public override IEnumerable <string> Process()
{
var countfiles = options.GetCountFiles();
Dictionary <string, FeatureItem> featureMap = new Dictionary <string, FeatureItem>();
List <string> samples = new List <string>();
for (int i = 0; i < countfiles.Count; i++)
{
var file = countfiles[i];
samples.Add(file.Name);
Progress.SetMessage("Reading {0}/{1} {2}...", i + 1, countfiles.Count, file.File);
var mapped = new FeatureItemGroupXmlFormat().ReadFromFile(file.File);
mapped.GetQueries().ForEach(m => m.Sample = file.Name);
//merge data by feature
foreach (var group in mapped)
{
foreach (var curFeature in group)
{
FeatureItem existFeature;
if (featureMap.TryGetValue(curFeature.Name, out existFeature))
{
var existLocationMap = existFeature.Locations.ToDictionary(l => l.GetLocation());
foreach (var curLocation in curFeature.Locations)
{
FeatureLocation existLocation;
if (existLocationMap.TryGetValue(curLocation.GetLocation(), out existLocation))
{
existLocation.SamLocations.AddRange(curLocation.SamLocations);
}
else
{
existFeature.Locations.Add(curLocation);
}
}
}
else // add to feature map
{
featureMap[curFeature.Name] = curFeature;
}
}
}
}
var features = featureMap.Values.ToList();
samples.Sort();
var allGroups = new List <FeatureItemGroup>();
var result = new List <string>();
var allTRNA = features.All(l => l.Name.StartsWith(SmallRNAConsts.tRNA));
if (!options.NoCategory)
{
if (!allTRNA)
{
//output miRNA
Progress.SetMessage("Grouping microRNA by sequence ...");
var miRNAGroup = features.Where(m => m.Name.StartsWith(SmallRNAConsts.miRNA)).GroupBySequence().OrderByDescending(m => m.GetEstimatedCount()).ThenBy(m => m.Name).ToList();
//Progress.SetMessage("Writing microRNA xml file ...");
//new FeatureItemGroupXmlFormat().WriteToFile(options.OutputFile + ".miRNA.xml", miRNAGroup);
Progress.SetMessage("Writing microRNA ...");
var miRNAFile = Path.ChangeExtension(options.OutputFile, SmallRNAConsts.miRNA + ".count");
result.AddRange(new MirnaNTACountTableWriter().WriteToFile(miRNAFile, miRNAGroup, samples, SmallRNAConsts.miRNA + ":"));
new SmallRNAPositionWriter().WriteToFile(miRNAFile + ".position", miRNAGroup);
allGroups.AddRange(miRNAGroup);
}
//output tRNA
Progress.SetMessage("Grouping tRNA by anticodon ...");
var tRNAs = features.Where(m => m.Name.StartsWith(SmallRNAConsts.tRNA)).ToList();
var tRNAGroup = tRNAs.GroupByFunction(SmallRNAUtils.GetTrnaAnticodon).OrderByDescending(m => m.GetEstimatedCount()).ThenBy(m => m.Name).ToList();
var tRNAFile = Path.ChangeExtension(options.OutputFile, SmallRNAConsts.tRNA + ".count");
Progress.SetMessage("Writing tRNA anticodon ...");
result.AddRange(new TrnaNTACountTableWriter().WriteToFile(tRNAFile, tRNAGroup, samples, SmallRNAConsts.tRNA + ":"));
Progress.SetMessage("Writing tRNA anticodon position ...");
new SmallRNAPositionWriter(m => SmallRNAUtils.GetTrnaAnticodon(m[0]), positionByPercentage: true).WriteToFile(tRNAFile + ".position", tRNAGroup);
new SmallRNAStartPositionWriter(m => SmallRNAUtils.GetTrnaAnticodon(m[0])).WriteToFile(tRNAFile + ".startpos", tRNAGroup);
allGroups.AddRange(tRNAGroup);
//output tRNA aminoacid
Progress.SetMessage("Grouping tRNA by amino acid ...");
tRNAGroup = tRNAs.GroupByFunction(SmallRNAUtils.GetTrnaAminoacid, true).OrderByDescending(m => m.GetEstimatedCount()).ThenBy(m => m.Name).ToList();
tRNAFile = Path.ChangeExtension(options.OutputFile, SmallRNAConsts.tRNA + ".aminoacid.count");
Progress.SetMessage("Writing tRNA amino acid ...");
result.AddRange(new SmallRNACountTableWriter().WriteToFile(tRNAFile, tRNAGroup, samples, SmallRNAConsts.tRNA + ":"));
Progress.SetMessage("Writing tRNA aminoacid position ...");
new SmallRNAPositionWriter(m => SmallRNAUtils.GetTrnaAminoacid(m[0]), positionByPercentage: true).WriteToFile(tRNAFile + ".position", tRNAGroup);
if (!allTRNA)
{
var exportBiotypes = SmallRNAUtils.GetOutputBiotypes(options);
foreach (var biotype in exportBiotypes)
{
OutputBiotype(samples, features, allGroups, result, biotype, m => m.StartsWith(biotype), !biotype.Equals(SmallRNABiotype.rRNA.ToString()), !biotype.Equals(SmallRNABiotype.rRNA.ToString()));
}
var biotypes = new[] { SmallRNAConsts.miRNA, SmallRNAConsts.tRNA }.Union(exportBiotypes).ToList();
OutputBiotype(samples, features, allGroups, result, "", m => !biotypes.Any(l => m.StartsWith(l)), false, false);
}
}
else
{
Progress.SetMessage("Grouping features by identical query ...");
allGroups = features.GroupByIdenticalQuery().OrderByDescending(m => m.GetEstimatedCount()).ThenBy(m => m.Name).ToList();
}
//output all smallRNA
Progress.SetMessage("Writing all smallRNA ...");
result.AddRange(new SmallRNACountTableWriter().WriteToFile(options.OutputFile, allGroups, samples, ""));
Progress.SetMessage("Done ...");
return(result);
}
