public override IEnumerable <string> Process()
{
var conf = CountMappingSummaryBuilderConfiguration.Read(options.InputFile);
var data = (from a in conf.SampleFiles
select new
{
Sample = a.Item1,
Data = (from b in a.Item2
let map = File.ReadAllLines(b).Where(m => !m.StartsWith("#")).ToDictionary(m => m.StringBefore("\t"), m => m.StringAfter("\t"))
let totalreads = map.ContainsKey("TotalReads") ? map["TotalReads"] : map["Total reads"]
let mappedreads = map.ContainsKey("MappedReads") ? map["MappedReads"] : map["Mapped reads"]
let featurereads = map.ContainsKey("FeatureReads") ? map["FeatureReads"] : map["Feature reads"]
select new { TotalReads = totalreads, MappedReads = mappedreads, FeatureReads = featurereads }).ToList()
}).ToList();
using (var sw = new StreamWriter(options.OutputFile))
{
sw.WriteLine("Sample\t" + (from s in conf.SearchTypes
let ss = new[] { s + "_TotalReads", s + "_MappedReads", s + "_FeatureReads" }
from sss in ss
select sss).Merge("\t"));
foreach (var d in data)
{
sw.Write(d.Sample);
foreach (var dd in d.Data)
{
sw.Write("\t{0}\t{1}\t{2}", dd.TotalReads, dd.MappedReads, dd.FeatureReads);
}
sw.WriteLine();
}
}
return(new[] { options.OutputFile });
}
public static CountMappingSummaryBuilderConfiguration Read(string fileName)
{
var result = new CountMappingSummaryBuilderConfiguration();
var lines = File.ReadAllLines(fileName).Where(m => !string.IsNullOrWhiteSpace(m)).ToArray();
result.SearchTypes = lines[0].Split('\t').Skip(1).ToList();
result.SampleFiles = (from l in lines.Skip(1)
let parts = l.Split('\t')
let sample = parts[0]
let files = parts.Skip(1).ToList()
select new Tuple<string, List<string>>(sample, files)).ToList();
return result;
}
public static CountMappingSummaryBuilderConfiguration Read(string fileName)
{
var result = new CountMappingSummaryBuilderConfiguration();
var lines = File.ReadAllLines(fileName).Where(m => !string.IsNullOrWhiteSpace(m)).ToArray();
result.SearchTypes = lines[0].Split('\t').Skip(1).ToList();
result.SampleFiles = (from l in lines.Skip(1)
let parts = l.Split('\t')
let sample = parts[0]
let files = parts.Skip(1).ToList()
select new Tuple <string, List <string> >(sample, files)).ToList();
return(result);
}
