/// <summary>
/// Adds a link to the map if it passes the link filter criteria.
/// </summary>
/// <param name="tssMap">Tss map.</param>
/// <param name="LocusMap">Locus map.</param>
/// <param name="filter">Filter.</param>
/// <param name="link">Link.</param>
private static void AddLink(
ref TssRegulatoryMap tssMap,
ref LocusRegulatoryMap LocusMap,
MapLinkFilter filter,
MapLink link)
{
if (filter.IsValidLink(link.Strand, link.LinkLength, link.ConfidenceScore, link.Correlation))
{
filter.ApplyLinkFilterType(link, tssMap, LocusMap);
}
}
public void AddReplaceLink(
MapLink link,
LocusRegulatoryMap map,
Func <MapLink, LocusRegulatoryMap, bool> test)
{
this.EnsureKey(link, map);
if (test(link, map))
{
map[link.LocusName].Clear();
map[link.LocusName].Add(link.TranscriptName, link);
}
}
public void EnsureKey(MapLink link, LocusRegulatoryMap LocusMap)
{
if (!LocusMap.ContainsKey(link.LocusName))
{
LocusMap.Add(link.LocusName, new Dictionary <MapLink.Tss, MapLink>());
}
if (LocusMap[link.LocusName].ContainsKey(link.TranscriptName))
{
throw new Exception(string.Format("Duplicate Locus-TSS link {0}-{1} in map", link.LocusName, link.TranscriptName));
}
}
/// <summary>
/// Loads the map.
/// </summary>
/// <returns>The map.</returns>
/// <param name="mapFileName">Map file name.</param>
/// <param name="filter">Filter of map links.</param>
public static TssRegulatoryMap LoadMap(
string mapFileName,
MapLinkFilter filter)
{
using (TextReader tr = new StreamReader(mapFileName))
{
string line = null;
TssRegulatoryMap tssMap = new TssRegulatoryMap();
LocusRegulatoryMap LocusMap = new LocusRegulatoryMap();
while ((line = tr.ReadLine()) != null)
{
var fields = line.Split('\t');
var transcriptName = fields[3];
var confidence = double.Parse(fields[8]);
var correlation = double.Parse(fields[7]);
var distance = int.Parse(fields[9]);
var LocusName = fields[6];
var strand = fields[5];
var link = new MapLink
{
ConfidenceScore = confidence,
Correlation = correlation,
LinkLength = distance,
TranscriptName = transcriptName,
TssName = transcriptName,
LocusName = LocusName,
Strand = strand,
Chromosome = fields[0],
TssPosition = int.Parse(fields[1]),
HistoneName = fields[10],
GeneName = fields[11],
};
if ((filter.TranscriptSet == null || (filter.TranscriptSet != null && filter.TranscriptSet.Contains(transcriptName))) &&
(filter.LocusSet == null || (filter.LocusSet != null && filter.LocusSet.Contains(LocusName))))
{
AddLink(ref tssMap, ref LocusMap, filter, link);
}
}
return(filter.PostProcessLinkFilterType(tssMap, LocusMap));
}
}
/// <summary>
/// Determines whether this given link is closest gene the specified link map.
/// </summary>
/// <returns><c>true</c> if this instance is closest gene the specified link map; otherwise, <c>false</c>.</returns>
/// <param name="link">Link.</param>
/// <param name="map">Map.</param>
private bool IsBestGene(MapLink link, LocusRegulatoryMap LocusMap)
{
return(!LocusMap[link.LocusName].Any(x => x.Value.ConfidenceScore < link.ConfidenceScore));
}
/// <summary>
/// Determines whether this given link is closest gene the specified link map.
/// </summary>
/// <returns><c>true</c> if this instance is closest gene the specified link map; otherwise, <c>false</c>.</returns>
/// <param name="link">Link.</param>
/// <param name="map">Map.</param>
public bool IsClosestGene(MapLink link, LocusRegulatoryMap LocusMap)
{
return(!LocusMap[link.LocusName].Any(x => x.Value.AbsLinkLength < link.AbsLinkLength));
}
public TssRegulatoryMap PostProcessLinkFilterType(TssRegulatoryMap tssMap, LocusRegulatoryMap LocusMap)
{
switch (this.LinkTypeFilter)
{
case MapLinkFilter.LinkType.NearestGene:
return(LocusMap.Invert());
case MapLinkFilter.LinkType.NearestBestGene:
return(new TssRegulatoryMap(LocusMap.Links
.ToLookup(x => x.TranscriptName, x => x)
.Select(x => x.OrderBy(y => y.ConfidenceScore).First())));
case MapLinkFilter.LinkType.NearestLocusOfNearestGene:
return(new TssRegulatoryMap(LocusMap.Links
.ToLookup(x => x.TranscriptName, x => x)
.Select(x => x.OrderBy(y => y.AbsLinkLength).First())));
case MapLinkFilter.LinkType.BestGeneLink:
return(LocusMap.Invert());
case MapLinkFilter.LinkType.NearestLocusOrGene:
return(new TssRegulatoryMap(tssMap.Links.Concat(LocusMap.Links)));
case MapLinkFilter.LinkType.NearestLocusAndGene:
return(new TssRegulatoryMap(tssMap.Links.Where(LocusMap.Links.Contains)));
case MapLinkFilter.LinkType.BestLocusNearestGene:
return(new TssRegulatoryMap(tssMap.Links.Where(LocusMap.Links.Contains)));
case MapLinkFilter.LinkType.BestLocusBestGene:
return(new TssRegulatoryMap(tssMap.Links.Where(LocusMap.Links.Contains)));
case MapLinkFilter.LinkType.NotNearestGene:
return(new TssRegulatoryMap(tssMap.Links.Where(link => LocusMap.Links.Contains(link))));
case MapLinkFilter.LinkType.NotNearestLocusOrGene:
var Locus2nnmap = LocusMap.GetNearestNeighborMap(5);
return(new TssRegulatoryMap(Locus2nnmap.Links.Where(link => !this.IsClosestLocus(link, tssMap) && !this.IsClosestGene(link, LocusMap))));
case MapLinkFilter.LinkType.BestLocusNotNearestLocusOrGene:
return(new TssRegulatoryMap(LocusMap.Links
.Where(link => !this.IsClosestLocus(link, tssMap) &&
!this.IsClosestGene(link, LocusMap) &&
this.auxiliaryMap.Links.Contains(link))));
case MapLinkFilter.LinkType.BestDistalLocus:
{
var distalLinks = tssMap.Links
.Where(link => !this.IsClosestLocus(link, this.auxiliaryMap) &&
!this.IsClosestGene(link, LocusMap));
TssRegulatoryMap bestDistalMap = new TssRegulatoryMap();
foreach (var link in distalLinks)
{
this.EnsureKey(link, bestDistalMap);
this.AddReplaceLink(link, bestDistalMap, IsBestLocus);
}
return(bestDistalMap);
}
default:
return(tssMap);
}
}
/// <summary>
/// Determines whether this instance is valid link type the specified link map.
