public static List <SeedItem> BuildTargetSeeds(ITargetBuilderOptions options, Func <SeedItem, bool> acceptSeed, IProgressCallback progress)
{
List <SeedItem> seeds = new List <SeedItem>();
var mapped = GetTargetCoverageRegion(options, progress);
progress.SetMessage("Building seeds ...");
progress.SetRange(0, mapped.Count);
progress.SetPosition(0);
foreach (var l in mapped)
{
progress.Increment(1);
for (int i = 0; i < l.Sequence.Length - options.MinimumSeedLength; i++)
{
SeedItem si = GetSeed(l, i, options.MinimumSeedLength, options.MinimumCoverage);
if (si != null && acceptSeed(si))
{
seeds.Add(si);
}
}
}
progress.End();
progress.SetMessage("Total {0} {1}mers seeds were built.", seeds.Count, options.MinimumSeedLength);
return(seeds);
}
/// <summary>
/// Transfer bed format (zero-based) to gff format (one-based)
/// </summary>
/// <param name="options"></param>
/// <param name="progress"></param>
/// <returns></returns>
public static List <CoverageRegion> GetTargetCoverageRegionFromBed(ITargetBuilderOptions options, IProgressCallback progress)
{
var result = new List <CoverageRegion>();
var groups = new BedItemFile <BedItem>().ReadFromFile(options.TargetFile);
progress.SetMessage("Total {0} potential target group read from file {1}", groups.Count, options.TargetFile);
foreach (var utr in groups)
{
var rg = new CoverageRegion();
rg.Name = utr.Name;
rg.Seqname = utr.Seqname.StringAfter("chr");
rg.Start = utr.Start + 1;
rg.End = utr.End;
rg.Strand = utr.Strand;
for (var i = rg.Start; i < rg.End; i++)
{
rg.Coverages.Add(new CoverageSite(DEFAULT_COVERAGE));
}
result.Add(rg);
}
return(result);
}
public static List <CoverageRegion> GetTargetCoverageRegion(ITargetBuilderOptions options, IProgressCallback progress, bool removeRegionWithoutSequence = true)
{
List <CoverageRegion> result;
if (options.TargetFile.EndsWith(".xml"))
{
result = GetTargetCoverageRegionFromXml(options, progress);
}
else
{
result = GetTargetCoverageRegionFromBed(options, progress);
}
var dic = result.ToGroupDictionary(m => m.Seqname);
progress.SetMessage("Filling sequence from {0}...", options.GenomeFastaFile);
using (var sr = new StreamReader(options.GenomeFastaFile))
{
var ff = new FastaFormat();
Sequence seq;
while ((seq = ff.ReadSequence(sr)) != null)
{
progress.SetMessage("Processing chromosome {0} ...", seq.Reference);
var seqname = seq.Name.StringAfter("chr");
List <CoverageRegion> lst;
if (dic.TryGetValue(seqname, out lst))
{
foreach (var l in lst)
{
l.Sequence = seq.SeqString.Substring((int)(l.Start - 1), (int)l.Length);
if (l.Strand == '+')
{
l.ReverseComplementedSequence = SequenceUtils.GetReverseComplementedSequence(l.Sequence);
}
}
}
}
}
if (removeRegionWithoutSequence)
{
result.RemoveAll(l => string.IsNullOrEmpty(l.Sequence));
}
progress.SetMessage("Filling sequence finished.");
var namemap = new MapReader(1, 12).ReadFromFile(options.RefgeneFile);
result.ForEach(m =>
{
var gene = m.Name.StringBefore("_utr3");
m.GeneSymbol = namemap.ContainsKey(gene) ? namemap[gene] : string.Empty;
});
return(result);
}
public static Dictionary <string, List <SeedItem> > BuildTargetSeedMap(ITargetBuilderOptions options, Func <SeedItem, bool> acceptSeed, IProgressCallback progress)
{
//Read 6 mers from target
var targetSeeds = BuildTargetSeeds(options, acceptSeed, progress);
progress.SetMessage("Grouping seeds by sequence ...");
var result = targetSeeds.ToGroupDictionary(m => m.Sequence.ToUpper());
progress.SetMessage("Total {0} unique {1}mers seeds were built.", result.Count, options.MinimumSeedLength);
return(result);
}
public static List <SeedItem> BuildTargetSeeds(ITargetBuilderOptions options, List <string> seeds, IProgressCallback progress)
{
List <SeedItem> result = new List <SeedItem>();
var mapped = GetTargetCoverageRegion(options, progress);
progress.SetMessage("Building seeds ...");
progress.SetRange(0, mapped.Count);
progress.SetPosition(0);
foreach (var l in mapped)
{
progress.Increment(1);
foreach (var seed in seeds)
{
var curseq = l.Strand == '+' ? l.ReverseComplementedSequence : l.Sequence;
