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)
{
Console.WriteLine("Oligonucleotides frq calculation.");
string seq = string.Empty;
//string fileName = @"/home/alvydas/Sequencies/H**o.sapience/Cromosome1.fasta";
//string fileName = @"/home/alvydas/Sequencies/Virus/Hepatitis.delta.fasta";
//string fileName = "//home//alvydas//Sequencies//Bacteria//Lactococcus.lactis.fasta";
//seq = "aaacagatcacccgctgagcgggttatctgtt";
seq = "aaaaacaagaatacaaccacgactagaagcaggagtataatcatgattcaacaccagcatccacccccgcctcgacgccggcgtctactcctgcttgaagacgaggatgcagccgcggctggaggcgggggtgtagtcgtggtttaatactagtattcatcctcgtcttgatgctggtgtttattcttgttt";
/*
* string fileName = @"/home/alvydas/Sequencies/Bacteria/Escherichia.coli.fasta";
*
* var fileStream = new FileStream(fileName, FileMode.Open, FileAccess.Read);
* using (var streamReader = new StreamReader(fileStream))
* {
* seq = streamReader.ReadToEnd().ToLower().Replace("\n", string.Empty);
* }
* Console.WriteLine(fileName);
* /*
* string [ ] mono = { "a" , "c" , "g" , "t" };
* foreach(var item1 in mono )
* {
* foreach ( var item2 in mono )
* {
* foreach ( var item3 in mono )
* {
* foreach ( var item4 in mono )
* {
* seq += item1 + item2 + item3 + item4;
* }
* }
* }
* }
*/
DinucCalc dinucCalc = new DinucCalc(seq);
var diCalc = dinucCalc.Calculation();
TrinucCalc trinucCalc = new TrinucCalc();
var triCalc = trinucCalc.Calculation("FromBoard", seq);
TetranucCalc tetranucCalc = new TetranucCalc(seq);
var tetraCalc = tetranucCalc.Calculation( );
}
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);
}
}
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 ();
}
}
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($"Calc seq cds trinucs for { Path.GetFileName(fileName) }");
GBSequence gbSequence = new GBSequence(fileName);
var gbSeq = gbSequence.GbSeq();
GBSeqFeatures gBSeqFeatures = new GBSeqFeatures(fileName);
List <GBFeat> cdsFeatures = gBSeqFeatures.FeaturesSeparation();
List <GBFeat> completeFeatures = gBSeqFeatures.CompleteSeparation(cdsFeatures);
List <TrinucDiff> triDiff = new List <TrinucDiff>();
foreach (var item in completeFeatures)
{
string subSeq = string.Empty;
Console.Write($"{item.SeqType}\t{item.SeqStart}\t{item.SeqEnd}\t");
if (item.SeqEnd - item.SeqStart > 40)
{
subSeq = gbSeq.Seq.Substring(item.SeqStart, item.SeqEnd - item.SeqStart + 1);
if (item.SeqType == "CDS" || item.SeqType == "JCDS" || item.SeqType == "NCDS")
{
Console.Write($"{subSeq.Substring(0, 10)}...{subSeq.Substring(subSeq.Length - 10)}\t");
TrinucCalc trinucCalc = new TrinucCalc();
TrinucDiff trinucDiff = trinucCalc.Calculation(item.SeqType, subSeq);
Console.WriteLine($"{ trinucDiff.DiffSum1st2nd.ToString("0.0000") }\t" +
$"{ trinucDiff.DiffSum1st3rd.ToString("0.0000") }\t" +
$"{ trinucDiff.DiffSum2nd3rd.ToString("0.0000") }\t" +
