/// <summary>
/// Execute the analysis
/// </summary>
/// <param name = "commandArgs"></param>
override public void Execute(Args commandArgs)
{
Console.WriteLine(commandArgs.StringEnumArgs[Arguments.Tissue]);
var nullMapBuilder = new NullMapBuilder(commandArgs.StringEnumArgs[Arguments.Config]);
IMapBuilder builder = IUnknown.QueryInterface <IMapBuilder>(nullMapBuilder);
if (commandArgs.StringEnumArgs.ContainsKey(Arguments.LocusFileName))
{
builder.LocusFileName = commandArgs.StringEnumArgs[Arguments.LocusFileName];
}
if (commandArgs.StringEnumArgs.ContainsKey(Arguments.MapFileName))
{
builder.MapFileName = commandArgs.StringEnumArgs[Arguments.MapFileName];
nullMapBuilder.GeneMap = commandArgs.Flags.Contains(Arguments.GeneMap.ToString());
}
builder.OutDir = commandArgs.StringEnumArgs.ContainsKey(Arguments.OutDir) ?
commandArgs.StringEnumArgs[Arguments.OutDir] :
builder.OutDir = ".";
builder.Tissue = commandArgs.StringEnumArgs[Arguments.Tissue];
builder.RnaSource = commandArgs.StringEnumArgs[Arguments.RnaSource];
builder.LocusFilterRange = commandArgs.IntArgs.ContainsKey(Arguments.RemoveGeneBodyTranscripts.ToString()) ?
commandArgs.IntArgs[Arguments.RemoveGeneBodyTranscripts.ToString()] :
0;
if (commandArgs.StringEnumArgs.ContainsKey(Arguments.TissueSources))
{
builder.TissueSources = commandArgs.StringEnumArgs[Arguments.TissueSources].Split('\t');
}
Stage stage = (Stage)Enum.Parse(typeof(Stage), commandArgs.StringEnumArgs[Arguments.Stage]);
switch (stage)
{
case Stage.Preprocess:
builder.PreprocessExpression();
break;
case Stage.BuildMap:
builder.BuildMap();
break;
case Stage.RunPipeline:
builder.PreprocessExpression();
builder.BuildMap();
break;
case Stage.FilterMap:
nullMapBuilder.FilterMap((MapLinkFilter.LinkType)Enum.Parse(typeof(MapLinkFilter.LinkType), commandArgs.StringEnumArgs[Arguments.MapType]));
break;
default:
throw new Exception("Invalid stage argument: " + commandArgs.StringEnumArgs[Arguments.Stage] + "\nValid values: Preprocess, BuildMap");
}
}
/// <summary>
/// Execute the analysis for which this class is the factor with the given command line arguments.
/// </summary>
/// <param name="commandArgs">Command arguments.</param>
public override void Execute(Args commandArgs)
{
IMapBuilder builder = IUnknown.QueryInterface <IMapBuilder>(new CorrelationMapBuilder(
commandArgs.StringEnumArgs[Arguments.Config],
commandArgs.StringEnumArgs.GetOptional(Arguments.OmittedTissues)));
this.ReflectStringArgs(builder, new Arguments[]
{
Arguments.Tissue,
Arguments.HistoneName,
Arguments.RnaSource,
});
this.ReflectOptionalStringArgs(builder, new Arguments[]
{
Arguments.LocusFileName,
Arguments.MapFileName,
});
this.ReflectOptionalString(builder, Arguments.OutDir, ".");
this.ReflectFlag(builder, Arguments.UseGenes);
this.ReflectOptionalInt(builder, Arguments.LocusFilterRange, 0);
Stage stage = (Stage)Enum.Parse(typeof(Stage), commandArgs.StringEnumArgs[Arguments.Stage]);
switch (stage)
{
case Stage.Preprocess:
builder.PreprocessExpression();
break;
case Stage.BuildMap:
builder.BuildMap();
break;
case Stage.RunPipeline:
builder.PreprocessExpression();
builder.BuildMap();
break;
default:
throw new Exception("Invalid stage argument: " + commandArgs.StringArgs["Stage"] + "\nValid values: Preprocess, BuildMap");
}
}
/// <summary>
/// Factory method for implementations of this interface
/// </summary>
/// <returns>The expression data.</returns>
/// <param name="filename">Filename.</param>
/// <param name="rnaType">Rna type.</param>
/// <param name="filetype">Filetype.</param>
/// <param name="annotation">Annotation.</param>
public static IExpressionData LoadExpressionData(string filename, string rnaType, string filetype, IAnnotation annotation)
{
Console.WriteLine("\tLoading expression file " + filename + " ... ");
IExpressionData data = null;
if (filetype == "gtf" || filetype == ".gtf")
{
data = IUnknown.QueryInterface <IExpressionData>(new GtfExpressionFile(GtfExpressionFile.ExpressionTypeFromString(rnaType), filename, annotation));
}
else
{
data = IUnknown.QueryInterface <IExpressionData>(new BedExpressionFile(filename, BedFile.BedExpression, annotation));
}
Console.WriteLine("\ttranscript count: " + data.Transcripts.Count);
Console.WriteLine("\tgene count: " + data.Genes.Count);
return(data);
}
/// <summary>
/// Convert the map to genes.
/// </summary>
public void Convert()
{
MapLinkFilter filter = new MapLinkFilter
{
MaximumLinkLength = this.MaxRange,
ConfidenceThreshold = this.PvalueThreshold,
LinkTypeFilter = MapLinkFilter.LinkType.Any,
};
TssRegulatoryMap map = TssRegulatoryMap.LoadMap(this.MapFileName, filter);
var expression = new GtfExpressionFile(
GtfExpressionFile.ExpressionTypeFromString(this.RnaSource),
this.AnnotationFileName);
var geneMap = map.ConvertToGenes(IUnknown.QueryInterface <IExpressionData>(expression));
foreach (var link in geneMap.Links)
{
var geneLocation = expression.Transcripts[link.TranscriptName];
string[] lineData = new string[]
{
geneLocation.Chromosome,
geneLocation.Start.ToString(),
geneLocation.End.ToString(),
link.GeneName,
"NA",
geneLocation.Strand,
link.LocusName,
link.Correlation.ToString(),
link.ConfidenceScore.ToString(),
link.LinkLength.ToString(),
this.HistoneName,
link.TranscriptName,
};
Console.WriteLine(string.Join("\t", lineData));
}
}