public static List <MutableTranscript> InvestigateInconsistentCdnaMaps(this List <MutableTranscript> transcripts,
TranscriptMergerLogger logger, string transcriptId)
{
var index = 0;
foreach (var transcript in transcripts)
{
string onReverseStrand = transcript.Gene.OnReverseStrand ? "R" : "F";
if (transcript.Exons.Length != transcript.CdnaMaps.Length)
{
logger.Log(transcriptId, $"Found different exon & cDNA maps counts ({transcript.Exons.Length} vs {transcript.CdnaMaps.Length}) (index: {index}, {onReverseStrand})");
}
if (transcript.Exons.Length == transcript.CdnaMaps.Length &&
DiffExonsAndCdnaMaps(transcript.Exons, transcript.CdnaMaps))
{
logger.Log(transcriptId, $"Found different start/end coordinates between exons & cDNA maps. (index: {index}, {onReverseStrand})");
}
index++;
}
return(transcripts);
}
public static List <MutableTranscript> FixGeneSymbolSource(this List <MutableTranscript> transcripts,
TranscriptMergerLogger logger)
{
if (transcripts.Count == 1)
{
return(transcripts);
}
var symbolSources = transcripts.GetSet(x => x.Gene.SymbolSource);
if (symbolSources.Count == 1)
{
return(transcripts);
}
if (symbolSources.Contains(GeneSymbolSource.Unknown))
{
symbolSources.Remove(GeneSymbolSource.Unknown);
}
if (symbolSources.Count != 1)
{
throw new NotImplementedException("Cannot handle multiple gene symbol sources at this time");
}
var targetSymbolSource = symbolSources.First();
foreach (var transcript in transcripts)
{
transcript.Gene.SymbolSource = targetSymbolSource;
}
logger.Log(transcripts[0].Id, "Normalized gene symbol source");
return(transcripts.Unique());
}
/// <summary>
/// separates the transcripts by ID and clusters the transcripts into overlapping
/// islands. From there we can resolve differences and return a unique transcript
/// for each cluster.
/// </summary>
public static List <MutableTranscript> Merge(TranscriptMergerLogger logger, IEnumerable <MutableTranscript> transcripts,
Dictionary <string, GenbankEntry> idToGenbankEntry)
{
var idToTranscripts = transcripts.GetMultiValueDict(x => x.Id + "|" + x.Start + "|" + x.End);
var mergedTranscripts = idToTranscripts.Select(kvp => Merge(logger, kvp.Value, idToGenbankEntry)).ToList();
return(mergedTranscripts.OrderBy(x => x.Start).ThenBy(x => x.End).ToList());
}
private static List <MutableTranscript> UnsupervisedFixGeneSymbols(this IReadOnlyList <MutableTranscript> transcripts,
TranscriptMergerLogger logger, List <string> symbols)
{
var nonLocGeneSymbols = symbols.FindAll(x => !string.IsNullOrEmpty(x) && !x.StartsWith("LOC"));
string symbol = nonLocGeneSymbols.Count > 0 ? nonLocGeneSymbols[0] : symbols[0];
foreach (var transcript in transcripts)
{
transcript.Gene.Symbol = symbol;
}
logger.Log(transcripts[0].Id, "Normalized gene symbol (unsupervised)");
return(transcripts.Unique());
}
public static List <MutableTranscript> RemoveFailedTranscripts(
this List <MutableTranscript> transcripts, TranscriptMergerLogger logger)
{
if (transcripts.Count == 1)
{
return(transcripts);
}
var filteredTranscripts = transcripts.Where(transcript => transcript.BamEditStatus != "failed").ToList();
if (filteredTranscripts.Count == 0)
{
return(transcripts);
}
logger.Log(transcripts[0].Id, "Filtered transcripts with failed BAM status.");
return(filteredTranscripts.Unique());
}
public static List <MutableTranscript> ChooseEditedTranscripts(
this List <MutableTranscript> transcripts, TranscriptMergerLogger logger)
{
if (transcripts.Count == 1)
{
return(transcripts);
}
var filteredTranscripts = transcripts.Where(transcript => transcript.RnaEdits != null || transcript.BamEditStatus == "ok").ToList();
if (filteredTranscripts.Count == 0)
{
return(transcripts);
}
logger.Log(transcripts[0].Id, "Filtered transcripts without RNA edits or BAM edit status");
