public static void Main(string[] args)
{
Expression <Func <object, object> > exp = x => ((MyClass)x).Value.Length;
var m = new MyClass {
Value = "ssdf",
/*Nested = new MyClass {
* Value = "asd"
* }*/
};
RUtils <MyClass> .TrySet(m, "Nested.Nested.Nested.Value", "fdg");
RUtils <MyClass> .TryGet(m, "Nested.Nested.Nested.Value", out var value);
RUtils <MyClass> .Set(obj, "Value", "asd");
RUtils <MyClass> .Get(obj, "Value");
var summary = BenchmarkRunner.Run <RUtils_Benchmarks>(new Config());
Console.WriteLine();
Console.WriteLine("\nString value set and then get");
var runCount = summary.Reports.Length;// / 2;
foreach (var report in summary.Reports.Take(runCount).OrderBy(x => x.ResultStatistics.Median))
{
var ns = $"{report.ResultStatistics.Median:N1} ns";
var spase = new string(' ', 10 - ns.Length);
Console.WriteLine($"{ns}{spase}{Info(report)}");
}
/*
* Console.WriteLine("\nString value set and then get");
* foreach (var report in summary.Reports.Skip(runCount).Take(runCount).OrderBy(x => x.ResultStatistics.Median)) {
* var ns = $"{report.ResultStatistics.Median:N1} ns";
* var spase = new string(' ', 10 - ns.Length);
*
* Console.WriteLine($"{ns}{spase}{Info(report)}");
* }*/
/*
* Console.WriteLine("\nString value set and then get");
* foreach (var report in summary.Reports.Skip(16).OrderBy(x => x.ResultStatistics.Median)) {
* var ns = $"{report.ResultStatistics.Median:N1} ns";
* var spase = new string(' ', 10 - ns.Length);
*
* Console.WriteLine($"{ns}{spase}{Info(report)}");
* }
*/
Console.WriteLine();
Console.ReadLine();
}
public string REtilsTrySetValue()
{
RUtils <MyClass> .TrySet(obj, "Value", "asd");
RUtils <MyClass> .TryGet(obj, "Value", out object value);
return((string)value);
}
private List <string> SummarizeBasicResult()
{
var result = new List <string>();
var qcitems = (from dir in Directory.GetDirectories(options.InputDir)
select new
{
Sample = Path.GetFileName(dir),
Data = (from subdir in Directory.GetDirectories(dir, "*_fastqc")
let summaryFile = Path.Combine(subdir, "summary.txt")
select FastQCSummaryItem.ReadFromFile(summaryFile)).ToArray()
}).ToList();
using (var sw = new StreamWriter(options.OutputFile))
{
sw.WriteLine("File\tCategory\tQCResult");
foreach (var qc in qcitems)
{
var filename = qc.Sample;
WriteData(sw, filename, "Basic Statistics", qc.Data, m => m.BasicStatistics);
WriteData(sw, filename, "Per base sequence quality", qc.Data, m => m.PerBaseSequenceQuality);
WriteData(sw, filename, "Per tile sequence quality", qc.Data, m => m.PerTileSequenceQuality);
WriteData(sw, filename, "Per sequence quality scores", qc.Data, m => m.PerSequenceQualityScore);
WriteData(sw, filename, "Per base sequence content", qc.Data, m => m.PerBaseSequenceContent);
WriteData(sw, filename, "Per sequence GC content", qc.Data, m => m.PerSequenceGCContent);
WriteData(sw, filename, "Per base N content", qc.Data, m => m.PerBaseNContent);
WriteData(sw, filename, "Sequence Length Distribution", qc.Data, m => m.SequenceLengthDistribution);
WriteData(sw, filename, "Sequence Duplication Levels", qc.Data, m => m.SequenceDuplicatonLevels);
WriteData(sw, filename, "Overrepresented sequences", qc.Data, m => m.OverrepresentedSequences);
WriteData(sw, filename, "Adapter Content", qc.Data, m => m.AdapterContent);
}
}
result.Add(options.OutputFile);
var rfile = new FileInfo(FileUtils.GetTemplateDir() + "/fastqc_summary.r").FullName;
if (File.Exists(rfile))
{
var targetrfile = options.OutputFile + ".r";
var resultfile = options.OutputFile + ".png";
var definitions = new List <string>();
definitions.Add(string.Format("outputdir<-\"{0}\"", Path.GetDirectoryName(Path.GetFullPath(options.OutputFile)).Replace("\\", "/")));
definitions.Add(string.Format("inputfile<-\"{0}\"", Path.GetFileName(options.OutputFile)));
definitions.Add(string.Format("outputfile<-\"{0}\"", Path.GetFileName(resultfile)));
RUtils.PerformRByTemplate(rfile, targetrfile, definitions);
if (File.Exists(resultfile))
{
result.Add(resultfile);
}
}
return(result);
}
/// <summary>
/// Returns whole <paramref name="entity"/>, represented as sequence of <typeparamref name="TParameter"/>.
