public override IEnumerable<string> Process(string fileName)
{
this.Progress.SetMessage("Parsing fastqc result ...");
var fMap = new FastQCItemReader().ReadFromRootDirectory(fastqcDir).ToDictionary(m => m.Name);
this.Progress.SetMessage("Parsing RNASeQC result ...");
var rMap = new RNASeQCItemReader().ReadFromFile(this.rnaseqcMatrixFile).ToDictionary(m => m.Sample);
using (StreamWriter sw = new StreamWriter(fileName))
{
sw.WriteLine("Sample\tFileNames\tTotalSequences\tSequenceLength\tGC\t" +
"AlternativeAlignments\tMappedUnique\tMappedUniqueRate\tMappedPairs\tBaseMismatchRate\t" +
"IntragenicRate\tExonicRate\tIntronicRate\tIntergenicRate\tExpressionProfilingEfficiency\tTranscriptsDetected\tGenesDetected\tMeanPerBaseCoverage\tFragmentLengthMean\tFragmentLengthStdDev");
var keys = (from k in fMap.Keys
orderby k
select k).ToList();
foreach (var key in keys)
{
var fitem = fMap[key];
var ritem = rMap[key];
sw.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}\t{7:0.000}\t{8}\t{9:0.000}\t{10:0.000}\t{11:0.000}\t{12:0.000}\t{13:0.000}\t{14:0.000}\t{15}\t{16}\t{17}\t{18}\t{19}",
fitem.Name,
fitem.FileNames,
fitem.TotalSequences,
fitem.SequenceLength,
fitem.GC,
ritem.AlternativeAlignments,
ritem.MappedUnique,
ritem.MappedUnique * 1.0 / fitem.TotalSequences,
ritem.MappedPairs,
ritem.BaseMismatchRate,
ritem.IntragenicRate,
ritem.ExonicRate,
ritem.IntronicRate,
ritem.IntergenicRate,
ritem.ExpressionProfilingEfficiency,
ritem.TranscriptsDetected,
ritem.GenesDetected,
ritem.MeanPerBaseCoverage,
ritem.FragmentLengthMean,
ritem.FragmentLengthStdDev
);
}
}
return new string[] { fileName };
}
public void Test()
{
var items = new RNASeQCItemReader().ReadFromFile("../../../data/rnaseqc_metrics.tsv");
Assert.AreEqual(19, items.Count);
Assert.AreEqual("G1_7071", items[0].Sample);
Assert.AreEqual(2437915, items[0].AlternativeAlignments);
Assert.AreEqual(69485233, items[0].MappedUnique);
Assert.AreEqual(0.002318971, items[0].BaseMismatchRate);
Assert.AreEqual(33526847, items[0].MappedPairs);
Assert.AreEqual(218, items[0].FragmentLengthMean);
Assert.AreEqual(205, items[0].FragmentLengthStdDev);
Assert.AreEqual(1094795, items[0].ChimericPairs);
Assert.AreEqual(0.9299, items[0].IntragenicRate, 0.0001);
Assert.AreEqual(0.0879, items[0].IntronicRate, 0.0001);
Assert.AreEqual(0.8420, items[0].ExonicRate, 0.0001);
Assert.AreEqual(99, items[0].ReadLength);
Assert.AreEqual(134191, items[0].TranscriptsDetected);
Assert.AreEqual(23641, items[0].GenesDetected);
Assert.AreEqual(56.24, items[0].MeanPerBaseCoverage, 0.01);
Assert.AreEqual(0.8420, items[0].ExpressionProfilingEfficiency, 0.01);
}
