public override void LoadData(string filePath)
{
var vcfParser = new VCFParser(filePath);
var header = vcfParser.Header;
var collectionInformationList = new List<patient_variant_information>();
var patient = new patient();
// We pull out all of the metadata from the header (all lines) and write them as information
// lines associated with this result.
foreach (var headerItem in header.MetaDataInInputOrder)
{
if (headerItem.Key == "individual-id")
{
var individualParts = headerItem.Value.Replace("<", "").Replace(">", "").Split(new char[] { ',' });
var individualData = individualParts.Select(x => x.Split(new char[] { '=' })).ToArray();
var mrnParts = individualData.FirstOrDefault(x => x[0] == "Dbxref")[1].Split(':');
patient = patientRepo.AddPatient(mrnParts[1], mrnParts[0],
individualData.FirstOrDefault(x => x[0] == "First_name")[1],
individualData.FirstOrDefault(x => x[0] == "Last_name")[1],
DateTime.Parse(individualData.FirstOrDefault(x => x[0] == "DOB")[1]));
}
else if (headerItem.GetType() == typeof(VCFInfoHeaderLine))
{
var info = headerItem as VCFInfoHeaderLine;
collectionInformationList.Add(AddHeaderInformation(string.Format("VCF:{0}", headerItem.Key), CleanHeaderValue("INFO", info.ToString())));
}
else if (headerItem.GetType() == typeof(VCFFilterHeaderLine))
{
var filter = headerItem as VCFFilterHeaderLine;
collectionInformationList.Add(AddHeaderInformation(string.Format("VCF:{0}", headerItem.Key), CleanHeaderValue("FILTER", filter.ToString())));
}
else if (headerItem.GetType() == typeof(VCFFormatHeaderLine))
{
var format = headerItem as VCFFormatHeaderLine;
collectionInformationList.Add(AddHeaderInformation(string.Format("VCF:{0}", headerItem.Key), CleanHeaderValue("FORMAT", format.ToString())));
}
else
{
collectionInformationList.Add(AddHeaderInformation(string.Format("VCF:{0}", headerItem.Key), headerItem.Value));
}
}
var reference = header.MetaDataInInputOrder.First(x => x.Key == "reference").Value;
DateTime? resultDate = DateTime.ParseExact(header.MetaDataInInputOrder.First(x => x.Key == "fileDate").Value,
"yyyyMMdd", CultureInfo.InvariantCulture, DateTimeStyles.None);
var patientVariants = new List<patient_variants>();
var featureInformationList = new Dictionary<patient_variants, List<patient_variant_information>>();
while (vcfParser.MoveNext())
{
var current = vcfParser.Current;
var variant = variantRepo.AddVariant(null, current.ID, "dbSNP",
current.Chr, current.Start, current.End,
reference, current.Reference.BaseString);
var patientVariant = new patient_variants()
{
patient_id = patient.id,
reference_id = variant.id,
resulted_on = resultDate,
variant_type = Enums.PatientVariantType.SNP
};
SetVariantValues(patientVariant, current);
patientVariants.Add(patientVariant);
var attributeList = new List<patient_variant_information>();
foreach (var attribute in current.Attributes)
{
attributeList.Add(AddVariantInformation(string.Format("VCF:{0}", attribute.Key), attribute.Value.ToString()));
}
if (current.FiltersMaybeNull != null)
{
foreach (var filter in current.FiltersMaybeNull)
{
attributeList.Add(AddVariantInformation("VCF:Filter", filter));
}
}
foreach (var genotype in current.Genotypes)
{
attributeList.Add(AddVariantInformation("VCF:Genotype", genotype.ToMHGRString()));
}
attributeList.Add(AddVariantInformation("VCF:Quality", current.PhredScaledQual.ToString()));
attributeList.Add(AddVariantInformation("VCF:Filter", string.Join(",", current.Filters.ToArray())));
featureInformationList.Add(patientVariant, attributeList);
}
// Save the collection to get its ID
var source = sourceRepo.AddSource("VCF", "VCF file");
var file = AddResultFile(filePath, source);
var collection = patientRepo.AddCollection(patient, file);
// Save the collection-level header data
collectionInformationList.ForEach(x => x.item_id = collection.id);
variantRepo.AddPatientVariantInformationList(collectionInformationList);
variantRepo.AddPatientVariants(patientVariants);
// Save the individual attributes associated with each feature.
// Must be done after the patient variants are written to DB (above), since we
// rely on the ID being set.
foreach (var pair in featureInformationList)
{
foreach (var attribute in pair.Value)
{
attribute.item_id = pair.Key.id;
}
variantRepo.AddPatientVariantInformationList(pair.Value);
}
variantRepo.AddPatientVariantsToCollection(collection, patientVariants);
featureInformationList.Clear();
collectionInformationList.Clear();
patientVariants.Clear();
}
public override void LoadData(string filePath)
{
var vcfParser = new VCFParser(filePath);
var header = vcfParser.Header;
var patient = new patient();
var source = sourceRepo.AddSource("VCF", "VCF file");
var file = AddResultFile(filePath, source);
// Process the file-level pragmas
result_entities rootEntity = new result_entities()
{
attribute_id = EntityRepository.GetAttribute(null, null, "Variant Call Format result", null).id,
result_file_id = file.id
};
// We pull out all of the metadata from the header (all lines) and write them as information
// lines associated with this result.