/// </summary>
/// <returns><c>true</c> if this instance is valid link type the specified link map; otherwise, <c>false</c>.</returns>
/// <param name="link">Link.</param>
/// <param name="map">Map.</param>
public void ApplyLinkFilterType(MapLink link, TssRegulatoryMap tssMap, LocusRegulatoryMap LocusMap)
{
this.EnsureKey(link, tssMap);
if ((this.LinkTypeFilter == LinkType.BestLocusNotNearestLocusOrGene ||
this.LinkTypeFilter == LinkType.BestDistalLocus) &&
this.auxiliaryMap == null)
{
this.auxiliaryMap = new TssRegulatoryMap();
}
switch (this.LinkTypeFilter)
{
case MapLinkFilter.LinkType.Any:
tssMap[link.TranscriptName].Add(link.LocusName, link);
break;
case MapLinkFilter.LinkType.NearestLocus:
this.AddReplaceLink(link, tssMap, this.IsClosestLocus);
break;
case MapLinkFilter.LinkType.NearestGene:
case MapLinkFilter.LinkType.NearestLocusOfNearestGene:
this.AddReplaceLink(link, LocusMap, this.IsClosestGene);
break;
case MapLinkFilter.LinkType.NearestBestGene:
this.AddReplaceLink(link, LocusMap, this.IsClosestGene);
break;
case MapLinkFilter.LinkType.BestLocusNearestGene:
this.AddReplaceLink(link, tssMap, this.IsBestLocus);
this.AddReplaceLink(link, LocusMap, this.IsClosestGene);
break;
case MapLinkFilter.LinkType.BestLocusBestGene:
this.AddReplaceLink(link, tssMap, this.IsBestLocus);
this.AddReplaceLink(link, LocusMap, this.IsBestGene);
break;
case MapLinkFilter.LinkType.NearestLocusOrGene:
this.AddReplaceLink(link, tssMap, this.IsClosestLocus);
this.AddReplaceLink(link, LocusMap, this.IsClosestGene);
break;
case MapLinkFilter.LinkType.NearestLocusAndGene:
this.AddReplaceLink(link, tssMap, this.IsClosestLocus);
this.AddReplaceLink(link, LocusMap, this.IsClosestGene);
break;
case MapLinkFilter.LinkType.BestLocusLink:
this.AddReplaceLink(link, tssMap, this.IsBestLocus);
break;
case MapLinkFilter.LinkType.WorstLocusLink:
this.AddReplaceLink(link, tssMap, this.IsWorstLocus);
break;
case MapLinkFilter.LinkType.BestGeneLink:
this.AddReplaceLink(link, LocusMap, this.IsBestGene);
break;
case MapLinkFilter.LinkType.NotNearestLocus:
break;
case MapLinkFilter.LinkType.NotNearestGene:
tssMap[link.TranscriptName].Add(link.LocusName, link);
this.AddReplaceLink(link, LocusMap, this.IsClosestGene);
break;
case MapLinkFilter.LinkType.NotNearestLocusOrGene:
tssMap[link.TranscriptName].Add(link.LocusName, link);
this.EnsureKey(link, LocusMap);
LocusMap[link.LocusName].Add(link.TranscriptName, link);
break;
case MapLinkFilter.LinkType.BestLocusNotNearestLocusOrGene:
tssMap[link.TranscriptName].Add(link.LocusName, link);
this.EnsureKey(link, LocusMap);
LocusMap[link.LocusName].Add(link.TranscriptName, link);
this.EnsureKey(link, this.auxiliaryMap);
this.AddReplaceLink(link, this.auxiliaryMap, this.IsBestLocus);
break;
case MapLinkFilter.LinkType.BestDistalLocus:
tssMap[link.TranscriptName].Add(link.LocusName, link);
this.EnsureKey(link, LocusMap);
this.AddReplaceLink(link, LocusMap, this.IsClosestGene);
this.EnsureKey(link, this.auxiliaryMap);
this.AddReplaceLink(link, this.auxiliaryMap, this.IsClosestLocus);
break;
}
}