/// <summary>
/// parses the relevant data from each variant effect feature cache
/// </summary>
public static void ParseReference(ObjectValue objectValue, DataStructures.VEP.VariantEffectFeatureCache cache, ImportDataStore dataStore)
{
// loop over all of the key/value pairs in the cache object
foreach (AbstractData ad in objectValue)
{
switch (ad.Key)
{
case IntronsKey:
var intronsList = ad as ListObjectKeyValue;
if (intronsList != null)
{
Intron.ParseListReference(intronsList.Values, cache.Introns, dataStore);
}
break;
case MapperKey:
var mapperNode = ad as ObjectKeyValue;
if (mapperNode != null)
{
TranscriptMapper.ParseReference(mapperNode.Value, cache.Mapper, dataStore);
}
break;
case ProteinFunctionPredictionsKey:
var predictionsNode = ad as ObjectKeyValue;
if (predictionsNode != null)
{
ProteinFunctionPredictions.ParseReference(predictionsNode.Value, cache.ProteinFunctionPredictions, dataStore);
}
break;
}
}
}
/// <summary>
/// parses the relevant data from each variant effect feature cache
/// </summary>
public static DataStructures.VEP.VariantEffectFeatureCache Parse(ObjectValue objectValue, ImportDataStore dataStore)
{
var cache = new DataStructures.VEP.VariantEffectFeatureCache();
// loop over all of the key/value pairs in the cache object
foreach (AbstractData ad in objectValue)
{
// sanity check: make sure we know about the keys are used for
if (!KnownKeys.Contains(ad.Key))
{
throw new GeneralException(
$"Encountered an unknown key in the dumper variant effect feature cache object: {ad.Key}");
}
// handle each key
switch (ad.Key)
{
case SelenocysteinesKey:
case ThreePrimeUtrKey:
case SeqEditsKey:
case CodonTableKey:
case ProteinFeaturesKey:
// not used
break;
case IntronsKey:
var intronsList = ad as ListObjectKeyValue;
if (intronsList != null)
{
cache.Introns = Intron.ParseList(intronsList.Values, dataStore);
}
else if (DumperUtilities.IsUndefined(ad))
{
cache.Introns = null;
}
else
{
throw new GeneralException(
$"Could not transform the AbstractData object into a ListObjectKeyValue: [{ad.GetType()}]");
}
break;
case MapperKey:
var mapperNode = ad as ObjectKeyValue;
if (mapperNode != null)
{
cache.Mapper = TranscriptMapper.Parse(mapperNode.Value, dataStore);
}
else
{
throw new GeneralException(
$"Could not transform the AbstractData object into an ObjectKeyValue: [{ad.GetType()}]");
}
break;
case PeptideKey:
cache.Peptide = DumperUtilities.GetString(ad);
break;
case ProteinFunctionPredictionsKey:
var predictionsNode = ad as ObjectKeyValue;
if (predictionsNode != null)
{
cache.ProteinFunctionPredictions = ProteinFunctionPredictions.Parse(predictionsNode.Value);
}
else
{
throw new GeneralException(
$"Could not transform the AbstractData object into an ObjectKeyValue: [{ad.GetType()}]");
}
break;
case SortedExonsKey:
var exonsList = ad as ListObjectKeyValue;
if (exonsList != null)
{
cache.Exons = Exon.ParseList(exonsList.Values, dataStore);
}
else
{
throw new GeneralException($"Could not transform the AbstractData object into a ListObjectKeyValue: [{ad.GetType()}]");
}
break;
case TranslateableSeqKey:
cache.TranslateableSeq = DumperUtilities.GetString(ad);
break;
default:
throw new GeneralException($"Unknown key found: {ad.Key}");
}
}
return(cache);
}
