public override IEnumerable <string> Process()
{
Progress.SetMessage("Reading T2C smallRNA...");
var mappedSmallRNA = ParclipUtils.GetSmallRNACoverageRegion(options.InputFile, null, new string[] { SmallRNAConsts.lincRNA });
mappedSmallRNA.Sort((m1, m2) => m2.Coverages.Average().CompareTo(m1.Coverages.Average()));
Progress.SetMessage("Build target {0} mers...", options.MinimumSeedLength);
var targetSeedMap = ParclipUtils.BuildTargetSeedMap(options, m => true, progress: this.Progress);
Progress.SetMessage("Finding target...");
using (var sw = new StreamWriter(options.OutputFile))
{
sw.WriteLine("SmallRNA\tChr\tStart\tEnd\tStrand\tSeed\tSeedOffset\tSeedLength\tSeedCoverage\tTarget\tTargetCoverage\tTargetGeneSymbol\tTargetName");
foreach (var t2c in mappedSmallRNA)
{
var seq = t2c.Sequence.ToUpper();
int[] offsets = GetPossibleOffsets(t2c.Name);
foreach (var offset in offsets)
{
var seed = seq.Substring(offset, options.MinimumSeedLength);
var coverage = t2c.Coverages.Skip(offset).Take(options.MinimumSeedLength).Average();
if (coverage < options.MinimumCoverage)
{
continue;
}
List <SeedItem> target;
if (targetSeedMap.TryGetValue(seed, out target))
{
target.Sort((m1, m2) =>
{
return(m2.Coverage.CompareTo(m1.Coverage));
});
if (!t2c.Name.StartsWith(SmallRNAConsts.miRNA))
{
target = ParclipUtils.FindLongestTarget(target, t2c, seq, offset, options.MinimumSeedLength, int.MaxValue, options.MinimumCoverage);
}
for (int j = 0; j < target.Count; j++)
{
var finalSeed = seq.Substring(offset, target[0].Sequence.Length);
sw.Write("{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}\t{7}\t{8}", t2c.Name, t2c.Seqname, t2c.Start, t2c.End, t2c.Strand, finalSeed, offset, finalSeed.Length, Math.Round(coverage));
var t = target[j];
sw.WriteLine("\t{0}:{1}-{2}:{3}\t{4}\t{5}\t{6}",
t.Seqname,
t.Start,
t.End,
t.Strand,
t.Coverage,
t.GeneSymbol,
t.Name);
}
}
}
}
}
return(new[] { options.OutputFile });
}
public override IEnumerable <string> Process()
{
var candidates = options.ReadSeeds();
Progress.SetMessage("Total {0} seeds readed.", candidates.Length);
var offsets = GetPossibleOffsets(string.Empty);
Progress.SetMessage("Build target {0} mers...", options.MinimumSeedLength);
var seeds = (from seq in candidates
from offset in offsets
select seq.Substring(offset, options.MinimumSeedLength)).ToList();
var targetSeedMap = ParclipUtils.BuildTargetSeedMap(options, seeds, this.Progress);
//var seeds = new HashSet<string>(from seq in candidates
// from offset in offsets
// select seq.Substring(offset, options.MinimumSeedLength));
//var targetSeedMap = ParclipUtils.BuildTargetSeedMap(options, m => seeds.Contains(m.Sequence), this.Progress);
Progress.SetMessage("Finding target...");
using (var sw = new StreamWriter(options.OutputFile))
{
sw.WriteLine("Sequence\tSeed\tSeedOffset\tSeedLength\tTarget\tTargetCoverage\tTargetGeneSymbol\tTargetName");
foreach (var seq in candidates)
{
foreach (var offset in offsets)
{
if (seq.Length < offset + options.MinimumSeedLength)
{
break;
}
var seed = seq.Substring(offset, options.MinimumSeedLength);
List <SeedItem> target;
if (targetSeedMap.TryGetValue(seed, out target))
{
