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linguist/samples/HyPhy/MFPositiveSelection.bf
Mike Doud 585d74ecc9 add better HyPhy samples
2015-05-02 13:24:43 -07:00

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ModelNames = {{"Neutral",
"Selection",
"Discrete",
"Freqs",
"Gamma",
"2 Gamma",
"Beta",
"Beta & w",
"Beta & Gamma",
"Beta & (Gamma+1)",
"Beta & (Normal>1)",
"0 & 2 (Normal>1)",
"3 Normal",
"RE: Lognormal",
"RE: Gamma",
"RE: Discrete"}};
ParameterCount = {{0,
1,
3,
4,
2,
4,
2,
4,
5,
5,
5,
5,
6,
1,
2,
4
}};
MAXIMUM_ITERATIONS_PER_VARIABLE = 2000;
OPTIMIZATION_PRECISION = 0.001;
function SetWDistribution (resp)
{
if (rateType == 0)
{
global P = .5;
P:<1;
categFreqMatrix = {{P,1-P}};
categRateMatrix = {{0,1}};
category c = (2, categFreqMatrix , MEAN, ,categRateMatrix, 0, 1e25);
}
else
{
if (rateType == 1)
{
global P1 = 1/3;
global P2 = 0;
P1:<1;
P2:<1;
global W = 1;
categFreqMatrix = {{P1,(1-P1)*P2, (1-P1)*(1-P2)}} ;
categRateMatrix = {{0,1,W}};
category c = (3, categFreqMatrix , MEAN, ,categRateMatrix, 0, 1e25);
}
else
{
if (rateType == 2)
{
global P1 = 1/3;
global P2 = .5;
P1:<1;
P2:<1;
global W1 = .25;
global R1 = 4;
global R2 = 3;
R1:>1;
R2:>1;
categFreqMatrix = {{P1,(1-P1)*P2, (1-P1)*(1-P2)}} ;
categRateMatrix = {{W1,W1*R1,W1*R1*R2}};
category c = (3, categFreqMatrix , MEAN, ,categRateMatrix, 0, 1e25);
}
else
{
if (rateType == 3)
{
global P1 = 1/5;
global P2 = 1/4;
global P3 = 1/3;
global P4 = 1/2;
P1:<1;
P2:<1;
P3:<1;
P4:<1;
categFreqMatrix = {{P1,
(1-P1)P2,
(1-P1)(1-P2)*P3,
(1-P1)(1-P2)(1-P3)P4,
(1-P1)(1-P2)(1-P3)(1-P4)}} ;
categRateMatrix = {{0,1/3,2/3,1,3}};
category c = (5, categFreqMatrix , MEAN, ,categRateMatrix, 0, 1e25);
}
else
{
if (rateType == 4)
{
global alpha = .5;
global beta = 1;
alpha:>0.01;alpha:<100;
beta:>0.01;
beta:<200;
category c = (resp, EQUAL, MEAN, GammaDist(_x_,alpha,beta), CGammaDist(_x_,alpha,beta), 0 ,
1e25,CGammaDist(_x_,alpha+1,beta)*alpha/beta);
}
else
{
if (rateType == 5)
{
global alpha = .5;
global beta = 1;
global alpha2= .75;
global P = .5;
alpha:>0.01;alpha:<100;
beta:>0.01;
beta:<200;
P:<1;
alpha2:>0.01;alpha2:<100;
category c = (resp, EQUAL, MEAN, P*GammaDist(_x_,alpha,beta) + (1-P)*GammaDist(_x_,alpha2,alpha2)
, P*CGammaDist(_x_,alpha,beta) + (1-P)*CGammaDist(_x_,alpha2,alpha2),
0 , 1e25,
P*CGammaDist(_x_,alpha+1,beta)*alpha/beta + (1-P)*CGammaDist(_x_,alpha2+1,alpha2));
}
else
{
if (rateType == 6)
{
global betaP = 1;
global betaQ = 1;
betaP:>0.05;betaP:<85;
betaQ:>0.05;betaQ:<85;
