/// <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 SeedItem GetSeed(CoverageRegion cr, int offset, int seedLength, double minCoverage)
{
if (cr.Sequence.Length < offset + seedLength)
{
return null;
}
var coverage = cr.Coverages.Skip(offset).Take(seedLength).Average();
if (coverage < minCoverage)
{
return null;
}
var newseq = cr.Sequence.Substring(offset, seedLength);
var start = cr.Start + offset;
var end = cr.Start + offset + seedLength - 1;
if (cr.Strand == '+')
{
newseq = SequenceUtils.GetReverseComplementedSequence(newseq);
}
return new SeedItem()
{
Seqname = cr.Seqname,
Start = start,
End = end,
Strand = cr.Strand,
Coverage = coverage,
Name = cr.Name,
Sequence = newseq,
Source = cr,
SourceOffset = offset,
GeneSymbol = cr.GeneSymbol
};
}
public static List <SeedItem> FindLongestTarget(List <SeedItem> target, CoverageRegion t2c, string seq, int offset, int minimumSeedLength, int maximumSeedLength, double minimumCoverage)
{
var result = ExtendToLongestTarget(target, t2c, seq, offset, minimumSeedLength, maximumSeedLength, minimumCoverage);
var maxLength = result.Max(l => l.Length);
result.RemoveAll(l => l.Length < maxLength);
return(result);
}
public static List <CoverageRegion> GetSmallRNACoverageRegionFromXml(string featureFile, string[] includeSmallRNATags = null, string[] excudeSmallRNATags = null)
{
var smallRNAGroups = new FeatureItemGroupXmlFormat().ReadFromFile(featureFile);
if (includeSmallRNATags != null && includeSmallRNATags.Length > 0)
{
smallRNAGroups.ForEach(m => m.RemoveAll(l => includeSmallRNATags.All(k => !m.Name.StartsWith(k))));
smallRNAGroups.RemoveAll(m => m.Count == 0);
}
if (excudeSmallRNATags != null && excudeSmallRNATags.Length > 0)
{
smallRNAGroups.ForEach(m => m.RemoveAll(l => excudeSmallRNATags.Any(k => m.Name.StartsWith(k))));
smallRNAGroups.RemoveAll(m => m.Count == 0);
}
var result = new List <CoverageRegion>();
foreach (var sg in smallRNAGroups)
{
//since the items in same group shared same reads, only the first one will be used.
var smallRNA = sg[0];
smallRNA.Name = (from g in sg select g.Name).Merge("/");
smallRNA.Locations.RemoveAll(m => m.SamLocations.Count == 0);
smallRNA.CombineLocationByMappedReads();
//only first location will be used.
var loc = smallRNA.Locations[0];
//coverage in all position will be set as same as total query count
var rg = new CoverageRegion();
rg.Name = smallRNA.Name;
rg.Seqname = loc.Seqname;
rg.Start = loc.Start;
rg.End = loc.End;
rg.Strand = loc.Strand;
rg.Sequence = loc.Sequence;
var coverage = (from sloc in loc.SamLocations select sloc.SamLocation.Parent.QueryCount).Sum();
var uniqueRead = (from sloc in loc.SamLocations select sloc.SamLocation.Parent.Qname).Distinct().ToList();
for (int i = 0; i < loc.Length; i++)
{
rg.Coverages.Add(new CoverageSite(coverage, uniqueRead));
}
result.Add(rg);
}
return(result);
}
public static List<CoverageRegion> GetSmallRNACoverageRegion(string mappedFeatureXmlFile, string[] includeSmallRNATags = null, string[] excudeSmallRNATags = null)
{
var smallRNAGroups = new FeatureItemGroupXmlFormat().ReadFromFile(mappedFeatureXmlFile);
if (includeSmallRNATags != null && includeSmallRNATags.Length > 0)
{
smallRNAGroups.ForEach(m => m.RemoveAll(l => includeSmallRNATags.All(k => !m.Name.StartsWith(k))));
smallRNAGroups.RemoveAll(m => m.Count == 0);
}
if (excudeSmallRNATags != null && excudeSmallRNATags.Length > 0)
{
smallRNAGroups.ForEach(m => m.RemoveAll(l => excudeSmallRNATags.Any(k => m.Name.StartsWith(k))));
smallRNAGroups.RemoveAll(m => m.Count == 0);
}
var result = new List<CoverageRegion>();
foreach (var sg in smallRNAGroups)
{
//since the items in same group shared same reads, only the first one will be used.
