private void ReadPanelFile(string pathToDatabase)
{
using (
StreamReader reader = new StreamReader(pathToDatabase))
//new StreamReader(new EncryptedFileStream(pathToDatabase, passPhrase, FileAccess.Read)))
{
while (!reader.EndOfStream)
{
string line = reader.ReadLine();
if (line == null)
{
break;
}
line = line.Trim();
//check its not a header line or comment.
if (IsItAComment(line))
{
continue;
}
string[] data = line.Split('\t');
//check its not an empty line
if (data.Length > 5)
{
RefPanelEntry entry = new RefPanelEntry();
entry.LoadEntry(data);
AddEntryToTable(entry);
}
}
}
}
//examples of Therascreen detections:
//12ASP detected
//12CYS
//13ASP
//WT
//12VAL detected
//INVALID
public RuleApplier(string mutationDataBase)
{
if (!File.Exists(mutationDataBase))
{
Console.WriteLine($"{mutationDataBase} does not exist");
System.Environment.Exit(1);
}
using (StreamReader mutationDatabaseReader = new StreamReader(mutationDataBase))
{
while (!mutationDatabaseReader.EndOfStream)
{
string line = mutationDatabaseReader.ReadLine();
if (line == null)
{
break;
}
line = line.Trim();
//check its not a header line or comment.
if (IsItAComment(line))
{
continue;
}
string[] data = line.Split('\t');
//check its not an empty line
if (data.Length > 5)
{
RefPanelEntry entry = new RefPanelEntry();
entry.LoadEntry(data);
AddEntryToDictionaries(entry);
DetectableMutationEntries.Add(entry);
}
}
//generate the mutation information
foreach (var mutationEntry in DetectableMutationEntries)
{
string currentMutationSource;
string currentMutationConfirmed;
string mutationID = mutationEntry.Chr + "_" + mutationEntry.FwdStandFirstPositionOfMutation + "_" + mutationEntry.FwdStrandRefAllele + "_" +
mutationEntry.FwdStrandAltAllele;
//check the possible source
if (mutationEntry.Gene.Equals("KRAS") && mutationEntry.Exon.Equals("2"))
{
currentMutationSource = mutationEntry.Gene.Substring(0, 1).ToUpper() + mutationEntry.Exon + "_" + mutationEntry.Codon;
string theraAminoAcidChange = "KRAS_" + mutationEntry.AminoAcidPosition + mutationEntry.AminoAcidAlt.ToUpper();
if (AminoAcidToBaseChangeForTherascreenDictionary[theraAminoAcidChange].Count == 1)
{
currentMutationConfirmed = "confirmed";
}
else if (AminoAcidToBaseChangeForTherascreenDictionary[theraAminoAcidChange].Count > 1)
{
currentMutationConfirmed = "plausible";
}
else
{
Console.WriteLine($"unrecogonized: {theraAminoAcidChange}");
throw new Exception("unregonized mutation in therascreen List, must something wrong");
}
}
else
{
currentMutationSource = mutationEntry.Gene.Substring(0, 1).ToUpper() + mutationEntry.Exon + "_" + mutationEntry.Codon;
if (AminoAcidToBaseChangeForSangerDictionary[currentMutationSource].Count == 1)
{
currentMutationConfirmed = "confirmed";
}
else if (AminoAcidToBaseChangeForSangerDictionary[currentMutationSource].Count > 1)
{
currentMutationConfirmed = "plausible";
}
else
{
throw new Exception("unregonized mutation in sanger List, must something wrong");
}
}
//if (!MutationConfirmedInformationFromAminoAcid.ContainsKey(mutationID))
MutationConfirmedInformationFromAminoAcid.Add(mutationID,
new List <string>()
{
currentMutationSource, currentMutationConfirmed
});
}
}
}