category c = (resp, EQUAL, MEAN, _x_^(betaP-1)*(1-_x_)^(betaQ-1)/Beta(betaP,betaQ), IBeta(_x_,betaP,betaQ), 0 ,
1,IBeta(_x_,betaP+1,betaQ)*betaP/(betaP+betaQ));
}
else
{
if (rateType == 7)
{
global W = 2;
/*W:>1;*/
global P = 1-1/(resp+1);
global betaP = 1;
global betaQ = 2;
betaP:>0.05;
betaQ:>0.05;
betaP:<85;
betaQ:<85;
P:>0.0000001;
P:<0.9999999;
categFreqMatrix = {resp+1,1};
for (k=0; k<resp; k=k+1)
{
categFreqMatrix[k]:=P/resp__;
}
categFreqMatrix[resp]:=(1-P);
category c = (resp+1, categFreqMatrix, MEAN,
P*_x_^(betaP-1)*(1-Min(_x_,1))^(betaQ-1)/Beta(betaP,betaQ)+W-W,
P*IBeta(Min(_x_,1),betaP,betaQ)+(1-P)*(_x_>=W),
0,1e25,
P*IBeta(Min(_x_,1),betaP+1,betaQ)*betaP/(betaP+betaQ)+(1-P)*W*(_x_>=W));
}
else
{
if (rateType == 8)
{
global P = .5;
global betaP = 1;
global betaQ = 2;
betaP:>0.05;betaP:<85;
betaQ:>0.05;betaQ:<85;
global alpha = .5;
global beta = 1;
alpha:>0.01;alpha:<100;
beta:>0.01;
beta:<200;
P:<1;
category c = (resp, EQUAL, MEAN,
P*_x_^(betaP-1)*(1-Min(_x_,1))^(betaQ-1)/Beta(betaP,betaQ)+(1-P)*GammaDist(_x_,alpha,beta),
P*IBeta(Min(_x_,1),betaP,betaQ)+(1-P)*CGammaDist(_x_,alpha,beta),
0,1e25,
P*betaP/(betaP+betaQ)*IBeta(Min(_x_,1),betaP+1,betaQ)+(1-P)*alpha/beta*CGammaDist(_x_,alpha+1,beta));
}
else
{
if (rateType == 9)
{
global P = .5;
P:<1;
global betaP = 1;
betaP:>0.05;betaP:<85;
global betaQ = 2;
betaQ:>0.05;betaQ:<85;
global alpha = .5;
alpha:>0.01;alpha:<100;
global beta = 1;
beta:>0.01;beta:<500;
category c = (resp, EQUAL, MEAN,
P*_x_^(betaP-1)*(1-Min(_x_,1))^(betaQ-1)/Beta(betaP,betaQ)+(1-P)*(_x_>1)*GammaDist(Max(1e-20,_x_-1),alpha,beta),
P*IBeta(Min(_x_,1),betaP,betaQ)+(1-P)*CGammaDist(Max(_x_-1,0),alpha,beta),
0,1e25,
P*betaP/(betaP+betaQ)*IBeta(Min(_x_,1),betaP+1,betaQ)+
(1-P)*(alpha/beta*CGammaDist(Max(0,_x_-1),alpha+1,beta)+CGammaDist(Max(0,_x_-1),alpha,beta)));
}
else
{
if (rateType == 10)
{
global P = .5;
global betaP = 1;
global betaQ = 2;
betaP:>0.05;
betaQ:>0.05;
betaP:<85;
betaQ:<85;
global mu = 3;
global sigma = .01;
sigma:>0.0001;
sqrt2pi = Sqrt(8*Arctan(1));
P:<1;
category c = (resp, EQUAL, MEAN,
P*_x_^(betaP-1)*(1-Min(_x_,1))^(betaQ-1)/Beta(betaP,betaQ)+
(1-P)*(_x_>=1)*Exp(-(_x_-mu)(_x_-mu)/(2*sigma*sigma))/(sqrt2pi__*sigma)/ZCDF((mu-1)/sigma),
P*IBeta(Min(_x_,1),betaP,betaQ)+(1-P)*(_x_>=1)*(1-ZCDF((mu-_x_)/sigma)/ZCDF((mu-1)/sigma)),
0,1e25,
P*betaP/(betaP+betaQ)*IBeta(Min(_x_,1),betaP+1,betaQ)+
(1-P)*(_x_>=1)*(mu*(1-ZCDF((1-mu)/sigma)-ZCDF((mu-_x_)/sigma))+
sigma*(Exp((mu-1)(1-mu)/(2*sigma*sigma))-Exp((_x_-mu)(mu-_x_)/(2*sigma*sigma)))/sqrt2pi__)/ZCDF((mu-1)/sigma));
