public int Run(CanvasNormalizeParameters parameters)
{
_referenceGenerator.Run(parameters.weightedAverageNormalBedFile);
var ratios = _ratioCalculator.Run(parameters.tumorBedFile, parameters.weightedAverageNormalBedFile);
CanvasNormalizeUtilities.RatiosToCounts(ratios, parameters.ploidyBedFile, parameters.outBedFile);
CanvasNormalizeUtilities.WriteCndFile(parameters.tumorBedFile, parameters.weightedAverageNormalBedFile,
ratios, new FileLocation(parameters.outBedFile.FullName + CndFileSuffix));
return(0);
}
static int Main(string[] args)
{
CanvasCommon.Utilities.LogCommandLine(args);
CanvasNormalizeParameters parameters = CanvasNormalizeParameters.ParseCommandLine(args);
if (parameters == null)
{
return(1);
}
return(CanvasNormalize.Run(parameters));
}
static int Main(string[] args)
{
CanvasCommon.Utilities.LogCommandLine(args);
CanvasNormalizeParameters parameters = CanvasNormalizeParameters.ParseCommandLine(args);
if (parameters == null)
{
return(1);
}
CanvasNormalizeFactory factory = new CanvasNormalizeFactory(parameters);
return(new CanvasNormalize(factory.GetReferenceGenerator(), factory.GetRatioCalculator())
.Run(parameters));
}
public static int Run(CanvasNormalizeParameters parameters)
{
NexteraManifest manifest = string.IsNullOrEmpty(parameters.manifestPath) ? null : new NexteraManifest(parameters.manifestPath, null, Console.WriteLine);
switch (parameters.normalizationMode)
{
case CanvasNormalizeMode.BestLR2:
GetBestLR2BinCount(parameters.tumorBedPath, parameters.normalBedPaths, parameters.weightedAverageNormalBedPath,
manifest: manifest);
break;
case CanvasNormalizeMode.WeightedAverage:
GetWeightedAverageBinCount(parameters.normalBedPaths, parameters.weightedAverageNormalBedPath, manifest: manifest);
break;
default:
throw new Exception(string.Format("Invalid CanvasNormalize mode '{0}'", parameters.normalizationMode));
}
GetBinRatio(parameters.tumorBedPath, parameters.weightedAverageNormalBedPath, parameters.outBedPath, parameters.ploidyBedPath);
return 0;
}
public static int Run(CanvasNormalizeParameters parameters)
{
NexteraManifest manifest = string.IsNullOrEmpty(parameters.manifestPath) ? null : new NexteraManifest(parameters.manifestPath, null, Console.WriteLine);
switch (parameters.normalizationMode)
{
case CanvasNormalizeMode.BestLR2:
GetBestLR2BinCount(parameters.tumorBedPath, parameters.normalBedPaths, parameters.weightedAverageNormalBedPath,
manifest: manifest);
break;
case CanvasNormalizeMode.WeightedAverage:
GetWeightedAverageBinCount(parameters.normalBedPaths, parameters.weightedAverageNormalBedPath, manifest: manifest);
break;
default:
throw new Exception(string.Format("Invalid CanvasNormalize mode '{0}'", parameters.normalizationMode));
}
GetBinRatio(parameters.tumorBedPath, parameters.weightedAverageNormalBedPath, parameters.outBedPath,
parameters.ploidyBedPath, manifest: manifest);
return(0);
}
public static CanvasNormalizeParameters ParseCommandLine(string[] args)
{
CanvasNormalizeParameters parameters = new CanvasNormalizeParameters();
parameters.normalizationMode = CanvasCommon.CanvasNormalizeMode.WeightedAverage;
// Should I display a help message?
bool needHelp = false;
OptionSet p = new OptionSet()
{
{ "t|tumor=", "bed file containing bin counts for the tumor sample", v => parameters.tumorBedFile = new FileLocation(v) },
{ "n|normal=", "bed file containing bin counts for a normal sample. Pass this option multiple times, once for each normal sample.\nIn PCA mode, model file containing the mean vector and the axes for projection. Pass this option only once.", v => parameters.normalBedFiles.Add(new FileLocation(v)) },
{ "o|out=", "bed file to output containing normalized bin counts", v => parameters.outBedFile = new FileLocation(v) },
{ "w|weightedAverageNormal=", "bed file to output containing reference bin counts", v => parameters.weightedAverageNormalBedFile = new FileLocation(v) },
{ "f|manifest=", "Nextera manifest file", v => parameters.manifestFile = new FileLocation(v) },
{ "p|ploidyBedFile=", "bed file specifying reference ploidy (e.g. for sex chromosomes) (optional)", v => parameters.ploidyBedFile = new FileLocation(v) },
{ "r|referenceBinCountRange=", "reference bin count range for the PCA mode. Default: (1, infinity). Pass this option twice to specify the min and the max (optional)", v => parameters.referenceBinCountRange.Add(double.Parse(v)) },
{ "h|help", "show this message and exit", v => needHelp = v != null },
{ "m|mode=", "normalization mode (WeightedAverage/BestLR2/PCA). Default: " + parameters.normalizationMode, v => parameters.normalizationMode = CanvasCommon.Utilities.ParseCanvasNormalizeMode(v) },
};
Console.WriteLine("CanvasNormalize {0}", System.Reflection.Assembly.GetEntryAssembly().GetName().Version.ToString());
List <string> extraArgs = p.Parse(args);
// Check for required arguments. Display the help message if any of them are missing.
