public override IEnumerable <string> Process()
{
var countfiles = _options.GetCountFiles();
var reader = new MapItemReader(_options.KeyIndex, _options.ValueIndex, informationIndex: _options.InformationIndex, hasHeader: !_options.HasNoHeader);
reader.CheckEnd = m => m.StartsWith("__no_feature") || m.StartsWith("no_feature");
var counts = new List <SampleData>();
foreach (var file in countfiles)
{
Progress.SetMessage("Reading data from {0} ...", file.File);
var data = reader.ReadFromFile(file.File);
if (!string.IsNullOrEmpty(_options.KeyRegex))
{
var reg = new Regex(_options.KeyRegex);
counts.Add(new SampleData()
{
Name = file.Name, Data = data.ToDictionary(l => reg.Match(l.Key).Groups[1].Value, l => l.Value)
});
}
else
{
counts.Add(new SampleData()
{
Name = file.Name, Data = data
});
}
}
MapData namemap = null;
if (File.Exists(_options.MapFile))
{
Progress.SetMessage("Reading name map from {0} ...", _options.MapFile);
namemap = new MapDataReader(0, 1).ReadFromFile(_options.MapFile);
if (!string.IsNullOrEmpty(_options.KeyRegex))
{
var reg = new Regex(_options.KeyRegex);
namemap.Data = namemap.Data.ToDictionary(l => reg.Match(l.Key).Groups[1].Value, l => l.Value);
}
}
if (!string.IsNullOrEmpty(_options.KeyRegex))
{
Progress.SetMessage("Filtering key by pattern {0} ...", _options.KeyRegex);
var reg = new Regex(_options.KeyRegex);
counts.ForEach(m =>
{
var keys = m.Data.Keys.ToList();
foreach (var key in keys)
{
if (!reg.Match(key).Success)
{
m.Data.Remove(key);
}
}
});
}
var features = (from c in counts
from k in c.Data.Keys
select k).Distinct().OrderBy(m => m).ToList();
var missing = _options.FillMissingWithZero ? "0" : "NA";
var outputExtra = _options.ExportExtra && namemap != null && namemap.InfoNames.Count > 0;
Progress.SetMessage("Writing {0} features to {1} ...", features.Count, _options.OutputFile);
using (var sw = new StreamWriter(_options.OutputFile))
{
sw.Write("Feature");
if (namemap != null)
{
if (outputExtra)
{
sw.Write("\t{0}", (from v in namemap.InfoNames select "Feature_" + v).Merge("\t"));
}
sw.Write("\tFeature_{0}", namemap.ValueName);
}
sw.WriteLine("\t" + (from c in counts select c.Name).Merge("\t"));
foreach (var feature in features)
{
if ((from count in counts
where count.Data.ContainsKey(feature)
select count.Data[feature]).All(m => string.IsNullOrEmpty(m.Value) || m.Value.Equals("0")))
{
continue;
}
sw.Write(feature);
if (namemap != null)
{
var feature2 = feature.StringBefore(".");
if (namemap.Data.ContainsKey(feature))
{
if (outputExtra)
{
sw.Write("\t{0}", namemap.Data[feature].Informations.Merge("\t"));
}
sw.Write("\t{0}", namemap.Data[feature].Value);
}
else
{
var fea = feature.StringBefore(":");
var suffix = feature.Contains(":") ? ":" + feature.StringAfter(":") : string.Empty;
var feas = fea.Split('+');
var values = new List <string>();
var findFeature = feas.FirstOrDefault(m => namemap.Data.ContainsKey(m));
if (findFeature == null)
{
if (outputExtra)
{
sw.Write("\t{0}", (from f in namemap.InfoNames select string.Empty).Merge("\t"));
}
sw.Write("\t{0}", feature);
}
else
{
if (outputExtra)
{
for (int i = 0; i < namemap.InfoNames.Count; i++)
{
sw.Write("\t{0}", (from f in feas
select namemap.Data.ContainsKey(f) ? namemap.Data[f].Informations[i] : string.Empty).Merge(";"));
}
}
sw.Write("\t{0}", (from f in feas
select namemap.Data.ContainsKey(f) ? namemap.Data[f].Value : f).Merge("+") + suffix);
}
}
}
foreach (var count in counts)
{
if (count.Data.ContainsKey(feature))
{
sw.Write("\t" + count.Data[feature].Value);
}
else
{
sw.Write("\t" + missing);
}
}
sw.WriteLine();
}
}
//output proteincoding count table
bool hasProteinCoding = namemap != null && namemap.InfoNames.Count > 0 && namemap.InfoNames.Contains("gene_biotype");
if (hasProteinCoding)
{
WriteProteincodingFile(_options.OutputFile, ".count");
}
if (!_options.NoFPKM)
{
bool hasLength = namemap != null && namemap.InfoNames.Count > 0 && namemap.InfoNames.Contains("length");
if (hasLength)
{
Progress.SetMessage("Calculating FPKM values...");
var outputFile = Path.ChangeExtension(_options.OutputFile, ".fpkm.tsv");
new HTSeqCountToFPKMCalculator(new HTSeqCountToFPKMCalculatorOptions()
{
InputFile = _options.OutputFile,
GeneLengthFile = _options.MapFile,
KeyRegex = _options.KeyRegex,
OutputFile = outputFile
})
{
Progress = this.Progress
}.Process();
if (hasProteinCoding)
