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);
}
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);
}