if (parameters.tumorBedFile == null)
{
Console.Error.WriteLine("Please specify the tumor bed file.");
needHelp = true;
}
else if (!parameters.normalBedFiles.Any())
{
if (parameters.normalizationMode == CanvasNormalizeMode.PCA)
{
Console.Error.WriteLine("Please specify a model file.");
}
else
{
Console.Error.WriteLine("Please specify at least one normal bed file.");
}
needHelp = true;
}
else if (parameters.outBedFile == null)
{
Console.Error.WriteLine("Please specify an output file name.");
needHelp = true;
}
if (!parameters.referenceBinCountRange.Any()) // default to 1 and infinity
{
parameters.referenceBinCountRange = new List <double>()
{
1, double.PositiveInfinity
};
}
else if (parameters.referenceBinCountRange.Count != 2)
{
Console.Error.WriteLine("Please specify -r exactly twice.");
needHelp = true;
}
if (needHelp)
{
ShowHelp(p);
return(null);
}
// Does the tumor bed file exist?
if (!parameters.tumorBedFile.Exists)
{
Console.WriteLine("CanvasNormalize.exe: File {0} does not exist! Exiting.", parameters.tumorBedFile);
return(null);
}
// Does each of the normal bed files exist?
foreach (var normalBedFile in parameters.normalBedFiles)
{
if (!normalBedFile.Exists)
{
Console.WriteLine("CanvasNormalize.exe: File {0} does not exist! Exiting.", normalBedFile.FullName);
return(null);
}
}
// Does the manifest file exist?
if (parameters.manifestFile != null && !parameters.manifestFile.Exists)
{
Console.WriteLine("CanvasNormalize.exe: File {0} does not exist! Exiting.", parameters.manifestFile.FullName);
return(null);
}
// Does the ploidy bed file exist?
if (parameters.ploidyBedFile != null && !parameters.ploidyBedFile.Exists)
{
Console.WriteLine("CanvasNormalize.exe: File {0} does not exist! Exiting.", parameters.ploidyBedFile.FullName);
return(null);
}
// Do we have only one model file in the PCA mode?
if (parameters.normalizationMode == CanvasNormalizeMode.PCA && parameters.normalBedFiles.Count > 1)
{
Console.WriteLine("CanvasNormalize.exe: Please specify only one model file.");
return(null);
}
return(parameters);
}
public static CanvasNormalizeParameters ParseCommandLine(string[] args)
{
CanvasNormalizeParameters parameters = new CanvasNormalizeParameters();
// Should I display a help message?
bool needHelp = false;
OptionSet p = new OptionSet()
{
{ "t|tumor=", "bed file containing bin counts for the tumor sample", v => parameters.tumorBedPath = v },
{ "n|normal=", "bed file containing bin counts for a normal sample. Pass this option multiple times, once for each normal sample.", v => parameters.normalBedPaths.Add(v) },
{ "o|out=", "bed file to output containing normalized bin counts", v => parameters.outBedPath = v },
{ "w|weightedAverageNormal=", "bed file to output containing normalized bin counts", v => parameters.weightedAverageNormalBedPath = v },
{ "f|manifest=", "Nextera manifest file", v => parameters.manifestPath = v },
{ "p|ploidyBedFile=", "bed file specifying reference ploidy (e.g. for sex chromosomes) (optional)", v => parameters.ploidyBedPath = v},
{ "h|help", "show this message and exit", v => needHelp = v != null },
{ "m|mode=", "normalization mode", v => parameters.normalizationMode = CanvasCommon.Utilities.ParseCanvasNormalizeMode(v) },
};
Console.WriteLine("CanvasNormalize {0}", System.Reflection.Assembly.GetEntryAssembly().GetName().Version.ToString());
List<string> extraArgs = p.Parse(args);
// Check for required arguments. Display the help message if any of them are missing.
if (string.IsNullOrEmpty(parameters.tumorBedPath))
{
Console.Error.WriteLine("Please specify the tumor bed file.");
needHelp = true;
}
else if (!parameters.normalBedPaths.Any())
{
Console.Error.WriteLine("Please specify at least one normal bed file.");
needHelp = true;
}
else if (string.IsNullOrEmpty(parameters.outBedPath))
{
Console.Error.WriteLine("Please specify an output file name.");
needHelp = true;
}
if (needHelp)
{
ShowHelp(p);
return null;
}
// Does the tumor bed file exist?