{
WriteProteincodingFile(outputFile, ".tsv");
}
}
}
return(new[] { Path.GetFullPath(_options.OutputFile) });
}
public override IEnumerable<string> Process()
{
var countfiles = _options.GetCountFiles();
var reader = new MapItemReader(_options.KeyIndex, _options.ValueIndex, informationIndex: _options.InformationIndex, hasHeader: !_options.HasNoHeader);
reader.CheckEnd = m => m.StartsWith("__no_feature") || m.StartsWith("no_feature");
var counts = new List<SampleData>();
foreach (var file in countfiles)
{
Progress.SetMessage("Reading data from {0} ...", file.File);
var data = reader.ReadFromFile(file.File);
if (!string.IsNullOrEmpty(_options.KeyRegex))
{
var reg = new Regex(_options.KeyRegex);
counts.Add(new SampleData() { Name = file.Name, Data = data.ToDictionary(l => reg.Match(l.Key).Groups[1].Value, l => l.Value) });
}
else
{
counts.Add(new SampleData() { Name = file.Name, Data = data });
}
}
MapData namemap = null;
if (File.Exists(_options.MapFile))
{
Progress.SetMessage("Reading name map from {0} ...", _options.MapFile);
namemap = new MapDataReader(0, 1).ReadFromFile(_options.MapFile);
if (!string.IsNullOrEmpty(_options.KeyRegex))
{
var reg = new Regex(_options.KeyRegex);
namemap.Data = namemap.Data.ToDictionary(l => reg.Match(l.Key).Groups[1].Value, l => l.Value);
}
}
if (!string.IsNullOrEmpty(_options.KeyRegex))
{
Progress.SetMessage("Filtering key by pattern {0} ...", _options.KeyRegex);
var reg = new Regex(_options.KeyRegex);
counts.ForEach(m =>
{
var keys = m.Data.Keys.ToList();
foreach (var key in keys)
{
if (!reg.Match(key).Success)
{
m.Data.Remove(key);
}
}
});
}
var features = (from c in counts
from k in c.Data.Keys
select k).Distinct().OrderBy(m => m).ToList();
var missing = _options.FillMissingWithZero ? "0" : "NA";
var outputExtra = _options.ExportExtra && namemap != null && namemap.InfoNames.Count > 0;
Progress.SetMessage("Writing {0} features to {1} ...", features.Count, _options.OutputFile);
using (var sw = new StreamWriter(_options.OutputFile))
{
sw.Write("Feature");
if (namemap != null)
{
if (outputExtra)
{
sw.Write("\t{0}", (from v in namemap.InfoNames select "Feature_" + v).Merge("\t"));
}
sw.Write("\tFeature_{0}", namemap.ValueName);
}
sw.WriteLine("\t" + (from c in counts select c.Name).Merge("\t"));
foreach (var feature in features)
{
if ((from count in counts
where count.Data.ContainsKey(feature)
select count.Data[feature]).All(m => string.IsNullOrEmpty(m.Value) || m.Value.Equals("0")))
{
continue;
}
sw.Write(feature);
if (namemap != null)
{
var feature2 = feature.StringBefore(".");
if (namemap.Data.ContainsKey(feature))
{
if (outputExtra)
{
sw.Write("\t{0}", namemap.Data[feature].Informations.Merge("\t"));
}
sw.Write("\t{0}", namemap.Data[feature].Value);
}
else
{
var fea = feature.StringBefore(":");
var suffix = feature.Contains(":") ? ":" + feature.StringAfter(":") : string.Empty;
var feas = fea.Split('+');
var values = new List<string>();
var findFeature = feas.FirstOrDefault(m => namemap.Data.ContainsKey(m));
if (findFeature == null)
{
if (outputExtra)
{
sw.Write("\t{0}", (from f in namemap.InfoNames select string.Empty).Merge("\t"));
}
sw.Write("\t{0}", feature);
}
else
{
if (outputExtra)
{
for (int i = 0; i < namemap.InfoNames.Count; i++)
{
sw.Write("\t{0}", (from f in feas
select namemap.Data.ContainsKey(f) ? namemap.Data[f].Informations[i] : string.Empty).Merge(";"));
}
}
sw.Write("\t{0}", (from f in feas
select namemap.Data.ContainsKey(f) ? namemap.Data[f].Value : f).Merge("+") + suffix);
}
}
}
foreach (var count in counts)
{
if (count.Data.ContainsKey(feature))
{
sw.Write("\t" + count.Data[feature].Value);
}
else
{
sw.Write("\t" + missing);
}
}
sw.WriteLine();
}
}
if (!_options.NoFPKM)
{
if (File.Exists(_options.MapFile))
{
bool hasLength = false;
using (var sr = new StreamReader(_options.MapFile))
{
var line = sr.ReadLine();
if (line != null)
{
hasLength = line.Contains("length");
}
}
if (hasLength)
{
Progress.SetMessage("Calculating FPKM values...");
new HTSeqCountToFPKMCalculator(new HTSeqCountToFPKMCalculatorOptions()
{
InputFile = _options.OutputFile,
GeneLengthFile = _options.MapFile,
KeyRegex = _options.KeyRegex,
OutputFile = Path.ChangeExtension(_options.OutputFile, ".fpkm.tsv")
})
{
Progress = this.Progress
}.Process();
}
}
}
return new[] { Path.GetFullPath(_options.OutputFile) };
}
