/// <summary>
/// The main entry point for the application.
/// </summary>
static int Main(string[] args)
{
var handle = System.Diagnostics.Process.GetCurrentProcess().MainWindowHandle;
SetConsoleMode(handle, ENABLE_EXTENDED_FLAGS);
var clusterIdMap = new Dictionary <int, UMCClusterLight>();
try
{
if (args.Length < 2)
{
Console.WriteLine("MultiAlignSTACRunner crosstabDirectory databasePath outputName");
Console.WriteLine("\tThe cross-tab file will be named similar to the database path");
return(1);
}
// Setup the analysis processing
Logger.PrintMessage("Find all datasets", true);
var directoryPath = args[0].Replace("\r", "").Replace("\n", "");
var databasePath = args[1].Replace("\r", "").Replace("\n", "");
var name = args[2].Replace("\r", "").Replace("\n", "");
var files = Directory.GetFiles(directoryPath, "*.csv");
Logger.PrintMessage("Creating Log File");
var loggerPath = AnalysisPathUtils.BuildLogPath(Path.GetDirectoryName(name), Path.GetFileNameWithoutExtension(name));
Logger.LogPath = loggerPath;
Logger.PrintMessage("Saving Log Data to: " + loggerPath);
Logger.PrintMessage(string.Format("Creating STAC"), true);
// Hardcode bad, but per discussions with OHSU
var stac = new STACAdapter <UMCClusterLight>
{
Options = new FeatureMatcherParameters
{
UserTolerances =
{
MassTolerancePPM = 25,
NETTolerance = .035,
DriftTimeTolerance = 3
},
UseDriftTime = true
}
};
var clusterFilteringOptions = new FilteringOptions();
WriteOptionsToLogFile(clusterFilteringOptions);
WriteOptionsToLogFile(stac.Options);
// Read the cluster data
var allClusters = new List <UMCClusterLight>();
var clusterId = 0;
foreach (var file in files)
{
var filename = Path.GetFileName(file);
Logger.PrintMessage(string.Format("Reading {0}", filename));
const string chargeString = "charge";
if (filename == null)
{
continue;
}
if (!filename.Contains(chargeString))
{
continue;
}
// Read each file.
var start = DateTime.Now;
var xname = filename.Replace("_", "");
// ReSharper disable once StringIndexOfIsCultureSpecific.1
var indexOfChargeString = xname.IndexOf(chargeString);
var charge = Convert.ToInt32(xname.Substring(indexOfChargeString + chargeString.Length, 1));
var clusters = ReadClusters(file, clusterFilteringOptions);
var end = DateTime.Now;
Logger.PrintMessage(string.Format("\tReading Took {0:.00} seconds", end.Subtract(start).TotalSeconds));
foreach (var cluster in clusters)
{
clusterIdMap.Add(clusterId, cluster);
cluster.Id = clusterId++;
cluster.ChargeState = charge;
}
allClusters.AddRange(clusters);
}
// Load the database
Logger.PrintMessage(string.Format("Loading Mass Tag Database: {0}", Path.GetFileNameWithoutExtension(databasePath)));
var options = new MassTagDatabaseOptions();
var databaseDefinition = new InputDatabase
{
DatabaseFormat = MassTagDatabaseFormat.Sqlite,
LocalPath = databasePath
};
var database = MtdbLoaderFactory.LoadMassTagDatabase(databaseDefinition, options);
// Run stac
try
{
Logger.PrintMessage("Matching clusters to peptides in mass tag database.");
var matches = stac.PerformPeakMatching(allClusters, database);
Logger.PrintMessage(string.Format("Writing Results To {0}", name));
var duplicateMatches = new Dictionary <int, Dictionary <int, FeatureMatchLight <UMCClusterLight, MassTagLight> > >();
foreach (var match in matches)
{
if (!duplicateMatches.ContainsKey(match.Observed.Id))
{
duplicateMatches.Add(match.Observed.Id, new Dictionary <int, FeatureMatchLight <UMCClusterLight, MassTagLight> >());
}
if (!duplicateMatches[match.Observed.Id].ContainsKey(match.Target.Id))
{
duplicateMatches[match.Observed.Id].Add(match.Target.Id, match);
}
}
WriteClusterData(name, duplicateMatches, clusterIdMap);
Logger.PrintMessage("ANALYSIS SUCCESS");
return(0);
}
catch (Exception ex)
{
Logger.PrintMessage("Unhandled Error: " + ex.Message);
var innerEx = ex.InnerException;
while (innerEx != null)
{
Logger.PrintMessage("Inner Exception: " + innerEx.Message);
innerEx = innerEx.InnerException;
}
Logger.PrintMessage("Stack: " + ex.StackTrace);
Logger.PrintMessage("");
Logger.PrintMessage("ANALYSIS FAILED");
return(1);
}
}
catch (Exception ex)
{
Logger.PrintMessage("Unhandled Error: " + ex.Message, true);
var innerEx = ex.InnerException;
while (innerEx != null)
{
Logger.PrintMessage("Inner Exception: " + innerEx.Message);
innerEx = innerEx.InnerException;
}
Logger.PrintMessage("Stack: " + ex.StackTrace, true);
Logger.PrintMessage("");
Logger.PrintMessage("ANALYSIS FAILED");
return(1);
}
}
/// <summary>
/// The main entry point for the application.
