public List<Mutation> GetMutationList(string fileContentString)
{
List<Mutation> list = new List<Mutation>();
try
{
string[] fileLines = fileContentString.Split(Environment.NewLine.ToCharArray(), StringSplitOptions.RemoveEmptyEntries);
for (int i = 1; i < fileLines.Length; i++)
{
string fileLine = fileLines[i];
string[] items = fileLine.Split(",".ToCharArray(), StringSplitOptions.RemoveEmptyEntries);
Mutation m = new Mutation();
m.Gene = items[0];
m.Transscript = items[1];
m.AAMutation = items[2];
m.CDSMutation = new MutationPoint(items[3]);
m.Somaticstatus = items[4];
m.Zygosity = items[5];
m.Validated = items[6];
m.Type = items[7];
m.Position = items[8];
list.Add(m);
}
list = list.Where(x=> x.Type.ToUpper() =="SUBSTITUTION" ).ToList();
list = list.Where(x => x.Transscript.Substring(0,4).ToUpper() == "ENST").ToList();
}
catch { }
return list;
}
public Mutation GetMutationPattern(Mutation mutation, string geneSequence)
{
switch (mutation.Type.ToUpper())
{
case "SUBSTITUTION":
{
mutation.MC1Position = mutation.CDSMutation.Position % 3;
if (mutation.MC1Position == 0) mutation.MC1Position = 3;
string window = GetWindow(geneSequence, mutation.CDSMutation.Position - 1, mutation.MC1Position);
mutation.PreviousCodon = window.Substring(0, 3);
mutation.MutatedCodon = window.Substring(3, 3);
mutation.NextCodon = window.Substring(6, 3);
int positionOfMutInWindow = 2 + mutation.MC1Position;
mutation.CDSMutation.WA_ = "0";
mutation.CDSMutation.WRC_ = "0";
mutation.CDSMutation._CG = "0";
mutation.CDSMutation._GYW = "0";
mutation.CDSMutation.CG_ = "0";
switch (mutation.CDSMutation.WT.ToUpper())
{
case "A":
{
string site = window.Substring(positionOfMutInWindow - 1, 2);
if (site == "AA" || site == "TA") mutation.CDSMutation.WA_ = "1";
break;
}
case "G":
{
string site = window.Substring(positionOfMutInWindow , 3);
if (site == "GTA"
|| site == "GCA"
|| site == "GTT"
|| site == "GCT"
)
mutation.CDSMutation._GYW = "1";
else
{
site = window.Substring(positionOfMutInWindow -1, 2);
if (site == "CG") mutation.CDSMutation.CG_ = "1";
}
break;
}
case "C":
{
string site = window.Substring(positionOfMutInWindow - 2, 3);
if (site == "AAC"
|| site == "AGC"
|| site == "TAC"
|| site == "TGC"
)
mutation.CDSMutation.WRC_ = "1";
else
{
site = window.Substring(positionOfMutInWindow , 2);
if (site == "CG") mutation.CDSMutation._CG = "1";
}
break;
}
}
break;
}
}
return mutation;
}