public static Dictionary <string, string> GetEnstToGeneSymbols(ISequenceProvider sequenceProvider, TranscriptCacheData transcriptData)
{
var cache = transcriptData.GetCache();
var enstToGeneSymbols = new Dictionary <string, string>();
foreach (var chromIndex in sequenceProvider.RefIndexToChromosome.Keys)
{
var overlappingTranscripts =
cache.TranscriptIntervalForest.GetAllOverlappingValues(chromIndex, 1, int.MaxValue);
if (overlappingTranscripts == null)
{
continue;
}
foreach (var transcript in overlappingTranscripts)
{
if (transcript.Id.WithoutVersion.StartsWith("ENST"))
{
enstToGeneSymbols[transcript.Id.WithoutVersion] = transcript.Gene.Symbol;
}
}
}
return(enstToGeneSymbols);
}
public static Dictionary <ushort, IntervalArray <byte> > GetSpliceIntervals(ISequenceProvider sequenceProvider, TranscriptCacheData transcriptData)
{
var cache = transcriptData.GetCache();
var spliceIntervalDict = new Dictionary <ushort, IntervalArray <byte> >(sequenceProvider.RefIndexToChromosome.Count);
foreach (var chromIndex in sequenceProvider.RefIndexToChromosome.Keys)
{
var spliceIntervals = new List <Interval <byte> >(8 * 1024);
var overlappingTranscripts =
cache.TranscriptIntervalForest.GetAllOverlappingValues(chromIndex, 1, int.MaxValue);
if (overlappingTranscripts == null)
{
continue;
}
foreach (var transcript in overlappingTranscripts)
{
if (transcript.Id.IsPredictedTranscript())
{
continue;
}
bool isFirstExon = true;
foreach (var transcriptRegion in transcript.TranscriptRegions)
{
if (transcriptRegion.Type != TranscriptRegionType.Exon)
{
continue;
}
var firstSplicePosition = transcriptRegion.Start;
var secondSplicePosition = transcriptRegion.End;
var firstInterval = new Interval <byte>(firstSplicePosition - SpliceFlankLength, firstSplicePosition + SpliceFlankLength, 0);
var secondInterval = new Interval <byte>(secondSplicePosition - SpliceFlankLength, secondSplicePosition + SpliceFlankLength, 0);
if (!isFirstExon)
{
spliceIntervals.Add(firstInterval);
}
spliceIntervals.Add(secondInterval);
isFirstExon = false;
}
//remove the last added interval since this is the tail of the last exon- which is not a splice site
if (spliceIntervals.Count > 0)
{
spliceIntervals.RemoveAt(spliceIntervals.Count - 1);
}
}
spliceIntervalDict[chromIndex] = new IntervalArray <byte>(spliceIntervals.OrderBy(x => x.Begin).ThenBy(x => x.End).ToArray());
}
return(spliceIntervalDict);
}
public static Dictionary <ushort, IntervalArray <byte> > GetSpliceIntervals(ISequenceProvider sequenceProvider, TranscriptCacheData transcriptData)
{
var cache = transcriptData.GetCache();
var spliceIntervals = new Dictionary <ushort, IntervalArray <byte> >(sequenceProvider.RefIndexToChromosome.Count);
foreach (var chromIndex in sequenceProvider.RefIndexToChromosome.Keys)
{
var spliceInterval = new List <Interval <byte> >(8 * 1024);
var overlappingTranscripts =
cache.TranscriptIntervalForest.GetAllOverlappingValues(chromIndex, 1, int.MaxValue);
if (overlappingTranscripts == null)
{
continue;
}
foreach (var transcript in overlappingTranscripts)
{
if (transcript.Id.IsPredictedTranscript())
{
continue;
}
foreach (var transcriptRegion in transcript.TranscriptRegions)
{
if (transcriptRegion.Type != TranscriptRegionType.Exon)
{
continue;
}
var firstSplicePosition = transcriptRegion.Start;
var secondSplicePosition = transcriptRegion.End;
var firstInterval = new Interval <byte>(firstSplicePosition - SpliceFlankLength, firstSplicePosition + SpliceFlankLength, 0);
var secondInterval = new Interval <byte>(secondSplicePosition - SpliceFlankLength, secondSplicePosition + SpliceFlankLength, 0);
spliceInterval.Add(firstInterval);
spliceInterval.Add(secondInterval);
}
}
spliceIntervals[chromIndex] = new IntervalArray <byte>(spliceInterval.OrderBy(x => x.Begin).ThenBy(x => x.End).ToArray());
}
return(spliceIntervals);
}