int lastpos = -1;
while (true)
{
int pos = curseq.IndexOf(seed, lastpos + 1);
if (pos == -1)
{
break;
}
if (l.Strand == '+')
{
result.Add(GetSeed(l, curseq.Length - pos - options.MinimumSeedLength, options.MinimumSeedLength, options.MinimumCoverage));
}
else
{
result.Add(GetSeed(l, pos, options.MinimumSeedLength, options.MinimumCoverage));
}
lastpos = pos;
}
}
}
progress.End();
progress.SetMessage("Total {0} {1}mers seeds were built.", result.Count, options.MinimumSeedLength);
return(result);
}
public static Dictionary<string, List<SeedItem>> BuildTargetSeedMap(ITargetBuilderOptions options, Func<SeedItem, bool> acceptSeed, IProgressCallback progress)
{
//Read 6 mers from target
var targetSeeds = BuildTargetSeeds(options, acceptSeed, progress);
progress.SetMessage("Grouping seeds by sequence ...");
var result = targetSeeds.ToGroupDictionary(m => m.Sequence.ToUpper());
progress.SetMessage("Total {0} unique {1}mers seeds were built.", result.Count, options.MinimumSeedLength);
return result;
}
public static List<SeedItem> BuildTargetSeeds(ITargetBuilderOptions options, Func<SeedItem, bool> acceptSeed, IProgressCallback progress)
{
List<SeedItem> seeds = new List<SeedItem>();
var mapped = GetTargetCoverageRegion(options, progress);
progress.SetMessage("Building seeds ...");
progress.SetRange(0, mapped.Count);
progress.SetPosition(0);
foreach (var l in mapped)
{
progress.Increment(1);
for (int i = 0; i < l.Sequence.Length - options.MinimumSeedLength; i++)
{
SeedItem si = GetSeed(l, i, options.MinimumSeedLength, options.MinimumCoverage);
if (si != null && acceptSeed(si))
{
seeds.Add(si);
}
}
}
progress.End();
progress.SetMessage("Total {0} {1}mers seeds were built.", seeds.Count, options.MinimumSeedLength);
return seeds;
}
public static List<SeedItem> BuildTargetSeeds(ITargetBuilderOptions options, List<string> seeds, IProgressCallback progress)
{
List<SeedItem> result = new List<SeedItem>();
var mapped = GetTargetCoverageRegion(options, progress);
progress.SetMessage("Building seeds ...");
progress.SetRange(0, mapped.Count);
progress.SetPosition(0);
foreach (var l in mapped)
{
progress.Increment(1);
foreach (var seed in seeds)
{
var curseq = l.Strand == '+' ? l.ReverseComplementedSequence : l.Sequence;
int lastpos = -1;
while (true)
{
int pos = curseq.IndexOf(seed, lastpos + 1);
if (pos == -1)
{
break;
}
if (l.Strand == '+')
{
result.Add(GetSeed(l, curseq.Length - pos - options.MinimumSeedLength, options.MinimumSeedLength, options.MinimumCoverage));
}
else
{
result.Add(GetSeed(l, pos, options.MinimumSeedLength, options.MinimumCoverage));
}
lastpos = pos;
}
}
}
progress.End();
progress.SetMessage("Total {0} {1}mers seeds were built.", result.Count, options.MinimumSeedLength);
return result;
}
/// <summary>
/// Transfer bed format (zero-based) to gff format (one-based)
/// </summary>
/// <param name="options"></param>
/// <param name="progress"></param>
/// <returns></returns>
public static List<CoverageRegion> GetTargetCoverageRegionFromBed(ITargetBuilderOptions options, IProgressCallback progress)
{
var result = new List<CoverageRegion>();
var groups = new BedItemFile<BedItem>().ReadFromFile(options.TargetFile);
progress.SetMessage("Total {0} potential target group read from file {1}", groups.Count, options.TargetFile);
foreach (var utr in groups)
{
var rg = new CoverageRegion();
rg.Name = utr.Name;
rg.Seqname = utr.Seqname.StringAfter("chr");
rg.Start = utr.Start + 1;
rg.End = utr.End;
rg.Strand = utr.Strand;
for (var i = rg.Start; i < rg.End; i++)
{
rg.Coverages.Add(1000);
}
result.Add(rg);
}
return result;
}
public static List<CoverageRegion> GetTargetCoverageRegionFromXml(ITargetBuilderOptions options, IProgressCallback progress)
{
var result = new List<CoverageRegion>();
var groups = new FeatureItemGroupXmlFormat().ReadFromFile(options.TargetFile);
progress.SetMessage("Total {0} potential target group read from file {1}", groups.Count, options.TargetFile);
foreach (var group in groups)
{
//since the items in same group shared same reads, only the first one will be used.
