public void TestChaoChao(string specFilePath)
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
if (!File.Exists(specFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, specFilePath);
}
const string dbFilePath = @"D:\Research\Data\ChaoChao\database\H_sapiens_Uniprot_SPROT_2013-05-01_withContam.fasta";
if (!File.Exists(dbFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, dbFilePath);
}
const string outputDir = @"D:\Research\Data\ChaoChao\Ic\";
// Configure amino acid set
//var carbamidomethylC = new SearchModification(Modification.Carbamidomethylation, 'C', SequenceLocation.Everywhere, true);
//var oxM = new SearchModification(Modification.Oxidation, 'M', SequenceLocation.Everywhere, false);
//var acetylN = new SearchModification(Modification.Acetylation, '*', SequenceLocation.ProteinNTerm, false);
//var pyroGluQ = new SearchModification(Modification.PyroGluQ, 'Q', SequenceLocation.Everywhere, false);
//var deamdN = new SearchModification(Modification.Deamidation, 'N', SequenceLocation.Everywhere, false);
//var deamdQ = new SearchModification(Modification.Deamidation, 'Q', SequenceLocation.Everywhere, false);
const int numMaxModsPerProtein = 0;
var searchModifications = new List<SearchModification>
{
//carbamidomethylC,
//acetylN,
//oxM
};
var aaSet = new AminoAcidSet(searchModifications, numMaxModsPerProtein);
bool? tda = true; // true: target & decoy, false: target, null: decoy
const int minSequenceLength = 7; // 7
const int maxSequenceLength = 150; // 1000
const int minPrecursorIonCharge = 1; // 3
const int maxPrecursorIonCharge = 30; // 67
const int minProductIonCharge = 1; // 1
const int maxProductIonCharge = 15; // 15
const double precursorIonTolerancePpm = 10;
const double productIonTolerancePpm = 10;
const double corrThreshold = 0.7;
var bottomUpLauncher = new IcBottomUpLauncher(
specFilePath,
dbFilePath,
outputDir,
aaSet,
null)
{
MinSequenceLength = minSequenceLength,
MaxSequenceLength = maxSequenceLength,
MinPrecursorIonCharge = minPrecursorIonCharge,
MaxPrecursorIonCharge = maxPrecursorIonCharge,
MinProductIonCharge = minProductIonCharge,
MaxProductIonCharge = maxProductIonCharge,
PrecursorIonTolerancePpm = precursorIonTolerancePpm,
ProductIonTolerancePpm = productIonTolerancePpm,
RunTargetDecoyAnalysisBool = tda,
NumTolerableTermini = 0
};
bottomUpLauncher.RunSearch(corrThreshold);
}
private static void Main(string[] args)
{
var handle = Process.GetCurrentProcess().MainWindowHandle;
SetConsoleMode(handle, EnableExtendedFlags);
if (args.Length % 2 != 0)
{
PrintUsageInfo("The number of arguments must be even.");
return;
}
// initialize parameters
var paramDic = new Dictionary<string, string>
{
{"-s", null},
{"-d", null},
{"-o", null},
{"-e", "1"},
{"-ntt", "2"},
{"-mod", null},
{"-t", "10"},
{"-f", "10"},
{"-tda", "0"},
{"-minLength", "6"},
{"-maxLength", "40"},
{"-minCharge", "1"},
{"-maxCharge", "4"},
{"-minFragCharge", "1"},
{"-maxFragCharge", "3"}
};
for (var i = 0; i < args.Length / 2; i++)
{
var key = args[2 * i];
var value = args[2 * i + 1];
if (!paramDic.ContainsKey(key))
{
PrintUsageInfo("Invalid parameter: " + key);
return;
}
paramDic[key] = value;
}
var parameters = new BottomUpInputParameters();
var message = parameters.Parse(paramDic);
if (message != null)
{
PrintUsageInfo(message);
return;
}
Console.WriteLine(Name + " " + Version);
parameters.Display();
parameters.Write();
foreach (string specFilePath in parameters.SpecFilePaths)
{
var bottomUpLauncher = new IcBottomUpLauncher(
specFilePath,
parameters.DatabaseFilePath,
parameters.OutputDir,
parameters.AminoAcidSet,
parameters.Enzyme)
{
MinSequenceLength = parameters.MinSequenceLength,
MaxSequenceLength = parameters.MaxSequenceLength,
MinPrecursorIonCharge = parameters.MinPrecursorIonCharge,
MaxPrecursorIonCharge = parameters.MaxPrecursorIonCharge,
MinProductIonCharge = parameters.MinProductIonCharge,
MaxProductIonCharge = parameters.MaxProductIonCharge,
PrecursorIonTolerancePpm = parameters.PrecursorIonTolerancePpm,
ProductIonTolerancePpm = parameters.ProductIonTolerancePpm,
//RunTargetDecoyAnalysisBool = parameters.TdaBool,
RunTargetDecoyAnalysis = parameters.Tda,
NumTolerableTermini = parameters.NumTolerableTermini,
};
bottomUpLauncher.RunSearch(CorrThreshold);
}
}
public void TestBottomUpSearch(string specFilePath, string dbFilePath, string outputDir, AminoAcidSet aaSet, bool? tda, int ntt, double corrThreshold = 0.3)
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
// Search parameters
const int minSequenceLength = 6; // 7
const int maxSequenceLength = 40; // 1000
const int minPrecursorIonCharge = 1; // 3
const int maxPrecursorIonCharge = 4; // 67
const int minProductIonCharge = 1; // 1
const int maxProductIonCharge = 2; // 15
const int precursorIonTolerancePpm = 10;
const int productIonTolerancePpm = 10;
var enzyme = Enzyme.Trypsin;
var bottomUpLauncher = new IcBottomUpLauncher(
specFilePath,
dbFilePath,
outputDir,
aaSet,
enzyme)
{
MinSequenceLength = minSequenceLength,
MaxSequenceLength = maxSequenceLength,
MinPrecursorIonCharge = minPrecursorIonCharge,
MaxPrecursorIonCharge = maxPrecursorIonCharge,
MinProductIonCharge = minProductIonCharge,
MaxProductIonCharge = maxProductIonCharge,
PrecursorIonTolerancePpm = precursorIonTolerancePpm,
ProductIonTolerancePpm = productIonTolerancePpm,
RunTargetDecoyAnalysisBool = tda,
NumTolerableTermini = ntt
};
bottomUpLauncher.RunSearch(corrThreshold);
//topDownLauncher.RunIntactProteinSearch();
}