return(filteredTranscripts.Unique());
}
public static List <MutableTranscript> PickSpecificTranscript(
this List <MutableTranscript> transcripts, TranscriptMergerLogger logger, string transcriptId)
{
if (transcripts.Count == 1)
{
return(transcripts);
}
List <MutableTranscript> filteredTranscripts;
string logMessage;
switch (transcriptId)
{
case "NM_001005786":
filteredTranscripts = transcripts.Where(transcript => transcript.CdnaMaps[9].Start == 25419007).ToList();
logMessage = $"Filtered on exon 9 start: {transcriptId}";
break;
case "NM_001278597":
case "NM_001278596":
filteredTranscripts = transcripts.Where(transcript => transcript.CdnaMaps.Length == 26).ToList();
logMessage = $"Filtered on exon count (26): {transcriptId}";
break;
case "NM_016152":
filteredTranscripts = transcripts.Where(transcript => transcript.Exons[0].Phase == 0).ToList();
logMessage = $"Filtered on exon phase (0): {transcriptId}";
break;
default:
return(transcripts);
}
if (filteredTranscripts.Count == 0)
{
return(transcripts);
}
logger.Log(transcriptId, logMessage);
return(filteredTranscripts.Unique());
}
public static List <MutableTranscript> RemoveTranscriptsWithLowestVersion(
this List <MutableTranscript> transcripts, TranscriptMergerLogger logger)
{
if (transcripts.Count == 1)
{
return(transcripts);
}
var versionToTranscript = transcripts.GetMultiValueDict(x => x.Version);
if (versionToTranscript.Count == 1)
{
return(transcripts);
}
byte maxVersion = versionToTranscript.Keys.Max();
transcripts.RemoveAll(x => x.Version != maxVersion);
logger.Log(transcripts[0].Id, "Filtered transcripts with lower versions");
return(transcripts.Unique());
}
public static List <MutableTranscript> FixCodingRegionCdnaEnd(this List <MutableTranscript> transcripts,
TranscriptMergerLogger logger, IReadOnlyDictionary <string, GenbankEntry> idToGenbankEntry, string transcriptId)
{
if (transcripts.Count == 1 || idToGenbankEntry == null || !idToGenbankEntry.TryGetValue(transcriptId, out var genbankEntry))
{
return(transcripts);
}
var cdnaEndToTranscript = transcripts.GetMultiValueDict(x => x.CodingRegion.CdnaEnd);
if (cdnaEndToTranscript.Count == 1)
{
return(transcripts);
}
if (!cdnaEndToTranscript.TryGetValue(genbankEntry.CodingRegion.End, out var filteredTranscripts))
{
return(transcripts);
}
logger.Log(transcripts[0].Id, "Filtered transcripts by coding region cDNA end");
return(filteredTranscripts.Unique());
}
public static List <MutableTranscript> UnsupervisedFixGeneId(this List <MutableTranscript> transcripts,
TranscriptMergerLogger logger)
{
if (transcripts.Count == 1)
{
return(transcripts);
}
var geneIds = transcripts.GetSet(x => x.Gene.GeneId).ToList();
if (geneIds.Count == 1)
{
return(transcripts);
}
string geneId = geneIds[0];
foreach (var transcript in transcripts)
{
transcript.Gene.GeneId = geneId;
}
logger.Log(transcripts[0].Id, "Normalized gene ID (unsupervised)");
return(transcripts.Unique());
}
private static MutableTranscript Merge(TranscriptMergerLogger logger, IReadOnlyList <MutableTranscript> transcripts,
Dictionary <string, GenbankEntry> idToGenbankEntry)
{
string transcriptId = transcripts[0].Id;
if (transcripts.Count == 1)
{
transcripts.Unique().InvestigateInconsistentCdnaMaps(logger, transcriptId);
return(transcripts[0]);
}
var filteredTranscripts = transcripts
.Unique()
.InvestigateInconsistentCdnaMaps(logger, transcriptId)
.RemoveFailedTranscripts(logger)
.ChooseEditedTranscripts(logger)
.RemoveTranscriptsWithLowestVersion(logger)
.FixCodingRegionCdnaStart(logger, idToGenbankEntry, transcriptId)
.FixCodingRegionCdnaEnd(logger, idToGenbankEntry, transcriptId)
.FixGeneSymbolSource(logger)
.FixBioType(logger)
.FixGeneId(logger, idToGenbankEntry, transcriptId)