/// </summary>
/// <returns>IEnumerable (sequence) of TParameter</returns>
protected virtual IEnumerable <TParameter> ParametersFrom <TEntity>(IEntityInfo info, TEntity entity) where TEntity : class
{
return(info.PersistedProperties.Select(x => {
object value;
if (!RUtils <TEntity> .TryGet(entity, x.Key, out value))
{
throw new InvalidOperationException($"Entity of type {entity.GetType()} should contain property '{x.Key}', " +
"but in some reason value or that property could not be getted.");
}
var criterion = new DataCriterion {
Name = x.Key, Type = x.Value.PropertyType, Value = value
};
return ParameterWith(info, criterion);
}));
}
public static T To <T>([NotNull] this DataRow row, [NotNull] T item) where T : class
{
foreach (DataColumn column in row.Table.Columns)
{
var value = row[column];
if (value == DBNull.Value || value == null)
{
continue;
}
if (!RUtils <T> .TrySet(item, column.ColumnName, value))
{
Log.TraceEvent(TraceEventType.Warning, $"Can't set property {column.ColumnName} from '{typeof (T).FullName}' context.");
}
}
return(item);
}
private List <string> SummarizeCount()
{
var result = new List <string>();
var qcitems = (from dir in Directory.GetDirectories(options.InputDir)
select new
{
Sample = Path.GetFileName(dir),
Data = (from subdir in Directory.GetDirectories(dir, "*_fastqc")
let dataFile = Path.Combine(subdir, "fastqc_data.txt")
let line = File.ReadAllLines(dataFile).Where(m => m.StartsWith("Total Sequences")).First()
select int.Parse(line.StringAfter("\t"))).ToArray()
}).ToList();
var datafile = Path.ChangeExtension(options.OutputFile, ".reads.tsv");
var errors = qcitems.Where(m => m.Data.Any(l => l != m.Data.First())).ToArray();
if (errors.Length > 0)
{
var errorFile = datafile + ".error";
using (var sw = new StreamWriter(errorFile))
{
sw.WriteLine("Sample\tRead1\tRead2");
foreach (var qc in errors)
{
sw.WriteLine("{0}\t{1}\t{2}", qc.Sample, qc.Data[0], qc.Data[1]);
}
}
result.Add(errorFile);
}
using (var sw = new StreamWriter(datafile))
{
sw.WriteLine("Sample\tReads");
foreach (var qc in qcitems)
{
sw.WriteLine("{0}\t{1}", qc.Sample, qc.Data.Distinct().Sum());
}
}
result.Add(datafile);
var rfile = new FileInfo(FileUtils.GetTemplateDir() + "/fastqc_summary_count.r").FullName;
if (File.Exists(rfile))
{
var targetrfile = datafile + ".r";
var resultfile = datafile + ".png";
var definitions = new List <string>();
definitions.Add(string.Format("outputdir<-\"{0}\"", Path.GetDirectoryName(Path.GetFullPath(options.OutputFile)).Replace("\\", "/")));
definitions.Add(string.Format("inputfile<-\"{0}\"", Path.GetFileName(datafile)));
definitions.Add(string.Format("outputfile<-\"{0}\"", Path.GetFileName(resultfile)));
RUtils.PerformRByTemplate(rfile, targetrfile, definitions);
if (File.Exists(resultfile))
{
result.Add(resultfile);
}
}
return(result);
}
public string REtilsSetValue()
{
RUtils <MyClass> .Set(obj, "Value", "asd");
return((string)RUtils <MyClass> .Get(obj, "Value"));
}