$"{ trinucDiff.DiffSum.ToString("0.0000") }");
if (item.SeqType == "CDS" || item.SeqType == "NCDS")
{
triDiff.Add(new TrinucDiff {
SeqType = item.SeqType,
DiffSum1st2nd = trinucDiff.DiffSum1st2nd,
DiffSum1st3rd = trinucDiff.DiffSum1st3rd,
DiffSum2nd3rd = trinucDiff.DiffSum2nd3rd,
DiffSum = trinucDiff.DiffSum
});
}
}
else if (item.SeqType == "CCDS" || item.SeqType == "CJCDS")
{
GBSequenceComp gbSequenceComp = new GBSequenceComp(subSeq);
subSeq = gbSequenceComp.SeqComp();
Console.Write($"{subSeq.Substring(0, 10)}...{subSeq.Substring(subSeq.Length - 10)}\t");
TrinucCalc trinucCalc = new TrinucCalc();
TrinucDiff trinucDiff = trinucCalc.Calculation(item.SeqType, subSeq);
Console.WriteLine($"{ trinucDiff.DiffSum1st2nd.ToString("0.0000") }\t" +
$"{ trinucDiff.DiffSum1st3rd.ToString("0.0000") }\t" +
$"{ trinucDiff.DiffSum2nd3rd.ToString("0.0000") }\t" +
$"{ trinucDiff.DiffSum.ToString("0.0000") }");
triDiff.Add(new TrinucDiff {
SeqType = item.SeqType,
DiffSum1st2nd = trinucDiff.DiffSum1st2nd,
DiffSum1st3rd = trinucDiff.DiffSum1st3rd,
DiffSum2nd3rd = trinucDiff.DiffSum2nd3rd,
DiffSum = trinucDiff.DiffSum
});
}
}
else
{
Console.WriteLine("nnnnnnnnnn...nnnnnnnnnn\t0.0000");
}
}
Console.WriteLine();
string filePath = string.Empty;
StreamWriter FH;
filePath = "/home/alvydas/Oligonucleotides/TrinucCalc/cdsframe.dat";
FH = new StreamWriter(filePath);
foreach (var item in triDiff)
{
if (item.SeqType == "CDS" || item.SeqType == "CCDS")
{
Console.WriteLine($"{item.SeqType}\t{item.DiffSum1st2nd.ToString("0.0000")}\t{item.DiffSum1st3rd.ToString("0.0000")}\t{item.DiffSum2nd3rd.ToString("0.0000")}\t{item.DiffSum.ToString("0.0000")}");
FH.WriteLine($"{item.SeqType}\t{item.DiffSum1st2nd.ToString("0.0000")}\t{item.DiffSum1st3rd.ToString("0.0000")}\t{item.DiffSum2nd3rd.ToString("0.0000")}\t{item.DiffSum.ToString("0.0000")}");
}
}
FH.Close();
Console.WriteLine();
filePath = "/home/alvydas/Oligonucleotides/TrinucCalc/ncdsframe.dat";
FH = new StreamWriter(filePath);
foreach (var item in triDiff)
{
if (item.SeqType == "NCDS")
{
Console.WriteLine($"{item.SeqType}\t{item.DiffSum1st2nd.ToString("0.0000")}\t{item.DiffSum1st3rd.ToString("0.0000")}\t{item.DiffSum2nd3rd.ToString("0.0000")}\t{item.DiffSum.ToString("0.0000")}");
FH.WriteLine($"{item.SeqType}\t{item.DiffSum1st2nd.ToString("0.0000")}\t{item.DiffSum1st3rd.ToString("0.0000")}\t{item.DiffSum2nd3rd.ToString("0.0000")}\t{item.DiffSum.ToString("0.0000")}");
}
}
FH.Close();
string rpath = "/usr/bin/Rscript";
//string arg1 = "/home/alvydas/Oligonucleotides/TrinucCalc/R/cdsframe.dat";
//string arg2 = "/home/alvydas/Oligonucleotides/TrinucCalc/R/ncdsframe.dat";
string scriptpath = "/home/alvydas/Oligonucleotides/TrinucCalc/framefrq.R cdsframe.dat ncdsframe.dat";
string output = RScript.RunRScript(rpath, scriptpath);
}