public TrinucCalculation Calc()
{
TrinucCalculation tri = new TrinucCalculation();
TrinucArray trinucArray = new TrinucArray();
string seqTrinuc = string.Empty;
int trinucIndex = 0;
int firstFrame = 0;
int secondFrame = 0;
int thirdFrame = 0;
string seqCalc = seq + seq.Substring(0, 6);
for (int i = 0; i < seq.Length; i += 3)
{
seqTrinuc = seqCalc.Substring(i, 3);
trinucIndex = Array.FindIndex(trinucArray.trinuc, item => item == seqTrinuc);
tri.trinucleotides[trinucIndex].Trinuc1st += 1;
firstFrame += 1;
}
for (int i = 1; i < seq.Length + 1; i += 3)
{
seqTrinuc = seqCalc.Substring(i, 3);
trinucIndex = Array.FindIndex(trinucArray.trinuc, item => item == seqTrinuc);
tri.trinucleotides[trinucIndex].Trinuc2nd += 1;
secondFrame += 1;
}
for (int i = 2; i < seq.Length + 2; i += 3)
{
seqTrinuc = seqCalc.Substring(i, 3);
trinucIndex = Array.FindIndex(trinucArray.trinuc, item => item == seqTrinuc);
tri.trinucleotides[trinucIndex].Trinuc3rd += 1;
thirdFrame += 1;
}
foreach (var item in tri.trinucleotides)
{
item.TrinucFrq1st = (double)item.Trinuc1st / (double)firstFrame;
item.TrinucFrq2nd = (double)item.Trinuc2nd / (double)secondFrame;
item.TrinucFrq3rd = (double)item.Trinuc3rd / (double)thirdFrame;
}
foreach (var item in tri.trinucleotides)
{
item.TrinucDiff1st2nd = Math.Abs(item.TrinucFrq1st - item.TrinucFrq2nd);
item.TrinucDiff2nd3rd = Math.Abs(item.TrinucFrq2nd - item.TrinucFrq3rd);
item.TrinucDiff1st3rd = Math.Abs(item.TrinucFrq1st - item.TrinucFrq3rd);
}
foreach (var item in tri.trinucleotides)
{
item.TrinucDiffSum = item.TrinucDiff1st2nd + item.TrinucDiff2nd3rd + item.TrinucDiff1st3rd;
}
//TrinucOutput trinucOutput = new TrinucOutput(seq, trinucleotide);
//trinucOutput.TrinucOut();
return(tri);
}
public static void Main(string[] args)
{
Console.WriteLine("CDS search using trinuc frequencies in three frames.");
TrinucCalculation trinucCalculation = new TrinucCalculation();
string FASTAfileName = @"/home/alvydas/Sequencies/Bacteria/Escherichia.coli.fasta";
int seqLength = 3000;
int stepLength = 10;
int fragmentLengt = 100;
List <double> fragTrinucFrq = new List <double>();
string seq = string.Empty;
using (StreamReader streamReader = new StreamReader(FASTAfileName))
{
seq = streamReader.ReadToEnd().ToLower().Replace("\n", string.Empty);
}
string fragSeq = seq.Substring(0, seqLength);
for (int i = 0; i < fragSeq.Length - fragmentLengt + stepLength; i += stepLength)
{
string frag = fragSeq.Substring(i, fragmentLengt);
//Console.WriteLine(frag);
TriCalc triCalc = new TriCalc(frag);
var tri = triCalc.Calc();
double sum = 0;
foreach (var item in tri.trinucleotides)
{
sum += item.TrinucDiffSum;
}
fragTrinucFrq.Add(sum);
Console.WriteLine(i + "\t" + sum);
}
}
public TrinucDiff Calculation(string seqType, string seq)
{
TrinucCalculation trinucCalculation = new TrinucCalculation();
TrinucDiff trinucDiff = new TrinucDiff();
int trinucCount = 0;
string seqCalc = "nnn" + seq + seq.Substring(0, 9);
string oligoFrag = string.Empty;
for (int i = 0; i < seqCalc.Length - 9; i++)
{
oligoFrag = seqCalc.Substring(i, 3);
if (Array.IndexOf(trinucArray.trinuc, oligoFrag) < 0)
{
trinucleotideMatch.Add(new TrinucleotideMatch {
TrinucPosition = i, TrinucMatch = oligoFrag
});
continue;
}
if (i % 3 == 0)
{
var index = Array.FindIndex(trinucCalculation.trinucleotides, row => row.Trinuc == oligoFrag);
trinucCalculation.trinucleotides [index].Trinuc1st += 1;
trinucCount += 1;
}
else if ((i - 1) % 3 == 0)
{
var index = Array.FindIndex(trinucCalculation.trinucleotides, row => row.Trinuc == oligoFrag);
trinucCalculation.trinucleotides [index].Trinuc2nd += 1;
}
else if ((i - 2) % 3 == 0)
{
var index = Array.FindIndex(trinucCalculation.trinucleotides, row => row.Trinuc == oligoFrag);
trinucCalculation.trinucleotides [index].Trinuc3rd += 1;
}
}
trinucDiff.SeqType = seqType;
foreach (var item in trinucCalculation.trinucleotides)
{
item.TrinucFrq1st = ( double )item.Trinuc1st / trinucCount;
item.TrinucFrq2nd = ( double )item.Trinuc2nd / trinucCount;
item.TrinucFrq3rd = ( double )item.Trinuc3rd / trinucCount;
item.TrinucFrqDiff1st2nd = Math.Abs(item.TrinucFrq1st - item.TrinucFrq2nd);
item.TrinucFrqDiff1st3rd = Math.Abs(item.TrinucFrq1st - item.TrinucFrq3rd);
item.TrinucFrqDiff2nd3rd = Math.Abs(item.TrinucFrq2nd - item.TrinucFrq3rd);
}
foreach (var item in trinucCalculation.trinucleotides)
{
trinucDiff.DiffSum1st2nd += item.TrinucFrqDiff1st2nd;
trinucDiff.DiffSum1st3rd += item.TrinucFrqDiff1st3rd;
trinucDiff.DiffSum2nd3rd += item.TrinucFrqDiff2nd3rd;
}
trinucDiff.DiffSum = trinucDiff.DiffSum1st2nd + trinucDiff.DiffSum1st3rd + trinucDiff.DiffSum2nd3rd;
return(trinucDiff);
}