var headerEntities = new List<result_entities>();
foreach (var headerItem in header.MetaDataInInputOrder)
{
if (headerItem.Key == "individual-id")
{
var individualParts = headerItem.Value.Replace("<", "").Replace(">", "").Split(new char[] { ',' });
var individualData = individualParts.Select(x => x.Split(new char[] { '=' })).ToArray();
var mrnParts = individualData.FirstOrDefault(x => x[0] == "Dbxref")[1].Split(':');
patient = patientRepo.AddPatient(mrnParts[1], mrnParts[0],
individualData.FirstOrDefault(x => x[0] == "First_name")[1],
individualData.FirstOrDefault(x => x[0] == "Last_name")[1],
DateTime.Parse(individualData.FirstOrDefault(x => x[0] == "DOB")[1]));
}
else if (headerItem.Key == "fileDate")
{
DateTime resultDate = DateTime.ParseExact(headerItem.Value, "yyyyMMdd", CultureInfo.InvariantCulture, DateTimeStyles.None);
headerEntities.Add(CreateEntityAttribute("Resulted on", 0, file.id, rootEntity, resultDate.ToShortDateString()));
}
else if (headerItem.GetType() == typeof(VCFInfoHeaderLine))
{
var info = headerItem as VCFInfoHeaderLine;
var infoEntity = CreateEntityAttribute("INFO", 0, file.id, rootEntity, null);
headerEntities.Add(infoEntity);
headerEntities.Add(CreateEntityAttribute("ID", 0, file.id, infoEntity, info.ID));
headerEntities.Add(CreateEntityAttribute("Number", 0, file.id, infoEntity, info.CountType.ToString()));
headerEntities.Add(CreateEntityAttribute("Type", 0, file.id, infoEntity, info.Type.ToString()));
headerEntities.Add(CreateEntityAttribute("Description", 0, file.id, infoEntity, info.Description));
}
else if (headerItem.GetType() == typeof(VCFFilterHeaderLine))
{
var filter = headerItem as VCFFilterHeaderLine;
var filterEntity = CreateEntityAttribute("FILTER", 0, file.id, rootEntity, null);
headerEntities.Add(filterEntity);
foreach (var field in filter.GenericFields())
{
headerEntities.Add(CreateEntityAttribute(field.Key, 0, file.id, filterEntity, field.Value));
}
}
else if (headerItem.GetType() == typeof(VCFFormatHeaderLine))
{
var format = headerItem as VCFFormatHeaderLine;
var formatEntity = CreateEntityAttribute("FORMAT", 0, file.id, rootEntity, null);
headerEntities.Add(formatEntity);
headerEntities.Add(CreateEntityAttribute("ID", 0, file.id, formatEntity, format.ID));
headerEntities.Add(CreateEntityAttribute("Number", 0, file.id, formatEntity, format.CountType.ToString()));
headerEntities.Add(CreateEntityAttribute("Type", 0, file.id, formatEntity, format.Type.ToString()));
headerEntities.Add(CreateEntityAttribute("Description", 0, file.id, formatEntity, format.Description));
}
else
{
var headerEntity = CreateEntityAttribute(headerItem.Key, 0, file.id, rootEntity, headerItem.Value);
headerEntities.Add(headerEntity);
}
}
rootEntity.patient_id = patient.id;
headerEntities.ForEach(x => x.patient_id = patient.id);
var variantEntities = new List<result_entities>();
while (vcfParser.MoveNext())
{
var current = vcfParser.Current;
result_entities variantEntity = new result_entities()
{
attribute_id = EntityRepository.GetAttribute(null, null, "Variant Call Format variant", null).id,
result_file_id = file.id,
patient_id = patient.id,
parent = rootEntity
};
variantEntities.Add(variantEntity);
result_entities snpEntity = new result_entities()
{
attribute_id = EntityRepository.GetAttribute(current.ID, "dbSNP", null, null).id,
result_file_id = file.id,
patient_id = patient.id,
parent = variantEntity
};
variantEntities.Add(snpEntity);
SetVariantValues(current, patient.id, file.id, snpEntity, variantEntities);
variantEntities.Add(CreateEntityAttribute("Chromosome", patient.id, file.id, variantEntity, current.Chr));
variantEntities.Add(CreateEntityAttribute("Start position", patient.id, file.id, variantEntity, current.Start.ToString()));
variantEntities.Add(CreateEntityAttribute("End position", patient.id, file.id, variantEntity, current.End.ToString()));
variantEntities.Add(CreateEntityAttribute("Reference base", patient.id, file.id, variantEntity, current.Reference.BaseString));
variantEntities.Add(CreateEntityAttribute("Quality", patient.id, file.id, variantEntity, current.PhredScaledQual.ToString()));
foreach (var attr in current.Attributes)
{
variantEntities.Add(CreateEntityAttribute(string.Format("INFO:{0}", attr.Key), patient.id, file.id, variantEntity, attr.Value.ToString()));
}
if (current.FiltersMaybeNull != null)
{
foreach (var filter in current.FiltersMaybeNull)
{
variantEntities.Add(CreateEntityAttribute(string.Format("FILTER:{0}", filter), patient.id, file.id, variantEntity, string.Empty));
}
}
//foreach (var genotype in current.Genotypes)
//{
// attributeList.Add(AddVariantInformation("VCF:Genotype", genotype.ToMHGRString()));
//}
//attributeList.Add(AddVariantInformation("VCF:Quality", current.PhredScaledQual.ToString()));
//attributeList.Add(AddVariantInformation("VCF:Filter", string.Join(",", current.Filters.ToArray())));
//featureInformationList.Add(patientVariant, attributeList);
}
entityRepo.AddVCF(rootEntity, headerEntities, variantEntities);
}
