public List <SampleRecord> GetSampleData()
{
List <SampleRecord> records = new List <SampleRecord>();
using (StreamReader sr = new StreamReader(truthFile))
{
while (true)
{
string line = sr.ReadLine();
if (string.IsNullOrEmpty(line))
{
break;
}
string[] splat = line.Split('\t');
if (splat[0] == "SUBJID")
{
continue;
}
SampleRecord newRec = new SampleRecord();
newRec.SubjectId = splat[0].Trim();
newRec.SangerResult = splat[1].Trim();
newRec.TherascreenResult = splat[2].Trim();
newRec.Valid = (splat[3] == "VALID");
records.Add(newRec);
}
return(records);
}
}
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);
}