public void Link(MapLinkFilter.LinkType type)
{
this.Map = TssRegulatoryMap.LoadMap(this.MapFileName, new MapLinkFilter {
LinkTypeFilter = type
});
NullMapBuilder.WriteMap(this.Map, this.ExpressionData.Genes, this.HistoneName, this.OutputFile);
}
public void BestWorst(double fraction)
{
this.Map = TssRegulatoryMap.LoadMap(this.MapFileName, new MapLinkFilter {
});
var bestLinkMap = this.Map.GetBestNeighborMap(1);
var orderedLinks = bestLinkMap.Links.OrderBy(x => x.ConfidenceScore).ToList();
int linkCount = (int)(orderedLinks.Count * fraction);
var topLinks = orderedLinks
.Take(linkCount)
.OrderBy(x => x.AbsLinkLength)
.ToList();
var bottomLinks = orderedLinks
.OrderBy(x => - x.ConfidenceScore)
.Take(orderedLinks.Count - linkCount)
.ToList();
List <MapLink> bestLinks = new List <MapLink>();
List <MapLink> worstLinks = new List <MapLink>();
foreach (var link in topLinks)
{
int linkIndex = int.MaxValue;
for (int i = 0; i < bottomLinks.Count; i++)
{
var bottomLink = bottomLinks[i];
if (Math.Sign(link.LinkLength) == Math.Sign(bottomLink.LinkLength) &&
link.AbsLinkLength < bottomLink.AbsLinkLength * 1.01 &&
link.AbsLinkLength > bottomLink.AbsLinkLength * 0.99)
{
linkIndex = i;
break;
}
}
if (linkIndex != int.MaxValue)
{
bestLinks.Add(link);
worstLinks.Add(bottomLinks[linkIndex]);
bottomLinks.RemoveAt(linkIndex);
}
}
var bottomMapFile = this.OutputFile.Replace(".bed", ".bottom.bed");
NullMapBuilder.WriteMap(new TssRegulatoryMap(bestLinks), this.ExpressionData.Genes, this.HistoneName, this.OutputFile);
NullMapBuilder.WriteMap(new TssRegulatoryMap(worstLinks), this.ExpressionData.Genes, this.HistoneName, bottomMapFile);
}
public void Convert()
{
var contacts = Helpers.GetFileDataLines(this.ContactFileName, true).Select(line =>
{
var fields = line.Split('\t');
var pair = fields[6];
var ids = pair.Split('_');
return(new
{
Pair = pair,
Id1 = ids[0],
Chr1 = fields[0],
Start1 = int.Parse(fields[1]),
End1 = int.Parse(fields[2]),
Id2 = ids[1],
Chr2 = fields[3],
Start2 = int.Parse(fields[4]),
End2 = int.Parse(fields[5]),
Score = double.Parse(fields[7]),
});
}).ToList();
var locations = contacts.Select(x => new Location[]
{
new Location
{
Name = x.Id1, Chromosome = x.Chr1, Start = x.Start1, End = x.End1, AlternateName = x.Id2, Score = x.Score
},
new Location
{
Name = x.Id2, Chromosome = x.Chr2, Start = x.Start2, End = x.End2, AlternateName = x.Id1, Score = x.Score
},
}).SelectMany(x => x)
.ToList();
var uniqueLocations = locations
.ToLookup(x => x.Name)
.ToDictionary(x => x.Key, x => x.First());
var contactMap = locations
.ToLookup(x => x.Name, x => x)
.ToDictionary(x => x.Key, x => x
.ToDictionary(y => y.AlternateName, y => uniqueLocations[y.AlternateName]));
var indexedLocations = new BedFile(uniqueLocations);
var LocusFile = new BedFile(this.LocusFileName, BedFile.Bed3Layout);
var annotationSet = new GtfExpressionFile(GtfExpressionFile.ExpressionType.Cage, this.AnnotationFileName);
var LocusOverlaps = indexedLocations.Locations.ToDictionary(
x => x.Key,
x => TRFScorer.GetOverlaps(
x.Value,
LocusFile.ChromosomeIndexedLocations,
BedFile.IndexSize,
LocusFile.MaxLocationSize[x.Value.Chromosome]));
var tssOverlaps = indexedLocations.Locations.ToDictionary(
x => x.Key,
x => TRFScorer.GetOverlaps(
x.Value,
annotationSet.ChromosomeIndexedLocations,
BedFile.IndexSize,
annotationSet.MaxLocationSize[x.Value.Chromosome],
Location.OverlapsDirectionalStart));
var links = contactMap
.Where(x => tssOverlaps[x.Key] != null)
.ToDictionary(x => x.Key, x => x.Value.Where(y => LocusOverlaps[y.Key] != null))
.Where(x => x.Value.Any())
.Select(x => tssOverlaps[x.Key].Select(y => new {
Id1 = x.Key,
Tss = y.Name,
LocusList = x.Value
.Select(z => LocusOverlaps[z.Key]
.Select(a => new { Name = a.Name, Id2 = z.Key }))
.SelectMany(z => z).ToList()
})
.Select(y => y.LocusList.Select(z =>
{
var LocusLocation = LocusFile.Locations[z.Name];
var tssStart = annotationSet.Transcripts[y.Tss].DirectionalStart;
var linkLength = LocusLocation.End < tssStart ? LocusLocation.End - tssStart : LocusLocation.Start - tssStart;
return(new MapLink
{
TranscriptName = y.Tss,
TssName = y.Tss,
LocusName = z.Name,
ConfidenceScore = contactMap[y.Id1][z.Id2].Score,
LinkLength = linkLength,
});
}))
.SelectMany(y => y))
.SelectMany(x => x)
.ToList();
var convertedMap = new TssRegulatoryMap(links);
NullMapBuilder.WriteMap(convertedMap, annotationSet.Locations, "Contact", this.MapFileName);
}