public void WritePosition(IEnumerable <SupplementaryDataItem> saItems)
{
if (saItems == null)
{
return;
}
var gnomadItems = new List <GnomadItem>();
foreach (var item in saItems)
{
if (!(item is GnomadItem gnomadItem))
{
throw new InvalidDataException("Expected GnomadItems list!!");
}
gnomadItems.Add(gnomadItem);
}
SupplementaryDataItem.RemoveConflictingAlleles(gnomadItems);
foreach (var gnomadItem in gnomadItems)
{
_writer.AddEntry(gnomadItem.Chromosome.EnsemblName, gnomadItem.Start, gnomadItem.ReferenceAllele, gnomadItem.AlternateAllele, null, new List <string> {
gnomadItem.GetJsonString()
});
}
}
public void WritePosition(IEnumerable <SupplementaryDataItem> saItems)
{
if (saItems == null)
{
return;
}
var customItems = new List <CustomItem>();
foreach (var item in saItems)
{
if (!(item is CustomItem customItem))
{
throw new InvalidDataException("Expected customItem list!!");
}
customItems.Add(customItem);
}
if (customItems.Count == 0)
{
return;
}
var alleleGroupedItems = customItems.GroupBy(x => x.AlternateAllele);
foreach (var groupedItem in alleleGroupedItems)
{
var jsonStrings = groupedItem.Select(x => x.GetJsonString()).ToList();
// since the reference allele for different items in the group may be different, we only use the first base as it is supposed to be the common padding base.
_writer.AddEntry(groupedItem.First().Chromosome.EnsemblName,
groupedItem.First().Start,
groupedItem.First().ReferenceAllele,
groupedItem.Key, null, jsonStrings);
}
}
public void WritePosition(IEnumerable <SupplementaryDataItem> saItems)
{
if (saItems == null)
{
return;
}
var clinvarItems = new List <ClinVarItem>();
foreach (var item in saItems)
{
if (!(item is ClinVarItem clinvarItem))
{
throw new InvalidDataException("Expected ClinvarItems list!!");
}
clinvarItems.Add(clinvarItem);
}
if (clinvarItems.Count == 0)
{
return;
}
var alleleGroupDict = GroupByAltAllele(clinvarItems);
foreach (var kvp in alleleGroupDict)
{
var refAllele = kvp.Key.ReferenceAllele;
var altAllele = kvp.Key.AlternateAllele;
var groupedItems = kvp.Value;
var vcfString = string.Join(",", groupedItems.OrderBy(x => x.Id).Select(x => SupplementaryAnnotationUtilities.ConvertToVcfInfoString(x.Significance)));
var jsonStrings = groupedItems.OrderBy(x => x.Id).Select(x => x.GetJsonString()).ToList();
var firstItem = groupedItems[0];
_writer.AddEntry(firstItem.Chromosome.EnsemblName,
firstItem.Start,
refAllele,
altAllele, vcfString, jsonStrings);
}
// var alleleGroupedItems = clinvarItems.GroupBy(x => x.AlternateAllele);
//foreach (var groupedItem in alleleGroupedItems)
//{
// var uniqueItems = groupedItem.GroupBy(p => p.ID).Select(x => x.First()).ToList();
// var vcfString = string.Join(",", uniqueItems.Select(x => SupplementaryAnnotationUtilities.ConvertToVcfInfoString(x.Significance)));
// var jsonStrings = uniqueItems.Select(x => x.GetVariantJsonString()).ToList();
// // since the reference allele for different items in the group may be different, we only use the first base as it is supposed to be the common padding base.
// _writer.AddEntry(groupedItem.First().Chromosome,
// groupedItem.First().Start,
// groupedItem.First().ReferenceAllele,
// groupedItem.Key, vcfString, jsonStrings);
//}
}
public void WritePosition(IEnumerable <SupplementaryDataItem> saItems)
{
if (saItems == null)
{
return;
}
var onekGenItems = new List <OneKGenItem>();
foreach (var item in saItems)
{
if (!(item is OneKGenItem onekGenItem))
{
throw new InvalidDataException("Expected OnekGenItems list!!");
}
onekGenItems.Add(onekGenItem);
}
SupplementaryDataItem.RemoveConflictingAlleles(onekGenItems);
var totalAltAlleleFreq = 0.0;
var alleleFrequencies = new Dictionary <string, double>();
foreach (var onekGenItem in onekGenItems)
{
_onekgWriter.AddEntry(onekGenItem.Chromosome.EnsemblName, onekGenItem.Start,
onekGenItem.ReferenceAllele, onekGenItem.AlternateAllele,
onekGenItem.GetVcfString(), new List <string> {
onekGenItem.GetJsonString()
});
if (!IsSnv(onekGenItem.ReferenceAllele) || !IsSnv(onekGenItem.AlternateAllele))
{
continue;
}
if (onekGenItem.AllAlleleNumber != null && onekGenItem.AllAlleleCount != null)
{
var freq = 1.0 * onekGenItem.AllAlleleCount.Value / onekGenItem.AllAlleleNumber.Value;
totalAltAlleleFreq += freq;
alleleFrequencies[onekGenItem.AlternateAllele] = freq;
}
}
var isRefMinor = totalAltAlleleFreq >= SaDataBaseCommon.RefMinorThreshold;
if (isRefMinor)
{
_refMinorWriter.AddEntry(onekGenItems[0].Chromosome.EnsemblName, onekGenItems[0].Start, GetMajorAllele(alleleFrequencies), onekGenItems[0].ReferenceAllele);
}
}
public void WritePosition(IEnumerable <SupplementaryDataItem> saItems)
{
if (saItems == null)
{
return;
}
var cosmicItems = new List <CosmicItem>();
foreach (var item in saItems)
{
if (!(item is CosmicItem cosmicItem))
{
throw new InvalidDataException("Expected CosmicItem list!!");
}
cosmicItems.Add(cosmicItem);
}
if (cosmicItems.Count == 0)
{
return;
}
var combineStudies = CombineStudies(cosmicItems);
var alleleGroupDict = GroupByAltAllele(combineStudies);
foreach (var kvp in alleleGroupDict)
{
var refAllele = kvp.Key.Item1;
var altAllele = kvp.Key.Item2;
var groupedItems = kvp.Value;
var vcfString = string.Join(",", groupedItems.OrderBy(x => x.Id).Select(x => x.Id));
var jsonStrings = groupedItems.OrderBy(x => x.Id).Select(x => x.GetJsonString()).ToList();
var firstItem = groupedItems[0];
_writer.AddEntry(firstItem.Chromosome.EnsemblName,
firstItem.Start,
refAllele,
altAllele, vcfString, jsonStrings);
}
}
public void WritePosition(IEnumerable <SupplementaryDataItem> saItems)
{
if (saItems == null)
{
return;
}
var mitoMapMutItems = saItems.Select(x => x as MitoMapItem).ToList();
var uniqueMutations = MitoMapItem.AggregatedMutationsSomePosition(mitoMapMutItems);
foreach (var mutation in uniqueMutations)
{
_mitoMapVarWriter.AddEntry(
mutation.Value.Chromosome.EnsemblName,
mutation.Value.Start,
mutation.Key.Item1,
mutation.Key.Item2,
null,
new List <string> {
mutation.Value.GetVariantJsonString()
});
}
}