private void InitiateSampleTruth(SampleTruth sampleTruthInfor)
{
foreach (string mutation in DetectableMutationList)
{
MutationTruth mutationInfor = new MutationTruth(mutation, false, "FAIL", MutationConfirmedInformationFromAminoAcid[mutation]);
sampleTruthInfor.Variants.Add(mutationInfor);
}
}
private void setSangerResultIgnored(SampleTruth sampleTruthInfor)
{
setPartMutationStatus(sampleTruthInfor, "K3", "IGNORE");
setPartMutationStatus(sampleTruthInfor, "K4", "IGNORE");
setPartMutationStatus(sampleTruthInfor, "N2", "IGNORE");
setPartMutationStatus(sampleTruthInfor, "N3", "IGNORE");
setPartMutationStatus(sampleTruthInfor, "N4", "IGNORE");
}
private void setSangerResultWT(SampleTruth sampleTruthInfor)
{
setPartMutationStatus(sampleTruthInfor, "K3", "PASS");
setPartMutationStatus(sampleTruthInfor, "K4", "PASS");
setPartMutationStatus(sampleTruthInfor, "N2", "PASS");
setPartMutationStatus(sampleTruthInfor, "N3", "PASS");
setPartMutationStatus(sampleTruthInfor, "N4", "PASS");
}
public List <SampleTruth> ApplyRule(List <SampleRecord> sampleTruthRecords)
{
List <SampleTruth> SampleTruthItems = new List <SampleTruth>();
foreach (var sampleTruthRecord in sampleTruthRecords)
{
SampleTruth truthItem = ApplyRule(sampleTruthRecord);
SampleTruthItems.Add(truthItem);
}
return(SampleTruthItems);
}
private static void SetValueForDetectedTruthMutation(SampleTruth sampleTruthInfor, string mutationName,
string mutationDetectedName)
{
bool foundMutationInPanel = false;
foreach (var mutation in sampleTruthInfor.Variants)
{
if (mutation.MutationName.Equals(mutationName))
{
foundMutationInPanel = true;
mutation.MutationStatus = "PASS";
mutation.MutationExist = true;
break;
}
}
if (!foundMutationInPanel)
{
throw new Exception(
$"{mutationDetectedName} exist in panel table but {mutationName} is not found\n");
}
}
private void setPartMutationStatus(SampleTruth sampleTruthInfor, string failPart, string status)
{
if (ExonToPositionTable.ContainsKey(failPart))
{
foreach (string mutationName in ExonToPositionTable[failPart])
{
foreach (var variant in sampleTruthInfor.Variants)
{
if (variant.MutationName.Equals(mutationName))
{
variant.MutationExist = false;
variant.MutationStatus = status;
}
}
}
}
else
{
throw new Exception($"unregoniced exon name {failPart}");
}
}
private void setTherascreenResultWT(SampleTruth sampleTruthInfor)
{
setPartMutationStatus(sampleTruthInfor, "K2", "PASS");
}
public SampleTruth ApplyRule(SampleRecord sampleTruthRecord)
{
SampleTruth sampleTruthInfor = new SampleTruth(sampleTruthRecord.SubjectId);
InitiateSampleTruth(sampleTruthInfor);
//check the therascreen result
//if (sampleTruthRecord.TherascreenResult.ToUpper().Equals("INVALID"))
// Console.WriteLine($"sample thereascreen result is {sampleTruthRecord.TherascreenResult}\t in {sampleTruthRecord.SubjectId}");
if (sampleTruthRecord.TherascreenResult.ToUpper().Equals("WT"))
{
setTherascreenResultWT(sampleTruthInfor);
}
else
{
//since therascreen contain name like 12ASP and 12ASP dectected
string[] theraNameItems = sampleTruthRecord.TherascreenResult.Split();
string mutationTheraName = "KRAS_" + theraNameItems[0];
if (AminoAcidToBaseChangeForTherascreenDictionary.ContainsKey(mutationTheraName))
{
setSangerResultIgnored(sampleTruthInfor);
setPartMutationStatus(sampleTruthInfor, "K2", "PASS");
List <string> mutationNames = AminoAcidToBaseChangeForTherascreenDictionary[mutationTheraName];
foreach (var mutationName in mutationNames)
{
SetValueForDetectedTruthMutation(sampleTruthInfor, mutationName, mutationTheraName);
}
}
else if (!sampleTruthRecord.TherascreenResult.ToUpper().Equals("INVALID"))
{
throw new Exception("unrecogonized therascreen result: {sampleTruthRecord.TherascreenResult}");
}
}
//check the sanger result
// Console.WriteLine($"sample sanger result is {sampleTruthRecord.SangerResult}\t in {sampleTruthRecord.SubjectId}");
string[] sangerResultItems = sampleTruthRecord.SangerResult.Split(',');
if (sangerResultItems.Length == 2)
{
if (sangerResultItems[0].Trim().StartsWith("WT") && sangerResultItems[1].Trim().StartsWith("FAIL"))
{
setSangerResultWT(sampleTruthInfor);
string failParts = sangerResultItems[1].Trim().Substring(4);
if (failParts.Length < 2)
{
throw new Exception($"unrecogonized therascreen result: {sampleTruthRecord.SangerResult}");
}
char GeneParts = failParts[0];
failParts = failParts.Remove(0, 1);
while (failParts.Length > 0)
{
char currentChar = failParts[0];
if (currentChar >= '0' && currentChar <= '9')
{
char[] failChars = new char[2];
failChars[0] = GeneParts;
failChars[1] = currentChar;
string failPart = new string(failChars);
setPartMutationStatus(sampleTruthInfor, failPart.ToUpper(), "FAIL");
}
else if ((currentChar >= 'A' && currentChar <= 'Z') || (currentChar >= 'a' && currentChar <= 'z'))
{
GeneParts = currentChar;
}
failParts = failParts.Remove(0, 1);
}
}
else
{
throw new Exception($"unrecogonized therascreen result: {sampleTruthRecord.SangerResult}");
}
}
else if (sangerResultItems.Length == 1)
{
//ignore NA case, since already processed when dealing with therascreen result
if (sampleTruthRecord.SangerResult.ToUpper().Equals("NA"))
{
//continue
}
else if (sampleTruthRecord.SangerResult.ToUpper().Equals("WT"))
{
setSangerResultWT(sampleTruthInfor);
}
else if (sampleTruthRecord.SangerResult.ToUpper().Equals("FAIL"))
{
//need this case, in case of therascreen detected mutation but Sanger was performed and failed (unlikely)
setSangerResultFail(sampleTruthInfor);
}
else
{
//detected a mutation or other unrecognized result
if (AminoAcidToBaseChangeForSangerDictionary.ContainsKey(sampleTruthRecord.SangerResult))
{
setSangerResultWT(sampleTruthInfor);
List <string> mutationNames = AminoAcidToBaseChangeForSangerDictionary[sampleTruthRecord.SangerResult];
foreach (var mutationName in mutationNames)
{
SetValueForDetectedTruthMutation(sampleTruthInfor, mutationName, sampleTruthRecord.SangerResult);
}
}
else
{
throw new Exception($"unrecogonized sanger result: {sampleTruthRecord.SangerResult}");
}
}
}
else
{
throw new Exception($"unrecogonized sanger result: {sampleTruthRecord.SangerResult}");
}
return(sampleTruthInfor);
}