/// </summary>
static int Main(string[] args)
{
var handle = System.Diagnostics.Process.GetCurrentProcess().MainWindowHandle;
SetConsoleMode(handle, ENABLE_EXTENDED_FLAGS);
var clusterIdMap = new Dictionary<int, UMCClusterLight>();
try
{
if (args.Length < 2)
{
Console.WriteLine("MultiAlignSTACRunner crosstabDirectory databasePath outputName");
Console.WriteLine("\tThe cross-tab file will be named similar to the database path");
return 1;
}
// Setup the analysis processing
Logger.PrintMessage("Find all datasets", true);
var directoryPath = args[0].Replace("\r","").Replace("\n","");
var databasePath = args[1].Replace("\r","").Replace("\n","");
var name = args[2].Replace("\r","").Replace("\n","");
var files = Directory.GetFiles(directoryPath, "*.csv");
Logger.PrintMessage("Creating Log File");
var loggerPath = AnalysisPathUtils.BuildLogPath(Path.GetDirectoryName(name), Path.GetFileNameWithoutExtension(name));
Logger.LogPath = loggerPath;
Logger.PrintMessage("Saving Log Data to: " + loggerPath);
Logger.PrintMessage(string.Format("Creating STAC"), true);
// Hardcode bad, but per discussions with OHSU
var stac = new STACAdapter<UMCClusterLight>
{
Options = new FeatureMatcherParameters
{
UserTolerances =
{
MassTolerancePPM = 25,
NETTolerance = .035,
DriftTimeTolerance = 3
},
UseDriftTime = true
}
};
var clusterFilteringOptions = new FilteringOptions();
WriteOptionsToLogFile(clusterFilteringOptions);
WriteOptionsToLogFile(stac.Options);
// Read the cluster data
var allClusters = new List<UMCClusterLight>();
var clusterId = 0;
foreach (var file in files)
{
var filename = Path.GetFileName(file);
Logger.PrintMessage(string.Format("Reading {0}", filename));
const string chargeString = "charge";
if (filename == null)
continue;
if (!filename.Contains(chargeString))
continue;
// Read each file.
var start = DateTime.Now;
var xname = filename.Replace("_", "");
// ReSharper disable once StringIndexOfIsCultureSpecific.1
var indexOfChargeString = xname.IndexOf(chargeString);
var charge = Convert.ToInt32(xname.Substring(indexOfChargeString + chargeString.Length, 1));
var clusters = ReadClusters(file, clusterFilteringOptions);
var end = DateTime.Now;
Logger.PrintMessage(string.Format("\tReading Took {0:.00} seconds", end.Subtract(start).TotalSeconds));
foreach (var cluster in clusters)
{
clusterIdMap.Add(clusterId, cluster);
cluster.Id = clusterId++;
cluster.ChargeState = charge;
}
allClusters.AddRange(clusters);
}
// Load the database
Logger.PrintMessage(string.Format("Loading Mass Tag Database: {0}", Path.GetFileNameWithoutExtension(databasePath)));
var options = new MassTagDatabaseOptions();
var databaseDefinition = new InputDatabase
{
DatabaseFormat = MassTagDatabaseFormat.Sqlite,
LocalPath = databasePath
};
var database = MtdbLoaderFactory.LoadMassTagDatabase(databaseDefinition, options);
// Run stac
try
{
Logger.PrintMessage("Matching clusters to peptides in mass tag database.");
var matches = stac.PerformPeakMatching(allClusters, database);
Logger.PrintMessage(string.Format("Writing Results To {0}", name));
var duplicateMatches = new Dictionary<int, Dictionary<int, FeatureMatchLight<UMCClusterLight, MassTagLight>>>();
foreach (var match in matches)
{
if (!duplicateMatches.ContainsKey(match.Observed.Id))
duplicateMatches.Add(match.Observed.Id, new Dictionary<int, FeatureMatchLight<UMCClusterLight, MassTagLight>>());
