private void TestTopDownSearch(string specFilePath, string dbFilePath, string outputDir, AminoAcidSet aaSet,
int minSequenceLength, int maxSequenceLength,
int minPrecursorIonCharge, int maxPrecursorIonCharge,
int minProductIonCharge, int maxProductIonCharge,
double minSequenceMass, double maxSequenceMass,
DatabaseSearchMode tda, InternalCleavageType searchMode)
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
// Search parameters
const int maxNumNTermCleavages = 1; // 30
const int maxNumCTermCleavages = 0;
const int precursorIonTolerancePpm = 10;
const int productIonTolerancePpm = 10;
var topDownOptions = new MsPfParameters(
specFilePath,
dbFilePath,
outputDir,
aaSet, "")
{
MinSequenceLength = minSequenceLength,
MaxSequenceLength = maxSequenceLength,
MaxNumNTermCleavages = maxNumNTermCleavages,
MaxNumCTermCleavages = maxNumCTermCleavages,
MinPrecursorIonCharge = minPrecursorIonCharge,
MaxPrecursorIonCharge = maxPrecursorIonCharge,
MinProductIonCharge = minProductIonCharge,
MaxProductIonCharge = maxProductIonCharge,
MinSequenceMass = minSequenceMass,
MaxSequenceMass = maxSequenceMass,
PrecursorIonTolerancePpm = precursorIonTolerancePpm,
ProductIonTolerancePpm = productIonTolerancePpm,
TargetDecoySearchMode = tda,
InternalCleavageMode = searchMode,
};
var topDownLauncher = new IcTopDownLauncher(topDownOptions);
//topDownLauncher.ForceParallel = true;
//topDownLauncher.MaxNumThreads = -1;
topDownLauncher.RunSearch(0.7);
//topDownLauncher.RunIntactProteinSearch();
}
public void TestTopDownSearch(string specFilePath, string dbFilePath, string outputDir, AminoAcidSet aaSet,
int minSequenceLength, int maxSequenceLength,
int minPrecursorIonCharge, int maxPrecursorIonCharge,
int minProductIonCharge, int maxProductIonCharge,
double minSequenceMass, double maxSequenceMass,
bool?tda, int searchMode)
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
// Search parameters
const int maxNumNTermCleavages = 1; // 30
const int maxNumCTermCleavages = 0;
const int precursorIonTolerancePpm = 10;
const int productIonTolerancePpm = 10;
var topDownLauncher = new IcTopDownLauncher(
specFilePath,
dbFilePath,
outputDir,
aaSet, "")
{
MinSequenceLength = minSequenceLength,
MaxSequenceLength = maxSequenceLength,
MaxNumNTermCleavages = maxNumNTermCleavages,
MaxNumCTermCleavages = maxNumCTermCleavages,
MinPrecursorIonCharge = minPrecursorIonCharge,
MaxPrecursorIonCharge = maxPrecursorIonCharge,
MinProductIonCharge = minProductIonCharge,
MaxProductIonCharge = maxProductIonCharge,
MinSequenceMass = minSequenceMass,
MaxSequenceMass = maxSequenceMass,
PrecursorIonTolerancePpm = precursorIonTolerancePpm,
ProductIonTolerancePpm = productIonTolerancePpm,
RunTargetDecoyAnalysisBool = tda,
SearchModeInt = searchMode,
};
//topDownLauncher.ForceParallel = true;
//topDownLauncher.MaxNumThreads = -1;
topDownLauncher.RunSearch(0.7);
//topDownLauncher.RunIntactProteinSearch();
}
public static int Main(string[] args)
{
var errorCode = 0;
#if (!DEBUG)
try
#endif
{
var handle = Process.GetCurrentProcess().MainWindowHandle;
SetConsoleMode(handle, EnableExtendedFlags);
var entryAsmName = System.Reflection.Assembly.GetEntryAssembly().GetName().Name;
var parser = new CommandLineParser <TopDownInputParameters>(entryAsmName, Version);
parser.UsageExamples.Add(string.Format("Perform a target+decoy search with default parameters and a mods file:\n{0}.exe -s testfile.raw -d sampleProteins.fasta -mod mods.txt -tda 1", entryAsmName));
// TODO: add more examples, maybe a link to GitHub?