.FixCanonical(logger)
.FixHgncId(logger)
.FixGeneStart(logger)
.FixGeneEnd(logger)
.FixGeneSymbols(logger, idToGenbankEntry, transcriptId)
.UnsupervisedFixGeneId(logger)
.PickSpecificTranscript(logger, transcriptId);
if (filteredTranscripts.Count == 1)
{
return(filteredTranscripts[0]);
}
throw new NotImplementedException($"Could not merge down to one transcript: {filteredTranscripts.Count} transcripts ({transcriptId})");
}
private static ExitCodes ProgramExecution()
{
var transcriptSource = GetSource(_transcriptSource);
var sequenceReader = new CompressedSequenceReader(FileUtilities.GetReadStream(_inputReferencePath));
var vepRootDirectory = new VepRootDirectory(sequenceReader.RefNameToChromosome);
var refIndexToVepDir = vepRootDirectory.GetRefIndexToVepDir(_inputVepDirectory);
var genomeAssembly = GenomeAssemblyHelper.Convert(_genomeAssembly);
long vepReleaseTicks = DateTime.Parse(_vepReleaseDate).Ticks;
var idToGenbank = GetIdToGenbank(genomeAssembly, transcriptSource);
// =========================
// create the pre-cache file
// =========================
// process each VEP directory
int numRefSeqs = sequenceReader.NumRefSeqs;
var header = new IntermediateIoHeader(_vepVersion, vepReleaseTicks, transcriptSource, genomeAssembly, numRefSeqs);
string siftPath = _outputStub + ".sift.gz";
string polyphenPath = _outputStub + ".polyphen.gz";
string transcriptPath = _outputStub + ".transcripts.gz";
string regulatoryPath = _outputStub + ".regulatory.gz";
using (var mergeLogger = new TranscriptMergerLogger(FileUtilities.GetCreateStream(_outputStub + ".merge_transcripts.log")))
using (var siftWriter = new PredictionWriter(GZipUtilities.GetStreamWriter(siftPath), header, IntermediateIoCommon.FileType.Sift))
using (var polyphenWriter = new PredictionWriter(GZipUtilities.GetStreamWriter(polyphenPath), header, IntermediateIoCommon.FileType.Polyphen))
using (var transcriptWriter = new MutableTranscriptWriter(GZipUtilities.GetStreamWriter(transcriptPath), header))
using (var regulatoryRegionWriter = new RegulatoryRegionWriter(GZipUtilities.GetStreamWriter(regulatoryPath), header))
{
var converter = new VepCacheParser(transcriptSource);
var emptyPredictionDict = new Dictionary <string, List <int> >();
for (ushort refIndex = 0; refIndex < numRefSeqs; refIndex++)
{
var chromosome = sequenceReader.RefIndexToChromosome[refIndex];
if (!refIndexToVepDir.TryGetValue(refIndex, out string vepSubDir))
{
siftWriter.Write(chromosome, emptyPredictionDict);
polyphenWriter.Write(chromosome, emptyPredictionDict);
continue;
}
Console.WriteLine("Parsing reference sequence [{0}]:", chromosome.UcscName);
var rawData = converter.ParseDumpDirectory(chromosome, vepSubDir);
var mergedTranscripts = TranscriptMerger.Merge(mergeLogger, rawData.Transcripts, idToGenbank);
var mergedRegulatoryRegions = RegulatoryRegionMerger.Merge(rawData.RegulatoryRegions);
int numRawTranscripts = rawData.Transcripts.Count;
int numMergedTranscripts = mergedTranscripts.Count;
Console.WriteLine($"- # merged transcripts: {numMergedTranscripts}, # total transcripts: {numRawTranscripts}");
WriteTranscripts(transcriptWriter, mergedTranscripts);
WriteRegulatoryRegions(regulatoryRegionWriter, mergedRegulatoryRegions);
WritePredictions(siftWriter, mergedTranscripts, x => x.SiftData, chromosome);
WritePredictions(polyphenWriter, mergedTranscripts, x => x.PolyphenData, chromosome);
}
}
Console.WriteLine("\n{0} directories processed.", refIndexToVepDir.Count);
return(ExitCodes.Success);
}
public static List <MutableTranscript> FixBioType(this List <MutableTranscript> transcripts, TranscriptMergerLogger logger)
{
if (transcripts.Count == 1)
{
return(transcripts);
}
var biotypes = transcripts.GetSet(x => x.BioType);
if (biotypes.Count != 2)
