예제 #1
0
    public override IEnumerable<string> Process()
    {
      var data = new CnMOPsItemReader().ReadFromFile(options.InputFile);

      Dictionary<string, List<ItemRange>> result = MergeRange(data);
      var seqnames = result.Keys.OrderBy(m => m).ToList();
      GenomeUtils.SortChromosome(seqnames, l => l, l => 1);

      using (var sw = new StreamWriter(options.OutputFile))
      {
        sw.WriteLine("seqname\tstart\tend\tlocus\tsample\tsample_start\tsample_end\tsample_type");

        foreach (var seqname in seqnames)
        {
          var ranges = result[seqname];
          foreach (var range in ranges)
          {
            foreach (var cn in range.Items)
            {
              if (options.IgnoreCN1CN3 && (cn.CN.Equals("CN1") || cn.CN.Equals("CN3")))
              {
                continue;
              }
              sw.WriteLine("{0}\t{1}\t{2}\t{0}:{1}-{2}\t{3}\t{4}\t{5}\t{6}",
                seqname, range.Start, range.End, cn.FileName, cn.Start, cn.End, cn.CN);
            }
          }
        }
      }

      var filenames = (from d in data select d.FileName).Distinct().OrderBy(l => l).ToArray();

      using (var sw = new StreamWriter(options.OutputFile + ".cnvr"))
      {
        sw.WriteLine("seqname\tstart\tend\tfile\t{0}", filenames.Merge("\t"));

        foreach (var seqname in seqnames)
        {
          var ranges = result[seqname];
          foreach (var range in ranges)
          {
            var cns = (from filename in filenames
                       let cn = range.Items.Where(l => l.FileName.Equals(filename)).FirstOrDefault()
                       select cn == null ? "CN2" : cn.CN).ToArray();
            if (options.IgnoreCN1CN3 && cns.All(l => l.Equals("CN1") || l.Equals("CN2") || l.Equals("CN3")))
            {
              continue;
            }

            sw.WriteLine("{0}\t{1}\t{2}\t{0}_{1}_{2}\t{3}",
              seqname, range.Start, range.End, cns.Merge("\t"));
          }
        }
      }

      return new[] { options.OutputFile, options.OutputFile + ".cnvr" };
    }
예제 #2
0
    public void Test()
    {
      var data = new CnMOPsItemReader().ReadFromFile("../../../data/cnmops.txt");
      var focus_before = data.Where(l => l.Start > 3000000 && l.End < 9000000).ToList();
      var ranges = CnMOPSCallProcessor.MergeRange(focus_before);

      var focus = ranges["5"];

      Assert.AreEqual(1, focus.Count);
      Assert.AreEqual(3000100, focus[0].Start);
      Assert.AreEqual(8494963, focus[0].End);
      //focus.ForEach(l =>
      //{
      //  Console.WriteLine("{0}-{1}", l.Start, l.End);
      //  l.Items.ForEach(m =>
      //  {
      //    Console.WriteLine("\t{0}-{1}\t{2}\t{3}", m.Start, m.End, m.FileName, m.CN);
      //  });
      //});

    }