public static IntervalForest <IGene> GetGeneForest(IntervalArray <ITranscript>[] transcriptIntervalArrays)
{
int numChromosomes = transcriptIntervalArrays.Length;
var geneIntervalArrays = new IntervalArray <IGene> [numChromosomes];
var geneComparer = new GeneComparer();
for (var chrIndex = 0; chrIndex < numChromosomes; chrIndex++)
{
if (transcriptIntervalArrays[chrIndex] == null)
{
geneIntervalArrays[chrIndex] = EmptyIntervalArray;
continue; // assign an empty IntervalArray to this chr
}
var geneList = new List <IGene>(); // keeps the order of genes, as the intervals are already sorted at trasncripts level
var geneSet = new HashSet <IGene>(geneComparer);
foreach (var transcriptInterval in transcriptIntervalArrays[chrIndex].Array)
{
var transcript = transcriptInterval.Value;
var gene = transcript.Gene;
if (geneSet.Contains(gene))
{
continue;
}
geneSet.Add(gene);
geneList.Add(gene);
}
geneIntervalArrays[chrIndex] = new IntervalArray <IGene>(geneList.Select(GetGeneInterval).ToArray());
}
return(new IntervalForest <IGene>(geneIntervalArrays));
}
public GeneComparerTests()
{
_geneA = new Gene(ChromosomeUtilities.Chr1, 100, 200, false, "PAX", 123, CompactId.Convert("NM_123"), CompactId.Convert("ENST0000123"));
_geneB = new Gene(ChromosomeUtilities.Chr1, 100, 200, false, "PAX", 123, CompactId.Convert("NM_123"), CompactId.Convert("ENST0000123"));
_geneC = new Gene(ChromosomeUtilities.Chr1, 101, 200, false, "PAX", 123, CompactId.Convert("NM_123"), CompactId.Convert("ENST0000123"));
_geneComparer = new GeneComparer();
}
public GeneComparerTests()
{
var chromosome = new Chromosome("chr1", "1", 0);
_geneA = new Gene(chromosome, 100, 200, false, "PAX", 123, CompactId.Convert("NM_123"), CompactId.Convert("ENST0000123"));
_geneB = new Gene(chromosome, 100, 200, false, "PAX", 123, CompactId.Convert("NM_123"), CompactId.Convert("ENST0000123"));
_geneC = new Gene(chromosome, 101, 200, false, "PAX", 123, CompactId.Convert("NM_123"), CompactId.Convert("ENST0000123"));
_geneComparer = new GeneComparer();
}
public static IDictionary <IGene, int> CreateDictionary(IGene[] genes)
{
var geneComparer = new GeneComparer();
var geneToInternalId = new Dictionary <IGene, int>(geneComparer);
for (var geneIndex = 0; geneIndex < genes.Length; geneIndex++)
{
var gene = genes[geneIndex];
if (geneToInternalId.TryGetValue(gene, out int oldGeneIndex))
{
throw new UserErrorException($"Found a duplicate gene in the dictionary: {genes[geneIndex]} ({geneIndex} vs {oldGeneIndex})");
}
geneToInternalId[gene] = geneIndex;
}
return(geneToInternalId);
}
/// <summary>
/// writes the annotations to the current database file
/// </summary>
public void Write(TranscriptCacheData cacheData)
{
_blockStream.WriteHeader(_header.Write);
WriteItems(_writer, cacheData.Genes, x => x.Write(_writer));
WriteItems(_writer, cacheData.TranscriptRegions, x => x.Write(_writer));
WriteItems(_writer, cacheData.Mirnas, x => x.Write(_writer));
WriteItems(_writer, cacheData.PeptideSeqs, x => _writer.WriteOptAscii(x));
var geneComparer = new GeneComparer();
var transcriptRegionComparer = new TranscriptRegionComparer();
var intervalComparer = new IntervalComparer();
var geneIndices = CreateIndex(cacheData.Genes, geneComparer);
var transcriptRegionIndices = CreateIndex(cacheData.TranscriptRegions, transcriptRegionComparer);
var microRnaIndices = CreateIndex(cacheData.Mirnas, intervalComparer);
var peptideIndices = CreateIndex(cacheData.PeptideSeqs, EqualityComparer <string> .Default);
WriteIntervals(_writer, cacheData.RegulatoryRegionIntervalArrays, x => x.Write(_writer));
WriteIntervals(_writer, cacheData.TranscriptIntervalArrays, x => x.Write(_writer, geneIndices, transcriptRegionIndices, microRnaIndices, peptideIndices));
}
private static (IGene[] Genes, ITranscriptRegion[] TranscriptRegions, IInterval[] Mirnas, string[] PeptideSeqs) GetUniqueData(
IEnumerable <IntervalArray <ITranscript> > intervalArrays)
{
var intervalComparer = new IntervalComparer();
var transcriptRegionComparer = new TranscriptRegionComparer();
var geneComparer = new GeneComparer();
var geneSet = new HashSet <IGene>(geneComparer);
var transcriptRegionSet = new HashSet <ITranscriptRegion>(transcriptRegionComparer);
var mirnaSet = new HashSet <IInterval>(intervalComparer);
var peptideSet = new HashSet <string>();
foreach (var intervalArray in intervalArrays)
{
if (intervalArray == null)
{
continue;
}
foreach (var interval in intervalArray.Array)
{
var transcript = interval.Value;
geneSet.Add(transcript.Gene);
AddString(peptideSet, transcript.Translation?.PeptideSeq);
AddTranscriptRegions(transcriptRegionSet, transcript.TranscriptRegions);
AddIntervals(mirnaSet, transcript.MicroRnas);
}
}
var genes = GetUniqueGenes(geneSet);
var transcriptRegions = GetUniqueTranscriptRegions(transcriptRegionSet);
var mirnas = GetUniqueIntervals(mirnaSet);
var peptideSeqs = GetUniqueStrings(peptideSet);
return(genes, transcriptRegions, mirnas, peptideSeqs);
}
