public override IEnumerable <string> Process()
{
var format = new MappedItemGroupXmlFileFormat();
Progress.SetMessage("reading mapped reads from " + _options.CountFile + " ...");
var mapped = format.ReadFromFile(_options.CountFile);
var sequenceLocusSet = new HashSet <string>(from item in mapped
from mi in item
from mr in mi.MappedRegions
from al in mr.AlignedLocations
select string.Format("{0}:{1}:{2}", al.Parent.Sequence, al.Seqname, al.Start));
Progress.SetMessage("There are {0} unique sequence:locus", sequenceLocusSet.Count);
using (var sw = new StreamWriter(_options.OutputFile))
{
using (var sr = SAMFactory.GetReader(_options.BamFile, false))
{
sr.ReadHeaders().ForEach(m => sw.WriteLine(m));
int count = 0;
int accepted = 0;
string line;
while ((line = sr.ReadLine()) != null)
{
if (count % 1000 == 0)
{
if (Progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
}
if (count % 100000 == 0 && count > 0)
{
Progress.SetMessage("{0} candidates from {1} reads", accepted, count);
}
count++;
var parts = line.Split('\t');
var locus = string.Format("{0}:{1}:{2}", parts[SAMFormatConst.SEQ_INDEX], parts[SAMFormatConst.RNAME_INDEX], parts[SAMFormatConst.POS_INDEX]);
if (!sequenceLocusSet.Contains(locus))
{
continue;
}
sw.WriteLine(line);
accepted++;
}
}
}
return(new[] { _options.OutputFile });
}
public override IEnumerable <string> Process()
{
var result = new List <string>();
var samformat = _options.GetEngineFormat();
var format = new MappedItemGroupXmlFileFormat();
Progress.SetMessage("reading mapped reads from " + _options.InputFile1 + " ...");
var items1 = format.ReadFromFile(_options.InputFile1);
Progress.SetMessage("reading mapped reads from " + _options.InputFile2 + " ...");
var items2 = format.ReadFromFile(_options.InputFile2);
var reads1 = items1.GetQueries().ToDictionary(m => m.Qname);
var reads2 = items2.GetQueries().ToDictionary(m => m.Qname);
var qnames = reads1.Keys.Union(reads2.Keys).Distinct().ToList();
foreach (var qname in qnames)
{
if (!reads1.ContainsKey(qname) || !reads2.ContainsKey(qname))
{
continue;
}
var r1 = reads1[qname];
var r2 = reads2[qname];
var res = samformat.CompareScore(r1.AlignmentScore, r2.AlignmentScore);
if (res == 0)
{
items1.RemoveRead(qname);
items2.RemoveRead(qname);
}
else if (res < 0)
{
items2.RemoveRead(qname);
}
else
{
items1.RemoveRead(qname);
}
}
var writer = new MappedItemGroupSequenceWriter();
SaveItems(items1, _options.OutputFile1, writer, format, result);
SaveItems(items2, _options.OutputFile2, writer, format, result);
return(result);
}
private static void SaveItems(List <MappedItemGroup> items1, string outputFile, MappedItemGroupSequenceWriter writer,
MappedItemGroupXmlFileFormat format, List <string> result)
{
items1.RemoveAll(m => m.QueryCount == 0);
var xml1 = outputFile + ".xml";
if (items1.Any(m => m.Name.Contains(".tRNA")))
{
items1.SortTRna();
}
writer.WriteToFile(outputFile, items1);
format.WriteToFile(xml1, items1);
result.Add(outputFile);
result.Add(xml1);
}
public override IEnumerable <string> Process()
{
var format = new MappedItemGroupXmlFileFormat();
using (StreamWriter sw = new StreamWriter(options.OutputFile))
{
sw.WriteLine("File\tFeature\tStrand\tCount\tPosition\tPercentage");
foreach (var file in options.GetCountFiles())
{
var xmlfile = file.File.EndsWith(".xml") ? file.File : file.File + ".mapped.xml";
var count = format.ReadFromFile(xmlfile).OrderByDescending(m => m.GetEstimatedCount()).ToList();
foreach (var group in count)
{
var item = group[0];
Dictionary <long, double> positionCount = new Dictionary <long, double>();
foreach (var region in item.MappedRegions)
{
foreach (var loc in region.AlignedLocations)
{
for (long p = loc.Start; p <= loc.End; p++)
{
var offset = region.Region.Strand == '+' ? p - region.Region.Start + 1 : region.Region.End - p + 1;
double v;
if (!positionCount.TryGetValue(offset, out v))
{
v = 0;
}
positionCount[offset] = v + loc.Parent.GetEstimatedCount();
}
}
}
var allcount = item.GetEstimatedCount();
var keys = positionCount.Keys.ToList();
keys.Sort();
foreach (var key in keys)
{
sw.WriteLine("{0}\t{1}\t{2}\t{3:0.##}\t{4}\t{5:0.00}",
file.Name,
item.Name,
item.MappedRegions.First().Region.Strand,
item.GetEstimatedCount(),
key,
positionCount[key] / allcount);
}
}
}
}
var rfile = new FileInfo(FileUtils.GetTemplateDir() + "/smallrna_position.r").FullName;
if (File.Exists(rfile))
{
var targetr = Path.ChangeExtension(options.OutputFile, ".r").Replace("\\", "/");
var content = File.ReadAllText(rfile).Replace("$$workspace", Path.GetDirectoryName(Path.GetFullPath(options.OutputFile)).Replace("\\", "/"))
.Replace("$$positionfile", Path.GetFileName(options.OutputFile).Replace("\\", "/"));
File.WriteAllText(targetr, content);
if (File.Exists(targetr))
{
SystemUtils.Execute("R", "--vanilla -f " + targetr);
}
}
return(new string[] { Path.GetFullPath(options.OutputFile) });
}
