public override IEnumerable <string> Process()
{
var counts = new MappedCountItemList();
var features = counts.Parse(options, m => SmallRNAUtils.SortNames(m));
var featureCounts = (from feature in features
let count = MathNet.Numerics.Statistics.Statistics.Median(from c in counts
select c.DisplayNameGroupMap.ContainsKey(feature) ? c.DisplayNameGroupMap[feature].GetEstimatedCount() : 0)
select new { Feature = feature, Count = count }).OrderByDescending(m => m.Count).ToList();
using (StreamWriter sw = new StreamWriter(options.OutputFile))
{
sw.Write("Feature\tLocation");
var hassequence = !string.IsNullOrEmpty(counts.First().DisplayNameGroupMap.First().Value.First().Sequence);
if (hassequence)
{
sw.Write("\tSequence");
}
sw.WriteLine("\t" + (from c in counts select c.ItemName).Merge("\t"));
foreach (var fc in featureCounts)
{
var feature = fc.Feature;
var first = counts.FirstOrDefault(m => m.DisplayNameGroupMap.ContainsKey(feature));
var item = first.DisplayNameGroupMap[feature];
sw.Write(feature + "\t" + item.DisplayLocations);
if (hassequence)
{
sw.Write("\t" + item.DisplaySequence);
}
for (int i = 0; i < counts.Count; i++)
{
if (counts[i].DisplayNameGroupMap.ContainsKey(feature))
{
sw.Write("\t{0:0.##}", counts[i].DisplayNameGroupMap[feature].GetEstimatedCount());
}
else
{
sw.Write("\t0");
}
}
sw.WriteLine();
}
}
var result = new[] { Path.GetFullPath(options.OutputFile) }.ToList();
var infofile = Path.ChangeExtension(options.OutputFile, ".info");
if (CountUtils.WriteInfoSummaryFile(infofile, options.GetCountFiles().ToDictionary(m => m.Name, m => m.File)))
{
result.Add(infofile);
}
return(new string[] { Path.GetFullPath(options.OutputFile) });
}
protected virtual void FilterAlignedItems(List <SAMAlignedItem> result)
{
SmallRNAUtils.InitializeSmallRnaNTA(result);
result.ForEach(l =>
{
foreach (var loc in l.Locations)
{
if (loc.Seqname.StartsWith("chr"))
{
loc.Seqname = loc.Seqname.StringAfter("chr");
}
}
});
}