var results = parser.ParseArgs(args);
if (!results.Success)
{
// Wait for 1.5 seconds
System.Threading.Thread.Sleep(1500);
return(-3);
}
if (!results.ParsedResults.Validate())
{
parser.PrintHelp();
// Wait for 1.5 seconds
System.Threading.Thread.Sleep(1500);
return(-3);
}
var parameters = results.ParsedResults;
Console.WriteLine(Name + " " + Version);
parameters.Display();
parameters.MaxNumNTermCleavages = 1; // max number of N-term cleavages
parameters.MaxNumCTermCleavages = 0; // max number of C-term cleavages
foreach (var specFilePath in parameters.SpecFilePaths)
{
// Update the spec file path in the parameters for each search
parameters.SpecFilePath = specFilePath;
parameters.Write();
var topDownLauncher = new IcTopDownLauncher(parameters);
var success = topDownLauncher.RunSearch();
if (success)
{
continue;
}
// topDownLauncher returned false (not successful)
// NOTE: The DMS Analysis Manager looks for this text; do not change it
var errorMsg = "Error processing " + Path.GetFileName(specFilePath) + ": ";
if (string.IsNullOrWhiteSpace(topDownLauncher.ErrorMessage))
{
errorMsg += "unknown error";
}
else
{
errorMsg += topDownLauncher.ErrorMessage;
}
Console.WriteLine(errorMsg);
if (errorCode == 0)
{
// This is the first error encountered; update the error code
// (though we will continue processing the next file if there is one)
errorCode = -Math.Abs(errorMsg.GetHashCode());
if (errorCode == 0)
{
return(-1);
}
else
{
return(errorCode);
}
}
}
}
#if (!DEBUG)
catch (Exception ex)
{
// NOTE: The DMS Analysis Manager looks for this text; do not change it
Console.WriteLine("Exception while processing: " + ex.Message);
Console.WriteLine(ex.StackTrace);
errorCode = -Math.Abs(ex.Message.GetHashCode());
System.Threading.Thread.Sleep(1500);
if (errorCode == 0)
{
return(-1);
}
else
{
return(errorCode);
}
}
#endif
return(errorCode);
}
public static int Main(string[] args)
{
var errorCode = 0;
#if (!DEBUG)
try
{
#endif
var handle = Process.GetCurrentProcess().MainWindowHandle;
SetConsoleMode(handle, EnableExtendedFlags);
if (args.Length == 0)
{
PrintUsageInfo();
return(-1);
}
if (args.Length % 2 != 0)
{
PrintUsageInfo("The number of arguments must be even");
return(-1);
}
// initialize parameters
var paramDic = new Dictionary <string, string>
{
{ "-s", null },
{ "-d", null },
{ "-o", null },
{ "-m", "1" },
{ "-mod", null },
{ "-t", "10" },
{ "-f", "10" },
{ "-tda", "0" },
{ "-minLength", "21" },
{ "-maxLength", "300" },
{ "-minCharge", "2" },
{ "-maxCharge", "60" },
{ "-minFragCharge", "1" },
{ "-maxFragCharge", "20" },
{ "-minMass", "2000.0" },
{ "-maxMass", "50000.0" },
{ "-feature", null },
{ "-threads", "0" },
{ "-tagSearch", "1" },
};
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(-2);
}
paramDic[key] = value;
}
var parameters = new TopDownInputParameters();
var message = parameters.Parse(paramDic);
if (message != null)
{
PrintUsageInfo(message);
return(-3);
}
Console.WriteLine(Name + " " + Version);
parameters.Display();
parameters.Write();
foreach (var specFilePath in parameters.SpecFilePaths)
{
var topDownLauncher = new IcTopDownLauncher(
specFilePath,
parameters.DatabaseFilePath,
parameters.OutputDir,
parameters.AminoAcidSet,
parameters.FeatureFilePath)
{
MinSequenceLength = parameters.MinSequenceLength,
MaxSequenceLength = parameters.MaxSequenceLength,
MaxNumNTermCleavages = 1, // max number of N-term cleavages
MaxNumCTermCleavages = 0, // max number of C-term cleavages
MinPrecursorIonCharge = parameters.MinPrecursorIonCharge,
MaxPrecursorIonCharge = parameters.MaxPrecursorIonCharge,
MinProductIonCharge = parameters.MinProductIonCharge,
MaxProductIonCharge = parameters.MaxProductIonCharge,
MinSequenceMass = parameters.MinSequenceMass,
MaxSequenceMass = parameters.MaxSequenceMass,
PrecursorIonTolerancePpm = parameters.PrecursorIonTolerancePpm,
ProductIonTolerancePpm = parameters.ProductIonTolerancePpm,
//RunTargetDecoyAnalysisBool = parameters.TdaBool,
RunTargetDecoyAnalysis = parameters.Tda,
//SearchModeInt = parameters.SearchModeInt,
SearchMode = parameters.SearchMode,
MaxNumThreads = parameters.MaxNumThreads,
TagBasedSearch = parameters.TagBasedSearch
};
var success = topDownLauncher.RunSearch();
if (success)
{
continue;
}
// topDownLauncher returned false (not successful)
// NOTE: The DMS Analysis Manager looks for this text; do not change it
var errorMsg = "Error processing " + Path.GetFileName(specFilePath) + ": ";
if (string.IsNullOrWhiteSpace(topDownLauncher.ErrorMessage))
{
errorMsg += "unknown error";
}
else
{
errorMsg += topDownLauncher.ErrorMessage;
}
Console.WriteLine(errorMsg);
if (errorCode == 0)
{
// This is the first error encountered; update the error code
// (though we will continue processing the next file if there is one)
errorCode = -Math.Abs(errorMsg.GetHashCode());
if (errorCode == 0)
{
return(-1);
}
else
{
return(errorCode);
}
}
}
#if (!DEBUG)
}
catch (Exception ex)
{
// NOTE: The DMS Analysis Manager looks for this text; do not change it
Console.WriteLine("Exception while processing: " + ex.Message);
Console.WriteLine(ex.StackTrace);
errorCode = -Math.Abs(ex.Message.GetHashCode());
System.Threading.Thread.Sleep(1500);
if (errorCode == 0)
{
return(-1);
}
else
{
return(errorCode);
}
}
#endif
return(errorCode);
}