if (target.ConvertAll(l => l.Coverage).Distinct().Count() == 1)
{
GenomeUtils.SortChromosome(target, m => m.Seqname, m => m.Start);
}
else
{
target.Sort((m1, m2) =>
{
return(m2.Coverage.CompareTo(m1.Coverage));
});
}
var longest = ParclipUtils.ExtendToLongestTarget(target, null, seq, offset, options.MinimumSeedLength, int.MaxValue, options.MinimumCoverage);
for (int j = 0; j < longest.Count; j++)
{
var t = longest[j];
var finalSeed = seq.Substring(offset, (int)t.Length);
sw.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}:{5}-{6}:{7}\t{8}\t{9}\t{10}",
seq,
finalSeed,
offset,
finalSeed.Length,
t.Seqname,
t.Start,
t.End,
t.Strand,
t.Coverage,
t.GeneSymbol,
t.Name);
}
}
}
}
}
return(new[] { options.OutputFile });
}
public override IEnumerable <string> Process()
{
Progress.SetMessage("Reading smallRNA...");
//exclude lincRNA
var mappedSmallRNA = ParclipUtils.GetSmallRNACoverageRegion(options.InputFile, includeSmallRNATags: null, excudeSmallRNATags: SmallRNAConsts.lncRNA);
mappedSmallRNA.Sort((m1, m2) => m2.Coverages.Average(l => l.Coverage).CompareTo(m1.Coverages.Average(l => l.Coverage)));
Progress.SetMessage("Build target {0} mers...", options.MinimumSeedLength);
var targetSeedMap = ParclipUtils.BuildTargetSeedMap(options, m => true, progress: this.Progress);
Progress.SetMessage("Finding target...");
using (var sw = new StreamWriter(options.OutputFile))
{
sw.WriteLine("SmallRNA\tChr\tStart\tEnd\tStrand\tSeed\tSeedOffset\tSeedLength\tSeedCoverage\tTarget\tTargetCoverage\tTargetGeneSymbol\tTargetName\tTargetSeedOffset\tTargetSeedUniqueRead");
foreach (var t2c in mappedSmallRNA)
{
var seq = t2c.Sequence.ToUpper();
int[] offsets = GetPossibleOffsets(t2c.Name);
foreach (var offset in offsets)
{
if (offset + options.MinimumSeedLength >= seq.Length)
{
Console.Error.WriteLine("t2c={0}/{1}, seq={2}, offset={3}, minseed={4}", t2c.Name, t2c.GeneSymbol, seq, offset, options.MinimumSeedLength);
continue;
}
var seed = seq.Substring(offset, options.MinimumSeedLength);
var coverage = t2c.Coverages.Skip(offset).Take(options.MinimumSeedLength).Average(l => l.Coverage);
if (coverage < options.MinimumCoverage)
{
continue;
}
List <SeedItem> target;
if (targetSeedMap.TryGetValue(seed, out target))
{
target.Sort((m1, m2) =>
{
return(m2.Coverage.CompareTo(m1.Coverage));
});
var longest = ParclipUtils.FindLongestTarget(target, t2c, seq, offset, options.MinimumSeedLength, int.MaxValue, options.MinimumCoverage);
for (int j = 0; j < longest.Count; j++)
{
var t = longest[j];
var finalSeed = seq.Substring(offset, (int)t.Length);
sw.Write("{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}\t{7}\t{8}", t2c.Name, t2c.Seqname, t2c.Start, t2c.End, t2c.Strand, finalSeed, offset, finalSeed.Length, Math.Round(coverage));
var uniqueReadCount = (from c in t.Source.Coverages.Skip(t.SourceOffset).Take(finalSeed.Length)
from q in c.UniqueRead
select q).Distinct().Count();
sw.WriteLine("\t{0}:{1}-{2}:{3}\t{4}\t{5}\t{6}\t{7}\t{8}",
t.Seqname,
t.Start,
t.End,
t.Strand,
t.Coverage,
t.GeneSymbol,
t.Name,
t.SourceOffset,
t.GetSeedUniqueReadCount(finalSeed.Length));
}
}
}
}
}
return(new[] { options.OutputFile });
}