var smallRNA = sg[0];
smallRNA.Name = (from g in sg select g.Name).Merge("/");
smallRNA.Locations.RemoveAll(m => m.SamLocations.Count == 0);
smallRNA.CombineLocationByMappedReads();
//only first location will be used.
var loc = smallRNA.Locations[0];
//coverage in all position will be set as same as total query count
var rg = new CoverageRegion();
rg.Name = smallRNA.Name;
rg.Seqname = loc.Seqname;
rg.Start = loc.Start;
rg.End = loc.End;
rg.Strand = loc.Strand;
rg.Sequence = loc.Sequence;
var coverage = (from sloc in loc.SamLocations select sloc.SamLocation.Parent.QueryCount).Sum();
for (int i = 0; i < loc.Length; i++)
{
rg.Coverages.Add(coverage);
}
result.Add(rg);
}
return result;
}
public static SeedItem GetSeed(CoverageRegion cr, int offset, int seedLength, double minCoverage)
{
if (cr.Sequence.Length < offset + seedLength)
{
return(null);
}
var coverages = cr.Coverages.Skip(offset).Take(seedLength).ToList();
var coverage = coverages.Average(l => l.Coverage);
if (coverage < minCoverage)
{
return(null);
}
var newseq = cr.Sequence.Substring(offset, seedLength);
var start = cr.Start + offset;
var end = cr.Start + offset + seedLength - 1;
if (cr.Strand == '+')
{
newseq = SequenceUtils.GetReverseComplementedSequence(newseq);
}
return(new SeedItem()
{
Seqname = cr.Seqname,
Start = start,
End = end,
Strand = cr.Strand,
Coverage = coverage,
Name = cr.Name,
Sequence = newseq,
Source = cr,
SourceOffset = offset,
GeneSymbol = cr.GeneSymbol
});
}
public static List <CoverageRegion> GetSmallRNACoverageRegionFromFasta(string featureFile)
{
var sequences = SequenceUtils.Read(featureFile);
var result = new List <CoverageRegion>();
foreach (var smallRNA in sequences)
{
//coverage in all position will be set as same as total query count
var rg = new CoverageRegion();
rg.Name = smallRNA.Name;
rg.Seqname = "Unknown";
rg.Start = -1;
rg.End = -1;
rg.Strand = '*';
rg.Sequence = smallRNA.SeqString;
for (int i = 0; i < smallRNA.SeqString.Length; i++)
{
rg.Coverages.Add(new CoverageSite(DEFAULT_COVERAGE));
}
result.Add(rg);
}
return(result);
}
public static List<SeedItem> FindLongestTarget(List<SeedItem> target, CoverageRegion t2c, string seq, int offset, int minimumSeedLength, int maximumSeedLength, double minimumCoverage)
{
var result = ExtendToLongestTarget(target, t2c, seq, offset, minimumSeedLength, maximumSeedLength, minimumCoverage);
var maxLength = result.Max(l => l.Length);
result.RemoveAll(l => l.Length < maxLength);
return result;
}
public static List<SeedItem> ExtendToLongestTarget(List<SeedItem> target, CoverageRegion t2c, string seq, int offset, int minimumSeedLength, int maximumSeedLength, double minimumCoverage)
{
var individualSeeds = new List<SeedItem>();
var source = new List<SeedItem>(target);
var extendSeedLength = minimumSeedLength;
while (extendSeedLength < maximumSeedLength)
{
extendSeedLength++;
//check the coverage in smallRNA
if (t2c != null)
{
var extendCoverage = t2c.Coverages.Skip(offset).Take(extendSeedLength).Average();
if (extendCoverage < minimumCoverage)
{
break;
}
}
if (seq.Length < offset + extendSeedLength)
{
individualSeeds.AddRange(source);
break;
}
var extendSeed = seq.Substring(offset, extendSeedLength);
var extendTarget = new List<SeedItem>();
var doneTarget = new List<SeedItem>();
foreach (var utrTarget in source)
{
