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);
}
public void GetAccessionNumber_ReturnNumber_Ensembl()
{
const int expectedResult = 515242;
var observedResult = AccessionUtilities.GetAccessionNumber("ENST00000515242");
Assert.Equal(expectedResult, observedResult);
}
public void GetAccessionNumber_ReturnMinusOne()
{
const int expectedResult = -1;
var observedResult = AccessionUtilities.GetAccessionNumber(null);
Assert.Equal(expectedResult, observedResult);
}
public void GetAccessionNumber_ReturnNumber_RefSeq()
{
const int expectedResult = 4522;
var observedResult = AccessionUtilities.GetAccessionNumber("NM_004522");
Assert.Equal(expectedResult, observedResult);
}
public void GetAccessionNumber_ThrowException_IfUnderlineMissingRefSeq()
{
Assert.Throws <InvalidDataException>(delegate
{
// ReSharper disable once UnusedVariable
var observedResult = AccessionUtilities.GetAccessionNumber("NM004522");
});
}