{
return(transcripts);
}
var biotype = GetDesiredBioType(biotypes);
if (biotype == BioType.other)
{
return(transcripts);
}
foreach (var transcript in transcripts)
{
transcript.BioType = biotype;
}
logger.Log(transcripts[0].Id, "Normalized biotype");
return(transcripts.Unique());
}
private static void Log(this TranscriptMergerLogger logger, string transcriptId, string description) =>
logger.WriteLine($"{transcriptId}\t{description}");
public static List <MutableTranscript> FixGeneId(this List <MutableTranscript> transcripts, TranscriptMergerLogger logger,
Dictionary <string, GenbankEntry> idToGenbankEntry, string transcriptId)
{
if (transcripts.Count == 1 || idToGenbankEntry == null || !idToGenbankEntry.TryGetValue(transcriptId, out var genbankEntry))
{
return(transcripts);
}
var geneIds = transcripts.GetSet(x => x.Gene.GeneId);
if (geneIds.Count == 1)
{
return(transcripts);
}
if (!geneIds.Contains(genbankEntry.GeneId))
{
throw new InvalidDataException($"Could not find the Genbank gene ID ({genbankEntry.GeneId}) within the transcripts.");
}
foreach (var transcript in transcripts)
{
transcript.Gene.GeneId = genbankEntry.GeneId;
}
logger.Log(transcripts[0].Id, "Normalized gene ID");
return(transcripts.Unique());
}
public static List <MutableTranscript> FixGeneEnd(this List <MutableTranscript> transcripts, TranscriptMergerLogger logger)
{
if (transcripts.Count == 1)
{
return(transcripts);
}
var geneEnds = transcripts.GetSet(x => x.Gene.End);
if (geneEnds.Count == 1)
{
return(transcripts);
}
var transcriptEnds = transcripts.GetSet(x => x.End).ToArray();
if (transcriptEnds.Length > 1)
{
return(transcripts);
}
int closestEnd = GetClosest(geneEnds, transcriptEnds[0]);
foreach (var transcript in transcripts)
{
transcript.Gene.End = closestEnd;
}
logger.Log(transcripts[0].Id, "Normalized gene end");
return(transcripts.Unique());
}
public static List <MutableTranscript> FixHgncId(this List <MutableTranscript> transcripts, TranscriptMergerLogger logger)
{
if (transcripts.Count == 1)
{
return(transcripts);
}
var hgncIds = transcripts.GetSet(x => x.Gene.HgncId);
if (hgncIds.Count == 1)
{
return(transcripts);
}
if (hgncIds.Contains(-1))
{
hgncIds.Remove(-1);
}
int hgncId = hgncIds.First();
foreach (var transcript in transcripts)
{
transcript.Gene.HgncId = hgncId;
}
logger.Log(transcripts[0].Id, "Normalized HGNC ID");
return(transcripts.Unique());
}
public static List <MutableTranscript> FixCanonical(this List <MutableTranscript> transcripts, TranscriptMergerLogger logger)
{
if (transcripts.Count == 1)
{
return(transcripts);
}
var canonicals = transcripts.GetSet(x => x.IsCanonical);
if (canonicals.Count == 1)
{
return(transcripts);
}
foreach (var transcript in transcripts)
{
transcript.IsCanonical = false;
}
logger.Log(transcripts[0].Id, "Normalized canonical flag");
return(transcripts.Unique());
}
public static List <MutableTranscript> FixGeneSymbols(this List <MutableTranscript> transcripts, TranscriptMergerLogger logger,
Dictionary <string, GenbankEntry> idToGenbankEntry, string transcriptId)
{
if (transcripts.Count == 1)
{
return(transcripts);
}
var symbols = transcripts.GetSet(x => x.Gene.Symbol);
if (symbols.Count == 1)
{
return(transcripts);
}
if (symbols.Contains(null))
{
symbols.Remove(null);
}
if (idToGenbankEntry == null || !idToGenbankEntry.TryGetValue(transcriptId, out var genbankEntry))
{
return(transcripts.UnsupervisedFixGeneSymbols(logger, symbols.ToList()));
}
if (!symbols.Contains(genbankEntry.Symbol))
{
return(transcripts.UnsupervisedFixGeneSymbols(logger, symbols.ToList()));
}
foreach (var transcript in transcripts)
{
transcript.Gene.Symbol = genbankEntry.Symbol;
}
logger.Log(transcripts[0].Id, "Normalized gene symbol");
return(transcripts.Unique());
}