if (!duplicateMatches[match.Observed.Id].ContainsKey(match.Target.Id))
duplicateMatches[match.Observed.Id].Add(match.Target.Id, match);
}
WriteClusterData(name, duplicateMatches, clusterIdMap);
Logger.PrintMessage("ANALYSIS SUCCESS");
return 0;
}
catch (Exception ex)
{
Logger.PrintMessage("Unhandled Error: " + ex.Message);
var innerEx = ex.InnerException;
while (innerEx != null)
{
Logger.PrintMessage("Inner Exception: " + innerEx.Message);
innerEx = innerEx.InnerException;
}
Logger.PrintMessage("Stack: " + ex.StackTrace);
Logger.PrintMessage("");
Logger.PrintMessage("ANALYSIS FAILED");
return 1;
}
}
catch (Exception ex)
{
Logger.PrintMessage("Unhandled Error: " + ex.Message, true);
var innerEx = ex.InnerException;
while (innerEx != null)
{
Logger.PrintMessage("Inner Exception: " + innerEx.Message);
innerEx = innerEx.InnerException;
}
Logger.PrintMessage("Stack: " + ex.StackTrace, true);
Logger.PrintMessage("");
Logger.PrintMessage("ANALYSIS FAILED");
return 1;
}
}
private static bool ShouldFilterCluster(UMCClusterLight cluster, FilteringOptions options)
{
//
// Total dataset member count ~
// Ratio of members dataset : total
// 1 but not > 1.5-2
//
var datasetMemberCount = cluster.DatasetMemberCount;
if (datasetMemberCount < options.TotalDatasetMembers)
return true;
var totalMembers = cluster.MemberCount;
var ratio = Convert.ToDouble(totalMembers)/Convert.ToDouble(datasetMemberCount);
if (ratio <= options.MaxRatio && ratio >= options.MinRatio)
return false;
return true;
}
private static void WriteOptionsToLogFile(FilteringOptions clusterFilteringOptions)
{
Logger.PrintMessage("Cluster Filtering Options");
Logger.PrintMessage(string.Format("\tMax Cluster Total to Dataset Ratio:{0}", clusterFilteringOptions.MaxRatio));
Logger.PrintMessage(string.Format("\tMin Cluster Total to Dataset Ratio:{0}", clusterFilteringOptions.MinRatio));
Logger.PrintMessage(string.Format("\tRequired Total Members:{0}", clusterFilteringOptions.TotalDatasetMembers));
}
/// <summary>
/// Reads the clusters and filters cluster by cluster.
/// </summary>
private static List<UMCClusterLight> ReadClusters(string path, FilteringOptions options)
{
var clusters = new List<UMCClusterLight>();
var totalClusters = 0;
using (TextReader reader = File.OpenText(path))
{
reader.ReadLine();
string line;
while ((line = reader.ReadLine()) != null)
{
var data = line.Split(',');
var mass = Convert.ToDouble(data[CONST_COLUMN_MASS]);
var retentionTime = Convert.ToDouble(data[CONST_COLUMN_NET]);
var cluster = new UMCClusterLight
{
Id = Convert.ToInt32(data[CONST_COLUMN_ID]),
MassMonoisotopic = mass,
MassMonoisotopicAligned = mass,
NetAligned = retentionTime,
Net = retentionTime,
DriftTime = Convert.ToDouble(data[CONST_COLUMN_DRIFT]),
Tightness = Convert.ToDouble(data[CONST_COLUMN_TIGHTNESS]),
AmbiguityScore = Convert.ToDouble(data[CONST_COLUMN_AMBIGUITY]),
DatasetMemberCount = Convert.ToInt32(data[CONST_COLUMN_DATASET_MEMBERS]),
MemberCount = Convert.ToInt32(data[CONST_COLUMN_TOTAL_MEMBERS])
};
var shouldFilter = ShouldFilterCluster(cluster, options);
if (!shouldFilter)
clusters.Add(cluster);
totalClusters++;
}
}
Logger.PrintMessage(string.Format("Found {0} filtered clusters from {1} total clusters", clusters.Count, totalClusters));
return clusters;
}
