[i]));
}
// clean up
Directory.Delete(folderPath, true);
}
public static void InternalFragmentIonTest()
{
SearchTask searchTask = new SearchTask()
{
SearchParameters = new SearchParameters
{
MinAllowedInternalFragmentLength = 1
},
CommonParameters = new CommonParameters(
digestionParams: new DigestionParams("top-down"),
listOfModsVariable: new List <(string, string)> {
("Common Variable", "Oxidation on M"),
("Common Biological", "Acetylation on K"),
("Common Biological", "Acetylation on X")
})
};
string myFile = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\InternalTest.mgf");
string myDatabase = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\InternalTest.fasta");
DbForTask db = new DbForTask(myDatabase, false);
List <(string, MetaMorpheusTask)> taskList = new List <(string, MetaMorpheusTask)> {
("TestInternal", searchTask)
};
var engine = new EverythingRunnerEngine(taskList, new List <string> {
myFile
}, new List <DbForTask> {
new DbForTask(myDatabase, false)
}, Environment.CurrentDirectory);
engine.Run();
string outputPath = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestInternal\AllPSMs.psmtsv");
//var output = File.ReadAllLines(outputPath);
//read the psmtsv
List <PsmFromTsv> psms = PsmTsvReader.ReadTsv(outputPath, out var warning);
Assert.IsTrue(psms.Count == 1);
//check that it's been disambiguated
Assert.IsFalse(psms[0].FullSequence.Contains("|"));
int numTotalFragments = psms[0].MatchedIons.Count;
//test again but no variable acetyl on K. Make sure that internal fragments are still searched even without ambiguity
searchTask = new SearchTask()
{
SearchParameters = new SearchParameters
{
MinAllowedInternalFragmentLength = 1
},
CommonParameters = new CommonParameters(
digestionParams: new DigestionParams("top-down"),
listOfModsVariable: new List <(string, string)> {
("Common Variable", "Oxidation on M"),
("Common Biological", "Acetylation on X")
})
};
taskList = new List <(string, MetaMorpheusTask)> {
("TestInternal", searchTask)
};
engine = new EverythingRunnerEngine(taskList, new List <string> {
myFile
}, new List <DbForTask> {
new DbForTask(myDatabase, false)
}, Environment.CurrentDirectory);
engine.Run();
psms = PsmTsvReader.ReadTsv(outputPath, out warning);
Assert.IsTrue(psms.Count == 1);
Assert.IsTrue(psms[0].MatchedIons.Count == numTotalFragments);
Directory.Delete(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestInternal"), true);
}
public ProteinDbForDataGrid(DbForTask uu)
{
Use = true;
Contaminant = uu.IsContaminant;
FilePath = uu.FilePath;
}