var newoffset = utrTarget.Strand == '-' ? utrTarget.SourceOffset : utrTarget.SourceOffset - 1;
if (newoffset < 0)
{
doneTarget.Add(utrTarget);
continue;
}
var newseed = GetSeed(utrTarget.Source, newoffset, extendSeedLength, minimumCoverage);
if (newseed == null)
{
doneTarget.Add(utrTarget);
continue;
}
if (!extendSeed.Equals(newseed.Sequence))
{
doneTarget.Add(utrTarget);
continue;
}
extendTarget.Add(newseed);
}
individualSeeds.AddRange(doneTarget);
if (extendTarget.Count > 0)
{
source = extendTarget;
}
else
{
break;
}
}
//For each gene, only the longest one will be kept
var individualGenes = (from cs in individualSeeds.GroupBy(m => m.GeneSymbol)
let csitem = cs.GroupBy(l => l.Length).OrderByDescending(k => k.Key).First()
from ls in csitem
select ls).OrderByDescending(l => l.Length).ToList();
//Merge the seeds with same gene symbol, same location but different name
var final = new List<SeedItem>();
var rmap = individualGenes.GroupBy(l => l.GeneSymbol + "_" + l.GetLocation()).ToList();
foreach (var rm in rmap)
{
var item = rm.First();
item.Name = (from r in rm
select r.Name).Merge("/");
final.Add(item);
}
return final.OrderByDescending(l => l.Length).ToList();
}
/// <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 <SeedItem> ExtendToLongestTarget(List <SeedItem> target, CoverageRegion t2c, string seq, int offset, int minimumSeedLength, int maximumSeedLength, double minimumCoverage)
{
var individualSeeds = new List <SeedItem>();
var source = new List <SeedItem>(target);
var extendSeedLength = minimumSeedLength;
while (extendSeedLength < maximumSeedLength)
{
extendSeedLength++;
//check the coverage in smallRNA
if (t2c != null)
{
var extendCoverage = t2c.Coverages.Skip(offset).Take(extendSeedLength).Average(l => l.Coverage);
if (extendCoverage < minimumCoverage)
{
break;
}
}
if (seq.Length < offset + extendSeedLength)
{
individualSeeds.AddRange(source);
break;
}
var extendSeed = seq.Substring(offset, extendSeedLength);
var extendTarget = new List <SeedItem>();
var doneTarget = new List <SeedItem>();
foreach (var utrTarget in source)
{
var newoffset = utrTarget.Strand == '-' ? utrTarget.SourceOffset : utrTarget.SourceOffset - 1;
if (newoffset < 0)
{
doneTarget.Add(utrTarget);
continue;
}
var newseed = GetSeed(utrTarget.Source, newoffset, extendSeedLength, minimumCoverage);
if (newseed == null)
{
doneTarget.Add(utrTarget);
continue;
}
if (!extendSeed.Equals(newseed.Sequence))
{
doneTarget.Add(utrTarget);
continue;
}
extendTarget.Add(newseed);
}
individualSeeds.AddRange(doneTarget);
if (extendTarget.Count > 0)
{
source = extendTarget;
}
else
{
break;
}
}
//For each gene, only the longest one will be kept
var individualGenes = (from cs in individualSeeds.GroupBy(m => m.GeneSymbol)
let csitem = cs.GroupBy(l => l.Length).OrderByDescending(k => k.Key).First()
from ls in csitem
select ls).OrderByDescending(l => l.Length).ToList();
//Merge the seeds with same gene symbol, same location but different name
var final = new List <SeedItem>();
var rmap = individualGenes.GroupBy(l => l.GeneSymbol + "_" + l.GetLocation()).ToList();
foreach (var rm in rmap)
{
var item = rm.First();
item.Name = (from r in rm
select r.Name).Merge("/");
final.Add(item);
}
return(final.OrderByDescending(l => l.Length).ToList());
}
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);
}
