public static (int Start, int End, string Id, bool OnReverseStrand) Parse(IImportNode importNode)
{
var objectValue = importNode.GetObjectValueNode();
if (objectValue == null)
{
throw new InvalidDataException("Encountered a gene import node that could not be converted to an object value node.");
}
int start = -1;
int end = -1;
string stableId = null;
var onReverseStrand = false;
foreach (var node in objectValue.Values)
{
// sanity check: make sure we know about the keys are used for
if (!KnownKeys.Contains(node.Key))
{
throw new InvalidDataException($"Encountered an unknown key in the dumper gene object: {node.Key}");
}
// handle each key
switch (node.Key)
{
case ImportKeys.End:
end = node.GetInt32();
break;
case ImportKeys.StableId:
stableId = node.GetString();
break;
case ImportKeys.Start:
start = node.GetInt32();
break;
case ImportKeys.Strand:
onReverseStrand = TranscriptUtilities.GetStrand(node);
break;
default:
throw new InvalidDataException($"Unknown key found: {node.Key}");
}
}
return(start, end, stableId, onReverseStrand);
}
TranslateableSequence, string SiftData, string PolyPhenData, int[] SelenocysteinePositions) Parse(IImportNode importNode)
{
var objectValue = importNode.GetObjectValueNode();
if (objectValue == null)
{
throw new InvalidDataException("Encountered a variant effect feature cache node that could not be converted to an object value node.");
}
MutableTranscriptRegion[] cdnaMaps = null;
IInterval[] introns = null;
string peptideSequence = null;
string translateableSequence = null;
string siftData = null;
string polyphenData = null;
int[] selenocysteinePositions = null;
foreach (var node in objectValue.Values)
{
// sanity check: make sure we know about the keys are used for
if (!KnownKeys.Contains(node.Key))
{
throw new InvalidDataException($"Encountered an unknown key in the dumper variant effect feature cache object: {node.Key}");
}
switch (node.Key)
{
case ImportKeys.CodonTable:
case ImportKeys.FivePrimeUtr:
case ImportKeys.ProteinFeatures:
case ImportKeys.Selenocysteines:
case ImportKeys.SortedExons:
case ImportKeys.SplicedSequence:
case ImportKeys.ThreePrimeUtr:
// not used
break;
case ImportKeys.Introns:
introns = node.ParseListObjectKeyValueNode(ImportIntron.ParseList);
break;
case ImportKeys.Mapper:
cdnaMaps = node.ParseObjectKeyValueNode(ImportTranscriptMapper.Parse);
break;
case ImportKeys.Peptide:
peptideSequence = node.GetString();
break;
case ImportKeys.ProteinFunctionPredictions:
if (node is ObjectKeyValueNode predictionsNode)
{
(siftData, polyphenData) = ImportProteinFunctionPredictions.Parse(predictionsNode.Value);
}
else
{
throw new InvalidDataException($"Could not transform the AbstractData object into an ObjectKeyValue: [{node.GetType()}]");
}
break;
case ImportKeys.SeqEdits:
selenocysteinePositions = node.ParseListObjectKeyValueNode(ImportSeqEdits.Parse);
break;
case ImportKeys.TranslateableSeq:
translateableSequence = node.GetString();
break;
default:
throw new InvalidDataException($"Unknown key found: {node.Key}");
}
}
return(cdnaMaps, introns, peptideSequence, translateableSequence, siftData, polyphenData, selenocysteinePositions);
}
endExon) Parse(IImportNode importNode, IChromosome currentChromosome)
{
var objectValue = importNode.GetObjectValueNode();
if (objectValue == null)
{
throw new InvalidDataException("Encountered a translation import node that could not be converted to an object value node.");
}
int start = -1;
int end = -1;
string proteinId = null;
byte proteinVersion = 0;
MutableExon startExon = null;
MutableExon endExon = null;
foreach (var node in objectValue.Values)
{
// sanity check: make sure we know about the keys are used for
if (!KnownKeys.Contains(node.Key))
{
throw new InvalidDataException($"Encountered an unknown key in the dumper mapper object: {node.Key}");
}
ObjectKeyValueNode exonNode;
switch (node.Key)
{
case ImportKeys.Adaptor:
case ImportKeys.Sequence:
case ImportKeys.DbId:
case ImportKeys.Transcript:
// skip this key
break;
case ImportKeys.StartExon:
exonNode = node as ObjectKeyValueNode;
if (exonNode != null)
{
startExon = ImportExon.Parse(exonNode.Value, currentChromosome);
}
break;
case ImportKeys.EndExon:
exonNode = node as ObjectKeyValueNode;
if (exonNode != null)
{
endExon = ImportExon.Parse(exonNode.Value, currentChromosome);
}
break;
case ImportKeys.StableId:
proteinId = node.GetString();
break;
case ImportKeys.End:
end = node.GetInt32();
break;
case ImportKeys.Start:
start = node.GetInt32();
break;
case ImportKeys.Version:
proteinVersion = (byte)node.GetInt32();
break;
default:
throw new InvalidDataException($"Unknown key found: {node.Key}");
}
}
return(start, end, proteinId, proteinVersion, startExon, endExon);
}