public virtual void MapReadToFeatureAndRemoveFromMap(List <FeatureLocation> allFeatures, Dictionary <string, Dictionary <char, List <SAMAlignedLocation> > > chrStrandReadMap)
{
var features = allFeatures.Where(l => Accept(l)).ToList();
Progress.SetMessage("Mapping reads to {0} {1} entries.", features.Count, MapperName);
if (features.Count > 0)
{
MapReadToFeature(features, chrStrandReadMap);
var reads = SmallRNAUtils.GetMappedReads(features);
Progress.SetMessage("There are {0} SAM entries mapped to {1} entries.", reads.Count, MapperName);
SmallRNAUtils.RemoveReadsFromMap(chrStrandReadMap, reads);
}
else
{
Progress.SetMessage("There are 0 SAM entries mapped to {0} entries.", MapperName);
}
}
public override IEnumerable <string> Process()
{
var result = new List <string>();
//read regions
var featureLocations = options.GetSequenceRegions();
Progress.SetMessage("There are {0} coordinate entries", featureLocations.Count);
if (featureLocations.Count == 0)
{
throw new Exception(string.Format("No coordinate found in file {1}", options.CoordinateFile));
}
var trnaLocations = featureLocations.Where(l => l.Category.Equals(SmallRNAConsts.tRNA)).ToList();
var mirnaLocations = featureLocations.Where(l => l.Category.Equals(SmallRNAConsts.miRNA)).ToList();
var notTrnaLocations = featureLocations.Where(l => !l.Category.Equals(SmallRNAConsts.tRNA)).ToList();
var resultFilename = options.OutputFile;
result.Add(resultFilename);
Progress.SetMessage("Parsing tRNA alignment result ...");
//Parsing reads
List <QueryInfo> trnaQueries;
var trnaReads = ParseCandidates(options.InputFiles, resultFilename, out trnaQueries);
SmallRNAUtils.InitializeSmallRnaNTA(trnaReads);
var hasNTA = trnaReads.Any(l => l.NTA.Length > 0);
List <QueryInfo> otherrnaQueries;
var otherRNAReads = ParseCandidates(options.OtherFile, resultFilename + ".other", out otherrnaQueries);
SmallRNAUtils.InitializeSmallRnaNTA(otherRNAReads);
var featureGroups = new List <FeatureItemGroup>();
var mappedfile = resultFilename + ".mapped.xml";
if (File.Exists(mappedfile) && options.NotOverwrite)
{
Progress.SetMessage("Reading mapped feature items...");
featureGroups = new FeatureItemGroupXmlFormat().ReadFromFile(mappedfile);
}
else
{
Progress.SetMessage("Mapping to tRNA...");
//Draw tRNA mapping position graph
Progress.SetMessage("Drawing tRNA position pictures...");
var tRNAPositionFile = Path.ChangeExtension(options.OutputFile, SmallRNAConsts.tRNA + ".position");
if (!options.NotOverwrite || !File.Exists(tRNAPositionFile))
{
DrawPositionImage(trnaReads, trnaLocations, "tRNA", tRNAPositionFile);
}
//Map reads to tRNA
MapReadToSequenceRegion(trnaLocations, trnaReads, hasNTA);
var trnaMapped = trnaLocations.GroupByName();
trnaMapped.RemoveAll(m => m.GetEstimatedCount() == 0);
trnaMapped.ForEach(m => m.CombineLocations());
var trnaGroups = trnaMapped.GroupByIdenticalQuery();
if (trnaGroups.Count > 0)
{
Progress.SetMessage("Writing tRNA count ...");
var trnaCountFile = Path.ChangeExtension(resultFilename, "." + SmallRNAConsts.tRNA + ".count");
OrderFeatureItemGroup(trnaGroups);
new FeatureItemGroupTIGRTCountWriter().WriteToFile(trnaCountFile, trnaGroups);
result.Add(trnaCountFile);
featureGroups.AddRange(trnaGroups);
}
//Get all queries mapped to tRNA
var tRNAreads = new HashSet <string>(from read in SmallRNAUtils.GetMappedReads(trnaLocations)
select read.OriginalQname);
//Remove all reads mapped to tRNA
otherRNAReads.RemoveAll(m => tRNAreads.Contains(m.OriginalQname));
//Draw miRNA mapping position graph
Progress.SetMessage("Drawing miRNA position pictures...");
var miRNAPositionFile = Path.ChangeExtension(options.OutputFile, SmallRNAConsts.miRNA + ".position");
if (!options.NotOverwrite || !File.Exists(miRNAPositionFile))
{
DrawPositionImage(otherRNAReads, mirnaLocations, "miRNA", miRNAPositionFile);
}
//Map reads to not tRNA
MapReadToSequenceRegion(notTrnaLocations, otherRNAReads, hasNTA);
var notTrnaMapped = notTrnaLocations.GroupByName();
notTrnaMapped.RemoveAll(m => m.GetEstimatedCount() == 0);
notTrnaMapped.ForEach(m => m.CombineLocations());
var mirnaGroups = notTrnaMapped.Where(m => m.Name.StartsWith(SmallRNAConsts.miRNA)).GroupBySequence();
if (mirnaGroups.Count > 0)
{
Progress.SetMessage("writing miRNA count ...");
OrderFeatureItemGroup(mirnaGroups);
var mirnaCountFile = Path.ChangeExtension(resultFilename, "." + SmallRNAConsts.miRNA + ".count");
new SmallRNACountMicroRNAWriter(options.Offsets).WriteToFile(mirnaCountFile, mirnaGroups);
result.Add(mirnaCountFile);
featureGroups.AddRange(mirnaGroups);
}
var otherGroups = notTrnaMapped.Where(m => !m.Name.StartsWith(SmallRNAConsts.miRNA)).GroupByIdenticalQuery();
if (otherGroups.Count > 0)
{
Progress.SetMessage("writing other smallRNA count ...");
var otherCountFile = Path.ChangeExtension(resultFilename, ".other.count");
OrderFeatureItemGroup(otherGroups);
new FeatureItemGroupTIGRTCountWriter().WriteToFile(otherCountFile, otherGroups);
result.Add(otherCountFile);
featureGroups.AddRange(otherGroups);
}
Progress.SetMessage("writing all smallRNA count ...");
new FeatureItemGroupTIGRTCountWriter().WriteToFile(resultFilename, featureGroups);
result.Add(resultFilename);
Progress.SetMessage("writing mapping details...");
new FeatureItemGroupXmlFormat().WriteToFile(mappedfile, featureGroups);
result.Add(mappedfile);
}
var readSummary = GetReadSummary(featureGroups, new HashSet <string>(), trnaReads.Union(otherRNAReads).ToList(), trnaQueries.Union(otherrnaQueries).ToList());
var totalQueryCount = (from q in trnaQueries.Union(otherrnaQueries) select q.Name.StringBefore(SmallRNAConsts.NTA_TAG)).Distinct().Sum(m => Counts.GetCount(m));
var totalMappedCount = (from q in trnaReads select q.OriginalQname).Union(from q in otherRNAReads select q.OriginalQname).Distinct().Sum(m => Counts.GetCount(m));
var infoFile = Path.ChangeExtension(resultFilename, ".info");
WriteSummaryFile(infoFile, readSummary, featureGroups);
result.Add(infoFile);
Progress.End();
return(result);
}