public static void Main(string[] args)
{
string fileName = "/home/alvydas/Oligonucleotides/Sequencies/Bacteria/Escherichia.coli.test.gb";
GBSequence gbSequence = new GBSequence(fileName);
GBSeq gbSeq = gbSequence.GbSeq();
TrinucCalc trinucCalc = new TrinucCalc();
int scanStart = 20000;
int scanEnd = 40000;
string scanSeq = gbSeq.Seq.Substring(scanStart, scanEnd - scanStart);
int fragment = 65;
//int step = 66;
int step = 5;
try
{
for (int i = 0; i < scanSeq.Length; i += step)
{
string fragSeq = scanSeq.Substring(i, fragment);
//Console.WriteLine( fragSeq);
double trinucDiff = trinucCalc.Calculation("FRAG", fragSeq);
Console.WriteLine($"FRAG\t{fragSeq}\t{trinucDiff.ToString("0.0000")}");
}
}
catch (Exception e)
{
Console.WriteLine(e);
}
}
public static void Main(string[] args)
{
//string fileName = "/home/alvydas/Oligonucleotides/Sequencies/Bacteria/Escherichia.coli.gb";
string fileName = "/home/alvydas/Oligonucleotides/Sequencies/Bacteria/Escherichia.coli.test.gb";
//string fileName = "/home/alvydas/Oligonucleotides/Sequencies/Bacteria/Escherichia.coli.short.gb";
//string fileName = "/home/alvydas/Oligonucleotides/Sequencies/Bacteria/Escherichia.coli.short1.gb";
//string fileName = "/home/alvydas/Oligonucleotides/Sequencies/Bacteria/Escherichia.coli.short2.gb";
//string fileName = "/home/alvydas/Oligonucleotides/Sequencies/Bacteria/Escherichia.coli.short3.gb";
//string fileName = "/home/alvydas/Oligonucleotides/Sequencies/Bacteria/Escherichia.coli.shuffle.test.gb";
Console.WriteLine($"Calc seq cds trinucs for { Path.GetFileName(fileName) }");
GBSequence gbSequence = new GBSequence(fileName);
GBSeq gbSeq = gbSequence.GbSeq();
Console.WriteLine(gbSeq);
GBSeqFeatures gBSeqFeatures = new GBSeqFeatures(fileName);
List <GBFeat> cdsFeatures = gBSeqFeatures.FeaturesSeparation();
List <GBFeat> completeFeatures = gBSeqFeatures.CompleteSeparation(cdsFeatures);
TrinucCalc trinucCalc = new TrinucCalc();
Sequence mixSeq = new Sequence()
{
SeqName = "CDS and random seq mix"
};
RandSeq randSeq = new RandSeq();
double trinucDiff = 0;
foreach (var item in completeFeatures)
{
string subSeq = string.Empty;
string randomSubSeq = string.Empty;
if (item.SeqType == "CDS" && item.SeqEnd - item.SeqStart > 30)
{
Console.Write($"{item.SeqType}\t{item.SeqStart}\t{item.SeqEnd}\t");
subSeq = gbSeq.Seq.Substring(item.SeqStart, item.SeqEnd - item.SeqStart + 1);
//var trinucCalc = new TrinucCalc(item.SeqType, subSeq);
trinucDiff = trinucCalc.Calculation("CDS", subSeq);
Console.WriteLine($"{subSeq}\t{trinucDiff.ToString("0.0000")}");
mixSeq.Seq += subSeq;
int randSeqNumber = 20;
double averageRCDS1 = 0;
for (int i = 0; i < randSeqNumber; i++)
{
randomSubSeq = randSeq.RandomSeq(subSeq, 1);
Console.Write($"RCDS1\t{item.SeqStart}\t{item.SeqEnd}\t");
trinucDiff = trinucCalc.Calculation("RCDS1", randomSubSeq);
Console.WriteLine($"{randomSubSeq}\t{trinucDiff.ToString("0.0000")}");
averageRCDS1 += trinucDiff;
}
Console.WriteLine($"Average RCDS1 {(averageRCDS1/randSeqNumber).ToString("0.0000")}\n");
mixSeq.Seq += randomSubSeq;
double averageRCDS2 = 0;
for (int i = 0; i < randSeqNumber; i++)
{
randomSubSeq = randSeq.RandomSeq(subSeq, 2);
Console.Write($"RCDS2\t{item.SeqStart}\t{item.SeqEnd}\t");
trinucDiff = trinucCalc.Calculation("RCDS2", randomSubSeq);
Console.WriteLine($"{randomSubSeq}\t{trinucDiff.ToString("0.0000")}");
averageRCDS2 += trinucDiff;
}
Console.WriteLine($"Average RCDS2 {(averageRCDS2/ randSeqNumber).ToString("0.0000")}\n");
mixSeq.Seq += randomSubSeq;
double averageRCDS3 = 0;
for (int i = 0; i < randSeqNumber; i++)
{
randomSubSeq = randSeq.RandomSeq(subSeq, 3);
Console.Write($"RCDS3\t{item.SeqStart}\t{item.SeqEnd}\t");
trinucDiff = trinucCalc.Calculation("RCDS3", randomSubSeq);
Console.WriteLine($"{randomSubSeq}\t{trinucDiff.ToString("0.0000")}");
averageRCDS3 += trinucDiff;
}
Console.WriteLine($"Average RCDS3 {(averageRCDS3 / randSeqNumber).ToString("0.0000")}\n");
mixSeq.Seq += randomSubSeq;
Console.WriteLine("\n");
//Console.WriteLine(subSeq);
//Console.WriteLine(randomSubSeq);
//Console.WriteLine( );
}
}
//CDS search in artificial sequence mooving fragment by particular step.
//for (int i = 0; i < mixSeq.Seq.Length; i++)
//{
// if (i > 0 && i % 60 == 0) Console.Write("\n");
// Console.Write(mixSeq.Seq[i]);
//}
Console.WriteLine("\n");
string seq = mixSeq.Seq;
int fragment = 65;
//int step = 66;
int step = 5;
try
{
for (int i = 0; i < seq.Length; i += step)
{
string fragSeq = seq.Substring(i, fragment);
//Console.WriteLine( fragSeq);
trinucDiff = trinucCalc.Calculation("FRAG", fragSeq);
Console.WriteLine($"FRAG\t{fragSeq}\t{trinucDiff.ToString("0.0000")}");
}
}
catch (Exception e)
{
Console.WriteLine(e);
}
}
