private SortedDictionary <int, HashSet <TranscriptMetadata> > GetTranscriptsByEntrezGeneId(IEnumerable <MutableTranscript> transcripts)
{
var genes = new SortedDictionary <int, HashSet <TranscriptMetadata> >();
foreach (var transcript in transcripts)
{
string idWithVersion = transcript.Id + '.' + transcript.Version;
int cdsLength = transcript.CodingRegion?.Length ?? 0;
int transcriptLength = transcript.End - transcript.Start + 1;
bool isLrg = _lrgTranscriptIds.Contains(transcript.Id);
int accession = AccessionUtilities.GetAccessionNumber(transcript.Id);
var metadata = new TranscriptMetadata(idWithVersion, accession, transcriptLength, cdsLength, isLrg);
int geneId = ConvertGeneIdToInt(transcript.Gene.GeneId);
if (genes.TryGetValue(geneId, out var observedMetadata))
{
observedMetadata.Add(metadata);
}
else
{
genes[geneId] = new HashSet <TranscriptMetadata> {
metadata
}
};
}
return(genes);
}
/// <summary>
/// returns a dictionary that aggregates the transcripts by gene
/// </summary>
private SortedDictionary <int, HashSet <TranscriptMetadata> > AggregateGenes(List <Transcript> transcripts)
{
var genes = new SortedDictionary <int, HashSet <TranscriptMetadata> >();
foreach (var transcript in transcripts)
{
int geneId = GetGeneId(transcript);
int cdsLength = GetCdsLength(transcript);
int transcriptLength = transcript.End - transcript.Start + 1;
var isLrg = _lrgEntries.Contains(transcript.Id.ToString());
var metadata = new TranscriptMetadata(transcript.Id, transcriptLength, cdsLength, isLrg);
HashSet <TranscriptMetadata> observedMetadata;
if (genes.TryGetValue(geneId, out observedMetadata))
{
observedMetadata.Add(metadata);
}
else
{
observedMetadata = new HashSet <TranscriptMetadata> {
metadata
};
genes[geneId] = observedMetadata;
}
}
return(genes);
}
