private Dictionary <char, List <TargetVariant> > GetSubstitutionDeltaMass()
{
var result = new Dictionary <char, List <TargetVariant> >();
var aa = new Aminoacids();
var validAA = aa.GetVisibleAminoacids();
foreach (var ai in validAA)
{
foreach (var aj in validAA)
{
if (ai == aj)
{
continue;
}
if (this.IsSingleNucleotideMutationOnly && !MutationUtils.IsSingleNucleotideMutation(ai, aj))
{
continue;
}
if (this.IgnoreDeamidatedMutation && MutationUtils.IsDeamidatedMutation(ai, aj))
{
continue;
}
if (!result.ContainsKey(ai))
{
result[ai] = new List <TargetVariant>();
}
var deltaMass = aa[aj].MonoMass - aa[ai].MonoMass;
if (Math.Abs(deltaMass) < MinimumAminoacidSubstitutionDeltaMass)
{
continue;
}
result[ai].Add(new TargetVariant()
{
Source = ai.ToString(),
Target = new HashSet <string>(new[] { aj.ToString() }),
DeltaMass = deltaMass,
TargetType = VariantType.SingleAminoacidPolymorphism
});
}
}
foreach (var v in result.Values)
{
v.Sort((m1, m2) => m1.DeltaMass.CompareTo(m2.DeltaMass));
}
return(result);
}
private List <TargetVariant> GetExtensionDeltaMass()
{
var result = new List <TargetVariant>();
var aa = new Aminoacids();
var validAA = (from a in aa.GetVisibleAminoacids() where a != 'I' select a).ToArray();
foreach (var ai in validAA)
{
result.Add(new TargetVariant()
{
Source = string.Empty,
Target = new HashSet <string>(new[] { ai.ToString() }),
DeltaMass = aa[ai].MonoMass
});
foreach (var aj in validAA)
{
result.Add(new TargetVariant()
{
Source = string.Empty,
Target = new HashSet <string>(new[] { ai.ToString() + aj.ToString() }),
DeltaMass = aa[ai].MonoMass + aa[aj].MonoMass
});
foreach (var ak in validAA)
{
result.Add(new TargetVariant()
{
Source = string.Empty,
Target = new HashSet <string>(new[] { ai.ToString() + aj.ToString() + ak.ToString() }),
DeltaMass = aa[ai].MonoMass + aa[aj].MonoMass + aa[ak].MonoMass
});
}
}
}
var grp = result.GroupBy(m => m.DeltaMass).ToList().ConvertAll(l => l.ToList());
result.Clear();
foreach (var g in grp)
{
var tv = g.First();
for (int i = 1; i < g.Count; i++)
{
tv.Target.UnionWith(g[i].Target);
}
result.Add(tv);
}
return(result);
}
public void TestIsRnaEditing()
{
var aas = new Aminoacids();
var aasstr = aas.GetVisibleAminoacids();
for (int i = 0; i < aasstr.Length; i++)
{
for (int j = 0; j < aasstr.Length; j++)
{
if(i == j)
{
continue;
}
string mutationstr;
if (aas[aasstr[i]].IsRnaEditing(aas[aasstr[j]], out mutationstr))
{
Console.WriteLine(aasstr[i] + "->" + aasstr[j] + " : " + mutationstr);
}
}
}
}
public void TestIsRnaEditing()
{
var aas = new Aminoacids();
var aasstr = aas.GetVisibleAminoacids();
for (int i = 0; i < aasstr.Length; i++)
{
for (int j = 0; j < aasstr.Length; j++)
{
if (i == j)
{
continue;
}
string mutationstr;
if (aas[aasstr[i]].IsRnaEditing(aas[aasstr[j]], out mutationstr))
{
Console.WriteLine(aasstr[i] + "->" + aasstr[j] + " : " + mutationstr);
}
}
}
}
private static void PrepareRnaEditingMap()
{
RnaEditingMap = new Dictionary <Pair <char, char>, string>();
var aasstr = aas.GetVisibleAminoacids();
for (int i = 0; i < aasstr.Length; i++)
{
for (int j = 0; j < aasstr.Length; j++)
{
if (i == j)
{
continue;
}
string mutationstr = null;
if (DoIsRnaEditing(aas[aasstr[i]], aas[aasstr[j]], ref mutationstr))
{
RnaEditingMap[new Pair <char, char>(aasstr[i], aasstr[j])] = mutationstr;
}
}
}
}
