private static List <string> ProcessLine(ShowBy showBy, PredictorCollection predictorCollection, string line,
MerLength merLength, int?dOfCenter, HlaSetSpecification hlaSetSpecification, bool modelOnly)
{
try
{
string hlaOrSupertypeOrNull;
string inputPeptide = ExtractInputs(hlaSetSpecification, line, predictorCollection, out hlaOrSupertypeOrNull);
List <string> output = new List <string>();
foreach (List <Prediction> predictionList in predictorCollection.MaxProbabilityPredictions(showBy, inputPeptide, merLength, dOfCenter, hlaSetSpecification, hlaOrSupertypeOrNull, modelOnly).Values)
{
string outputLine = InsertMaterial(line, hlaSetSpecification.InputHeaderCollection().Length, Prediction.CollectionToString(predictionList, false, hlaSetSpecification.IncludeHlaInOutput()));
output.Add(outputLine);
}
return(output);
}
catch (Exception exception)
{
string errorString = SpecialFunctions.CreateTabString(
line,
string.Format("Error: {0}{1}", exception.Message, exception.InnerException == null ? "" : string.Format(" ({0})", exception.InnerException)));
List <string> output = new List <string>();
output.Add(errorString);
return(output);
}
}
static public string ExtractInputs(HlaSetSpecification hlaSetSpecification, string line, PredictorCollection predictorCollection, out string hlaOrSupertypeOrNull)
{
List <string> fieldCollection = SpecialFunctions.Split(line, '\t');
int inputLength = hlaSetSpecification.InputHeaderCollection().Length;
SpecialFunctions.CheckCondition(inputLength <= fieldCollection.Count, string.Format("Expected input to have at least {0} columns", inputLength));
string inputPeptide = fieldCollection[0];
hlaOrSupertypeOrNull = (inputLength > 1) ? fieldCollection[1] : null;
return(inputPeptide);
}
static public string CreateHeader(HlaSetSpecification hlaSetSpecification, TextReader textReader, bool inputHasHeader)
{
if (!inputHasHeader)
{
return(hlaSetSpecification.Header());
}
//!!!this code is very similar to that which processes the non-header lines. Could/should they be combined?
int splitPoint = hlaSetSpecification.InputHeaderCollection().Length;
string middleStuff = Prediction.ExtraHeader(hlaSetSpecification.IncludeHlaInOutput());
List <string> columnCollection = SpecialFunctions.Split(textReader.ReadLine(), '\t');
return(InsertMaterial(columnCollection, splitPoint, middleStuff));
}
public static void Main(string[] args)
{
try
{
// Parse arguments
ArgCollection argCollection = ArgCollection.GetInstance(args);
if (argCollection.ExtractOptionalFlag("Help"))
{
Console.WriteLine(HelpString);
return;
}
string modelName = argCollection.ExtractOptional("model", "LANLIEDB03062007");
bool modelOnly = argCollection.ExtractOptionalFlag("modelOnly");
bool inputHasHeader = argCollection.ExtractOptionalFlag("inputHasHeader");
MerLength merLength = argCollection.ExtractOptional <MerLength>("merLength", MerLength.scan);
int? dOfCenter = argCollection.ExtractOptional <int?>("withinDOfCenter", null);
ShowBy showBy = argCollection.ExtractOptional <ShowBy>("showBy", ShowBy.all);
string hlaSetName = argCollection.ExtractOptional <string>("hlaSet", "singleton");
HlaSetSpecification hlaSetSpecification = HlaSetSpecification.GetInstance(hlaSetName);
argCollection.CheckNoMoreOptions();
string inputFileName = argCollection.ExtractNext <string>("inputFile");
string outputFileName = argCollection.ExtractNext <string>("outputFile");
argCollection.CheckThatEmpty();
ReadInputCreatingOutput(showBy, modelName, inputHasHeader, merLength, dOfCenter, hlaSetSpecification, modelOnly, inputFileName, outputFileName);
}
catch (Exception exception)
{
Console.WriteLine("");
Console.WriteLine(exception.Message);
if (exception.InnerException != null)
{
Console.WriteLine(exception.InnerException.Message);
}
Console.Error.WriteLine("");
Console.Error.WriteLine(@"For more help:
Epipred -help");
System.Environment.Exit(-1);
}
}
private static void ReadInputCreatingOutput(ShowBy showBy, string modelName,
bool inputHasHeader, MerLength merLength, int?dOfCenter,
HlaSetSpecification hlaSetSpecification, bool modelOnly, string inputFileName, string outputFileName)
{
using (TextReader textReader = File.OpenText(inputFileName))
{
using (TextWriter textWriter = File.CreateText(outputFileName))
{
string header = CreateHeader(hlaSetSpecification, textReader, inputHasHeader);
textWriter.WriteLine(header);
PredictorCollection predictorCollection = PredictorCollection.GetInstance(modelName);
foreach (string line in SpecialFunctions.ReadEachLine(textReader))
{
foreach (string outputLine in ProcessLine(showBy, predictorCollection, line, merLength, dOfCenter, hlaSetSpecification, modelOnly))
{
textWriter.WriteLine(outputLine);
textWriter.Flush();
}
}
}
}
}
