CreateSequenceRangeGroupingsForVennDiagram
(
SequenceRangeGrouping srgA,
SequenceRangeGrouping srgB,
out SequenceRangeGrouping srgOnly_A,
out SequenceRangeGrouping srgOnly_B,
out SequenceRangeGrouping srgOnly_AB
)
{
// Create the proper intersected sets from the two original SequenceRangeGroups
SequenceRangeGrouping srgAB = srgA.MergeOverlaps(srgB); // use set terminology (Union) or boolean logic (Or)
srgOnly_A = srgAB.Subtract(srgB, 1, SubtractOutputType.NonOverlappingPiecesOfIntervals); // TODO: Subtract and Intersect should use same 'logic' (for bool 3rd arg)
srgOnly_B = srgAB.Subtract(srgA, 1, SubtractOutputType.NonOverlappingPiecesOfIntervals);
srgOnly_AB = srgA.Intersect(srgB, 1, IntersectOutputType.OverlappingPiecesOfIntervals);
}
CreateSequenceRangeGroupingsForVennDiagram
(
SequenceRangeGrouping srgA,
SequenceRangeGrouping srgB,
SequenceRangeGrouping srgC,
out SequenceRangeGrouping srgOnly_A,
out SequenceRangeGrouping srgOnly_B,
out SequenceRangeGrouping srgOnly_C,
out SequenceRangeGrouping srgOnly_AB,
out SequenceRangeGrouping srgOnly_AC,
out SequenceRangeGrouping srgOnly_BC,
out SequenceRangeGrouping srgOnly_ABC
)
{
// create the proper sets for a 3 circle Venn Diagram
SequenceRangeGrouping srgBC = srgB.MergeOverlaps(srgC);
srgOnly_A = srgA.Subtract(srgBC, 1, SubtractOutputType.NonOverlappingPiecesOfIntervals);
SequenceRangeGrouping srgAC = srgA.MergeOverlaps(srgC);
srgOnly_B = srgB.Subtract(srgAC, 1, SubtractOutputType.NonOverlappingPiecesOfIntervals);
SequenceRangeGrouping srgAB = srgA.MergeOverlaps(srgB);
srgOnly_C = srgC.Subtract(srgAB, 1, SubtractOutputType.NonOverlappingPiecesOfIntervals);
srgAB = srgA.Intersect(srgB, 1, IntersectOutputType.OverlappingPiecesOfIntervals);
srgOnly_AB = srgAB.Subtract(srgC, 1, SubtractOutputType.NonOverlappingPiecesOfIntervals);
srgAC = srgA.Intersect(srgC, 1, IntersectOutputType.OverlappingPiecesOfIntervals);
srgOnly_AC = srgAC.Subtract(srgB, 1, SubtractOutputType.NonOverlappingPiecesOfIntervals);
srgBC = srgB.Intersect(srgC, 1, IntersectOutputType.OverlappingPiecesOfIntervals);
srgOnly_BC = srgBC.Subtract(srgA, 1, SubtractOutputType.NonOverlappingPiecesOfIntervals);
srgOnly_ABC = srgAB.Intersect(srgC, 1, IntersectOutputType.OverlappingPiecesOfIntervals);
}
/// <summary>
/// Indentify hot spot chromosomes for length anamoly regions.
/// </summary>
/// <param name="inputFile"> Input file</param>
/// <param name="mean">Mean value</param>
/// <param name="standardDeviation">Standard deviation</param>
private void IdentifyLentghAnamolies(string filename,
float mean = -1, float deviation = -1)
{
bool calculateMeanNdeviation = false;
if (mean == -1 || deviation == -1)
{
calculateMeanNdeviation = true;
}
SequenceAlignmentMap alignmentMapobj = null;
if (!SAMInput)
{
BAMParser bamParser = new BAMParser();
alignmentMapobj = bamParser.ParseOne<SequenceAlignmentMap>(filename);
}
else
{
SAMParser samParser = new SAMParser();
alignmentMapobj = samParser.ParseOne<SequenceAlignmentMap>(filename);
}
// get reads from sequence alignment map object.
IList<PairedRead> pairedReads = null;
if (calculateMeanNdeviation)
{
pairedReads = alignmentMapobj.GetPairedReads();
}
else
{
pairedReads = alignmentMapobj.GetPairedReads(mean, deviation);
}
// Get the orphan regions.
var orphans = pairedReads.Where(PR => PR.PairedType == PairedReadType.Orphan);
if (orphans.Count() == 0)
{
Console.WriteLine("No Orphans to display");
}
List<ISequenceRange> orphanRegions = new List<ISequenceRange>(orphans.Count());
foreach (PairedRead orphanRead in orphans)
{
orphanRegions.Add(GetRegion(orphanRead.Read1));
}
// Get sequence range grouping for Orphan regions.
SequenceRangeGrouping orphanRangegroup = new SequenceRangeGrouping(orphanRegions);
// Get the Length anomalies regions.
var lengthAnomalies = pairedReads.Where(PE => PE.PairedType == PairedReadType.LengthAnomaly);
if (lengthAnomalies.Count() == 0)
{
Console.WriteLine("No Anomalies to display");
}
List<ISequenceRange> lengthAnomalyRegions = new List<ISequenceRange>(lengthAnomalies.Count());
foreach (PairedRead laRead in lengthAnomalies)
{
SequenceRange range = new SequenceRange();
range.ID = laRead.Read1.RName;
range.Start = laRead.Read1.Pos;
range.End = laRead.Read1.Pos + laRead.InsertLength;
lengthAnomalyRegions.Add(range);
}
// Get sequence range grouping for length anomaly regions.
SequenceRangeGrouping lengthAnomalyRangegroup =
new SequenceRangeGrouping(lengthAnomalyRegions);
if (lengthAnomalyRangegroup.GroupIDs.Count() == 0)
{
Console.Write("\r\nNo Length anomalies reads to display");
}
else
{
Console.Write("Region of length anomaly:");
DisplaySequenceRange(lengthAnomalyRangegroup);
}
if (orphanRangegroup.GroupIDs.Count() == 0)
{
Console.Write("\r\nNo Orphan reads to display");
}
else
{
Console.Write("\r\nRegion of Orphan reads:");
DisplaySequenceRange(orphanRangegroup);
}
SequenceRangeGrouping intersectedRegions =
lengthAnomalyRangegroup.Intersect(orphanRangegroup);
if (intersectedRegions.GroupIDs.Count() == 0)
{
Console.Write("\r\nNo Hot spots found");
}
else
{
Console.Write("\r\nChromosomal Hot spot of length anomaly and Orphan region:");
DisplaySequenceRange(intersectedRegions);
}
}