public ActionResult SeqIn(SequenceModels sequenceModels, string choose)
{
switch (choose)
{
//case "add-test":
//sequenceModels.TestSeq.TSeq = sequenceModels.TestSeq.TSeq;
//break;
case "make-random":
RandomSeq randomSeq = new RandomSeq();
sequenceModels.Seq.Seq = randomSeq.RandSeq();
break;
case "add-random":
sequenceModels.Seq.Seq = sequenceModels.RandomSeq.Seq;
break;
//case "add-from-list":
//SequenceFile sequenceFile = new SequenceFile();
//sequenceFile.SeqFile(sequenceModels);
//break;
}
return(View("~/Views/Home/Index.cshtml", sequenceModels));
}
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.shuffle.test.gb";
Console.WriteLine($"Calc seq cds trinucs for { Path.GetFileName (fileName) }");
GBSequence gbSequence = new GBSequence(fileName);
var gbSeq = gbSequence.GbSeq();
GBFeatures gbFeatures = new GBFeatures(fileName);
var gbCds = gbFeatures.Cds();
GBSeparation gBSeparation = new GBSeparation(gbSeq, gbCds);
gBSeparation.GBSeq();
TrinucDiff trinucDiff = new TrinucDiff();
Console.WriteLine($"Seq length {gbSeq.Seq.Length}\n{ gbSeq.Seq.Substring (0, 30)}....{ gbSeq.Seq.Substring (gbSeq.Seq.Length - 30)}\n");
int randFragLength = 1;
foreach (var item in gbCds)
{
if (item.CdsEnd - item.CdsStart >= 60)
{
TrinucCalc trinucCalc = new TrinucCalc();
double triDiff = trinucCalc.Calculation("CDS", item.CdsSeq);
Console.Write($"CDS\t{item.CdsStart}\t{item.CdsEnd}\t{item.CdsSeq.Substring (0, 9)}...{item.CdsSeq.Substring (item.CdsSeq.Length - 9)}\t");
Console.Write($"{trinucDiff.DiffSum1st2nd.ToString("0.0000")}\t{trinucDiff.DiffSum1st3rd.ToString ("0.0000")}\t{trinucDiff.DiffSum2nd3rd.ToString ("0.0000")}\t");
Console.WriteLine($"{triDiff.ToString("0.0000")}");
for (int i = 0; i < 10; i++)
{
RandomSeq randomSeq = new RandomSeq(item.CdsSeq);
string randSeq = randomSeq.RandomSeqByFragment(randFragLength);
TrinucCalc randtrinucCalc = new TrinucCalc();
triDiff = randtrinucCalc.Calculation("RCDS", randSeq);
Console.Write($"RCDS\t{item.CompCdsStart}\t{item.CompCdsEnd}\t{randSeq.Substring (0, 9)}...{randSeq.Substring (randSeq.Length - 9)}\t");
Console.Write($"{trinucDiff.DiffSum1st2nd.ToString ("0.0000")}\t{trinucDiff.DiffSum1st3rd.ToString ("0.0000")}\t{trinucDiff.DiffSum2nd3rd.ToString ("0.0000")}\t");
Console.WriteLine($"{triDiff.ToString ("0.0000")}");
}
}
if (item.CompCdsEnd - item.CompCdsStart >= 60)
{
TrinucCalc trinucCalc = new TrinucCalc();
double triDiff = trinucCalc.Calculation("CCDS", item.CompCdsSeq);
Console.Write($"CCDS\t{item.CompCdsStart}\t{item.CompCdsEnd}\t{item.CompCdsSeq.Substring (0, 9)}...{item.CompCdsSeq.Substring (item.CompCdsSeq.Length - 9)}\t");
Console.Write($"{trinucDiff.DiffSum1st2nd.ToString ("0.0000")}\t{trinucDiff.DiffSum1st3rd.ToString ("0.0000")}\t{trinucDiff.DiffSum2nd3rd.ToString ("0.0000")}\t");
Console.WriteLine($"{triDiff.ToString ("0.0000")}");
for (int i = 0; i < 10; i++)
{
RandomSeq randomSeq = new RandomSeq(item.CompCdsSeq);
string randSeq = randomSeq.RandomSeqByFragment(randFragLength);
TrinucCalc randtrinucCalc = new TrinucCalc();
triDiff = randtrinucCalc.Calculation("RCCDS", randSeq);
Console.Write($"RCCDS\t{item.CdsStart}\t{item.CdsEnd}\t{randSeq.Substring (0, 9)}...{randSeq.Substring (randSeq.Length - 9)}\t");
Console.Write($"{trinucDiff.DiffSum1st2nd.ToString ("0.0000")}\t{trinucDiff.DiffSum1st3rd.ToString ("0.0000")}\t{trinucDiff.DiffSum2nd3rd.ToString ("0.0000")}\t");
Console.WriteLine($"{triDiff.ToString ("0.0000")}");
}
}
//PrintOut printOut = new PrintOut (gbSeq, gbCds, 30, trinucDiff);
//printOut.SeqPrint ();
//printOut.CdsPrint ();
//printOut.CompCdsPrint ();
}
}