if (!File.Exists(parameters.tumorBedPath))
{
Console.WriteLine("CanvasNormalize.exe: File {0} does not exist! Exiting.", parameters.tumorBedPath);
return null;
}
// Does each of the normal bed files exist?
foreach (string normalBedPath in parameters.normalBedPaths)
{
if (!File.Exists(normalBedPath))
{
Console.WriteLine("CanvasNormalize.exe: File {0} does not exist! Exiting.", normalBedPath);
return null;
}
}
// Does the manifest file exist?
if (!string.IsNullOrEmpty(parameters.manifestPath) && !File.Exists(parameters.manifestPath))
{
Console.WriteLine("CanvasNormalize.exe: File {0} does not exist! Exiting.", parameters.manifestPath);
return null;
}
// Does the ploidy bed file exist?
if (!string.IsNullOrEmpty(parameters.ploidyBedPath) && !File.Exists(parameters.ploidyBedPath))
{
Console.WriteLine("CanvasNormalize.exe: File {0} does not exist! Exiting.", parameters.ploidyBedPath);
return null;
}
return parameters;
}
public CanvasNormalizeFactory(CanvasNormalizeParameters parameters)
{
_parameters = parameters;
_manifest = _parameters.manifestFile == null ? null
: new NexteraManifest(_parameters.manifestFile.FullName, null, Console.WriteLine);
}
public static CanvasNormalizeParameters ParseCommandLine(string[] args)
{
CanvasNormalizeParameters parameters = new CanvasNormalizeParameters();
// Should I display a help message?
bool needHelp = false;
OptionSet p = new OptionSet()
{
{ "t|tumor=", "bed file containing bin counts for the tumor sample", v => parameters.tumorBedPath = v },
{ "n|normal=", "bed file containing bin counts for a normal sample. Pass this option multiple times, once for each normal sample.", v => parameters.normalBedPaths.Add(v) },
{ "o|out=", "bed file to output containing normalized bin counts", v => parameters.outBedPath = v },
{ "w|weightedAverageNormal=", "bed file to output containing normalized bin counts", v => parameters.weightedAverageNormalBedPath = v },
{ "f|manifest=", "Nextera manifest file", v => parameters.manifestPath = v },
{ "p|ploidyBedFile=", "bed file specifying reference ploidy (e.g. for sex chromosomes) (optional)", v => parameters.ploidyBedPath = v },
{ "h|help", "show this message and exit", v => needHelp = v != null },
{ "m|mode=", "normalization mode", v => parameters.normalizationMode = CanvasCommon.Utilities.ParseCanvasNormalizeMode(v) },
};
Console.WriteLine("CanvasNormalize {0}", System.Reflection.Assembly.GetEntryAssembly().GetName().Version.ToString());
List <string> extraArgs = p.Parse(args);
// Check for required arguments. Display the help message if any of them are missing.
if (string.IsNullOrEmpty(parameters.tumorBedPath))
{
Console.Error.WriteLine("Please specify the tumor bed file.");
needHelp = true;
}
else if (!parameters.normalBedPaths.Any())
{
Console.Error.WriteLine("Please specify at least one normal bed file.");
needHelp = true;
}
else if (string.IsNullOrEmpty(parameters.outBedPath))
{
Console.Error.WriteLine("Please specify an output file name.");
needHelp = true;
}
if (needHelp)
{
ShowHelp(p);
return(null);
}
// Does the tumor bed file exist?
if (!File.Exists(parameters.tumorBedPath))
{
Console.WriteLine("CanvasNormalize.exe: File {0} does not exist! Exiting.", parameters.tumorBedPath);
return(null);
}
// Does each of the normal bed files exist?
foreach (string normalBedPath in parameters.normalBedPaths)
{
if (!File.Exists(normalBedPath))
{
Console.WriteLine("CanvasNormalize.exe: File {0} does not exist! Exiting.", normalBedPath);
return(null);
}
}
// Does the manifest file exist?
if (!string.IsNullOrEmpty(parameters.manifestPath) && !File.Exists(parameters.manifestPath))
{
Console.WriteLine("CanvasNormalize.exe: File {0} does not exist! Exiting.", parameters.manifestPath);
return(null);
}
// Does the ploidy bed file exist?
if (!string.IsNullOrEmpty(parameters.ploidyBedPath) && !File.Exists(parameters.ploidyBedPath))
{
Console.WriteLine("CanvasNormalize.exe: File {0} does not exist! Exiting.", parameters.ploidyBedPath);
return(null);
}
return(parameters);
}
