private static bool CheckPubmedIds(string xmlString, ClinVarItem clinVarItem)
{
var match = Regex.Match(xmlString, @"<a href=""/pubmed/(\d+)"">");
var pubmedHash = new HashSet <long>();
while (match.Success)
{
pubmedHash.Add(Convert.ToInt64(match.Groups[1].Value));
match = match.NextMatch();
}
// we are using xor here. if they are not the same, we return false.
if (clinVarItem.PubmedIds == null ^ pubmedHash.Count == 0)
{
PrintDiff(clinVarItem.ID.Split('.')[0], "pubmed", clinVarItem, pubmedHash);
return(false);
}
foreach (var pId in pubmedHash)
{
if (clinVarItem.PubmedIds == null)
{
return(false);
}
if (!clinVarItem.PubmedIds.Contains(pId))
{
PrintDiff(clinVarItem.ID.Split('.')[0], "pubmed", clinVarItem, pubmedHash);
return(false);
}
}
return(true);
}
public void AllSuppAnnotOutputTest()
{
const string altAllele = "C";
var sa = new SupplementaryAnnotationPosition(115256529);
var oneKg = new OneKGenAnnotation
{
OneKgAllAn = 5008,
OneKgAllAc = 2130,
OneKgAmrAn = 694,
OneKgAmrAc = 250
};
var dbSnp = new DbSnpAnnotation
{
DbSnp = new List <long> {
11554290
}
};
var saCreator = new SupplementaryPositionCreator(sa);
saCreator.AddExternalDataToAsa(DataSourceCommon.DataSource.OneKg, "C", oneKg);
saCreator.AddExternalDataToAsa(DataSourceCommon.DataSource.DbSnp, "C", dbSnp);
var cosmicItem1 = new CosmicItem("chr1", 115256529, "COSM1000", "T", altAllele, "TP53",
new HashSet <CosmicItem.CosmicStudy> {
new CosmicItem.CosmicStudy("", "carcinoma", "oesophagus")
}, 1,
altAllele);
var cosmicItem2 = new CosmicItem("chr1", 115256529, "COSM1001", "T", altAllele, "TP53",
new HashSet <CosmicItem.CosmicStudy> {
new CosmicItem.CosmicStudy("01", "carcinoma", "large_intestine")
}, 1,
altAllele);
cosmicItem1.AddCosmicToSa(saCreator);
cosmicItem2.AddCosmicToSa(saCreator);
var clinvarItem1 = new ClinVarItem(null, 0, null, altAllele, null, "RCV001",
null, null, new List <string> {
"ORPHA2462"
}, null, null, "other");
sa.ClinVarItems.Add(clinvarItem1);
var saReader = new MockSupplementaryAnnotationReader(sa);
var infoColumn = VcfUtilities.GetVcfColumn(saReader,
"chr1\t115256529\t.\tT\tC\t1000\tPASS\t.\tGT\t0/1", VcfCommon.InfoIndex);
Assert.Contains("AF1000G=0.425319", infoColumn);
Assert.Contains("cosmic=1|COSM1000,1|COSM1001", infoColumn);
Assert.Contains("clinvar=1|other", infoColumn);
}
public void ClinVarOutputTest()
{
var sa = new SupplementaryAnnotationPosition(115256529);
var clinvarItem1 = new ClinVarItem(null, 0, null, "C", null, "RCV001",
null, null, new List <string> {
"ORPHA2462"
}, null, null, "other");
sa.ClinVarItems.Add(clinvarItem1);
var saReader = new MockSupplementaryAnnotationReader(sa);
VcfUtilities.FieldContains(saReader,
"chr1\t115256529\t.\tT\tC\t1000\tPASS\t.\tGT\t0/1", "clinvar=1|other", VcfCommon.InfoIndex);
}
private bool ValidateRefAllele(ClinVarItem clinvarVariant)
{
if (string.IsNullOrEmpty(clinvarVariant.RefAllele) || clinvarVariant.RefAllele == "-")
{
return(true);
}
string refAllele = clinvarVariant.RefAllele;
if (string.IsNullOrEmpty(refAllele))
{
return(true);
}
int refLength = clinvarVariant.Stop - clinvarVariant.Position + 1;
return(refLength == refAllele.Length && _sequenceProvider.Sequence.Validate(clinvarVariant.Position, clinvarVariant.Stop, refAllele));
}
private bool ValidateRefAllele(ClinVarItem clinvarVariant)
{
if (string.IsNullOrEmpty(clinvarVariant.ReferenceAllele) || clinvarVariant.ReferenceAllele == "-")
{
return(true);
}
var refAllele = clinvarVariant.ReferenceAllele;
if (string.IsNullOrEmpty(refAllele))
{
return(true);
}
var refLength = clinvarVariant.Stop - clinvarVariant.Start + 1;
return(refLength == refAllele.Length && _sequenceProvider.Sequence.Validate(clinvarVariant.Start, clinvarVariant.Stop, refAllele));
//var stop = clinvarVariant.Start + refAllele.Length - 1;
//return _sequenceProvider.Sequence.Validate(clinvarVariant.Start, stop, refAllele);
}
private static void PrintDiff(string rcv, string fieldName, ClinVarItem clinVarItem, HashSet <long> pubmedHash)
{
Console.Write(rcv + '\t' + fieldName + '\t');
if (pubmedHash != null)
{
foreach (var id in pubmedHash.OrderBy(x => x))
{
Console.Write(id.ToString() + ',');
}
}
Console.Write('\t');
if (clinVarItem.PubmedIds != null)
{
foreach (var id in clinVarItem.PubmedIds.OrderBy(x => x))
{
Console.Write(id.ToString() + ',');
}
}
Console.WriteLine();
}
private static string GetAltAllele(ClinVarItem variant, ISequence compressedSequence)
{
return(variant == null ? null : compressedSequence.Substring(variant.Position - 1, variant.Stop - variant.Position + 1));
}
private static string GetReferenceAllele(ClinVarItem variant, ISequence compressedSequence)
{
return(variant == null ? null : compressedSequence.Substring(variant.Start - 1, variant.Stop - variant.Start + 1));
}