for (int i = 1; i < group.Count; i++)
{
group[0].Name = group[0].Name + "/" + group[i].Name;
}
group.RemoveRange(1, group.Count - 1);
var utr = group[0];
utr.Locations.RemoveAll(m => m.SamLocations.Count == 0);
utr.CombineLocationByMappedReads();
foreach (var loc in utr.Locations)
{
var map = new Dictionary<long, int>();
foreach (var sloc in loc.SamLocations)
{
for (long i = sloc.SamLocation.Start; i <= sloc.SamLocation.End; i++)
{
int count;
if (map.TryGetValue(i, out count))
{
map[i] = count + sloc.SamLocation.Parent.QueryCount;
}
else
{
map[i] = sloc.SamLocation.Parent.QueryCount;
}
}
}
var keys = (from k in map.Keys
orderby k
select k).ToList();
int start = 0;
int end = start + 1;
while (true)
{
if (end == keys.Count || keys[end] != keys[end - 1] + 1)
{
var rg = new CoverageRegion();
rg.Name = utr.Name;
rg.Seqname = loc.Seqname;
rg.Start = keys[start];
rg.End = keys[end - 1];
rg.Strand = loc.Strand;
for (int i = start; i < end; i++)
{
rg.Coverages.Add(map[keys[i]]);
}
result.Add(rg);
if (end == keys.Count)
{
break;
}
start = end;
end = start + 1;
}
else
{
end++;
}
}
}
}
return result;
}
public static List<CoverageRegion> GetTargetCoverageRegion(ITargetBuilderOptions options, IProgressCallback progress, bool removeRegionWithoutSequence = true)
{
List<CoverageRegion> result;
if (options.TargetFile.EndsWith(".xml"))
{
result = GetTargetCoverageRegionFromXml(options, progress);
}
else
{
result = GetTargetCoverageRegionFromBed(options, progress);
}
var dic = result.ToGroupDictionary(m => m.Seqname);
progress.SetMessage("Filling sequence from {0}...", options.GenomeFastaFile);
using (var sr = new StreamReader(options.GenomeFastaFile))
{
var ff = new FastaFormat();
Sequence seq;
while ((seq = ff.ReadSequence(sr)) != null)
{
progress.SetMessage("Processing chromosome {0} ...", seq.Reference);
var seqname = seq.Name.StringAfter("chr");
List<CoverageRegion> lst;
if (dic.TryGetValue(seqname, out lst))
{
foreach (var l in lst)
{
l.Sequence = seq.SeqString.Substring((int)(l.Start - 1), (int)l.Length);
if(l.Strand == '+')
{
l.ReverseComplementedSequence = SequenceUtils.GetReverseComplementedSequence(l.Sequence);
}
}
}
}
}
if (removeRegionWithoutSequence)
{
result.RemoveAll(l => string.IsNullOrEmpty(l.Sequence));
}
progress.SetMessage("Filling sequence finished.");
var namemap = new MapReader(1, 12).ReadFromFile(options.RefgeneFile);
result.ForEach(m =>
{
var gene = m.Name.StringBefore("_utr3");
m.GeneSymbol = namemap.ContainsKey(gene) ? namemap[gene] : string.Empty;
});
return result;
}
public static List <CoverageRegion> GetTargetCoverageRegionFromXml(ITargetBuilderOptions options, IProgressCallback progress)
{
var result = new List <CoverageRegion>();
var groups = new FeatureItemGroupXmlFormat().ReadFromFile(options.TargetFile);
progress.SetMessage("Total {0} potential target group read from file {1}", groups.Count, options.TargetFile);
foreach (var group in groups)
{
//since the items in same group shared same reads, only the first one will be used.
for (int i = 1; i < group.Count; i++)
{
group[0].Name = group[0].Name + "/" + group[i].Name;
}
group.RemoveRange(1, group.Count - 1);
var utr = group[0];
utr.Locations.RemoveAll(m => m.SamLocations.Count == 0);
utr.CombineLocationByMappedReads();
foreach (var loc in utr.Locations)
{
var map = new Dictionary <long, CoverageSite>();
foreach (var sloc in loc.SamLocations)
{
for (long i = sloc.SamLocation.Start; i <= sloc.SamLocation.End; i++)
{
CoverageSite count;
if (map.TryGetValue(i, out count))
{
count.Coverage = count.Coverage + sloc.SamLocation.Parent.QueryCount;
count.UniqueRead.Add(sloc.SamLocation.Parent.Qname);
}
else
{
map[i] = new CoverageSite(sloc.SamLocation.Parent.QueryCount, sloc.SamLocation.Parent.Qname);
}
}
}
var keys = (from k in map.Keys
orderby k
select k).ToList();
int start = 0;
int end = start + 1;
while (true)
{
if (end == keys.Count || keys[end] != keys[end - 1] + 1)
{
var rg = new CoverageRegion();
rg.Name = utr.Name;
rg.Seqname = loc.Seqname;
rg.Start = keys[start];
rg.End = keys[end - 1];
rg.Strand = loc.Strand;
for (int i = start; i < end; i++)
{
rg.Coverages.Add(map[keys[i]]);
}
result.Add(rg);
if (end == keys.Count)
{
break;
}
start = end;
end = start + 1;
}
else
{
end++;
}
}
}
}
return(result);
}