}
else
{
if (rateType == 11)
{
global P = 1/3;
global P1 = .5;
global mu = 3;
global sigma = .5;
sigma:>0.0001;
global sigma1 = 1;
sigma1:>0.0001;
sqrt2pi = Sqrt(8*Arctan(1));
P:<1;
P1:<1;
categFreqMatrix = {resp+1,1};
for (k=1; k<=resp; k=k+1)
{
categFreqMatrix[k]:=(1-P)/resp__;
}
categFreqMatrix[0]:=P;
category c = (resp+1, categFreqMatrix, MEAN,
(1-P)((1-P1)*Exp(-(_x_-mu)(_x_-mu)/(2*sigma1*sigma1))/(sqrt2pi__*sigma1)/ZCDF(mu/sigma1)+
P1*Exp(-(_x_-1)(_x_-1)/(2*sigma*sigma))/(sqrt2pi__*sigma)/ZCDF(1/sigma)),
P+(1-P)(_x_>1e-20)((1-P1)(1-ZCDF((mu-_x_)/sigma1)/ZCDF(mu/sigma1))+
P1*(1-ZCDF((1-_x_)/sigma)/ZCDF(1/sigma))),
0,1e25,
(1-P)((1-P1)(mu*(1-ZCDF(-mu/sigma1)-ZCDF((mu-_x_)/sigma1))+
sigma1*(Exp(-mu*mu/(2*sigma1*sigma1))-Exp((_x_-mu)(mu-_x_)/(2*sigma1*sigma1)))/sqrt2pi__)/ZCDF(mu/sigma1)+
P(1-ZCDF(-1/sigma)-ZCDF((1-_x_)/sigma)+
sigma*(Exp(-1/(2*sigma*sigma))-Exp((_x_-1)(1-_x_)/(2*sigma*sigma)))/sqrt2pi__)/ZCDF(1/sigma))
);
}
else
{
if (rateType == 12)
{
global P = 1/3;
global P1 = .5;
global mu = 3;
global sigma = .25;
global sigma1 = .5;
global sigma2 = 1;
sigma:>0.0001;
sigma1:>0.0001;
sigma2:>0.0001;
sqrt2pi = Sqrt(8*Arctan(1));
P:<1;
P1:<1;
category c = (resp, EQUAL , MEAN,
2*P*Exp(-_x_^2/(2*sigma*sigma))+
(1-P)((1-P1)*Exp((_x_-mu)(mu-_x_)/(2*sigma2*sigma2))/(sqrt2pi__*sigma2)/ZCDF(mu/sigma2)+
P1*Exp((1-_x_)(_x_-1)/(2*sigma1*sigma1))/(sqrt2pi__*sigma1)/ZCDF(1/sigma1)),
P*(1-2*ZCDF(-_x_/sigma))+
(1-P)((1-P1)(1-ZCDF((mu-_x_)/sigma2)/ZCDF(mu/sigma2))+
P1*(1-ZCDF((1-_x_)/sigma1)/ZCDF(1/sigma1))),
0,1e25,
2*P*sigma*(1-Exp(-_x_*_x_/(2*sigma*sigma)))/sqrt2pi__+
(1-P)((1-P1)(mu*(1-ZCDF(-mu/sigma2)-ZCDF((mu-_x_)/sigma2))+
sigma2*(Exp(-mu*mu/(2*sigma2*sigma2))-Exp((_x_-mu)(mu-_x_)/(2*sigma2*sigma2)))/sqrt2pi__)/ZCDF(mu/sigma2)+
P1(1-ZCDF(-1/sigma1)-ZCDF((1-_x_)/sigma1)+
sigma1*(Exp(-1/(2*sigma1*sigma1))-Exp((_x_-1)(1-_x_)/(2*sigma1*sigma1)))/sqrt2pi__)/ZCDF(mu/sigma1))
);
}
else
{
if (rateType == 13)
{
global sigma = .1;
sigma:>0.0001;sigma:<10;
sqrt2pi = Sqrt(8*Arctan(1));
global _x_:<1e200;
category c = (resp, EQUAL, MEAN,
Exp (-Log(_x_)*Log(_x_) / (2*sigma*sigma)) / (_x_*sigma*sqrt2pi__), /*density*/
ZCDF (Log(_x_)/sigma), /*CDF*/
1e-200, /*left bound*/
1e200, /*right bound*/
Exp (.5*sigma^2)*ZCDF (Log(_x_)/sigma-sigma),
CONSTANT_ON_PARTITION
);
}
else
{
if (rateType == 14)
{
global alpha = .5;
global beta = 1;
alpha:>0.01;alpha:<100;
beta:>0.01;
beta:<200;
category c = (resp, EQUAL, MEAN, GammaDist(_x_,alpha,beta), CGammaDist(_x_,alpha,beta), 0 ,
1e25,CGammaDist(_x_,alpha+1,beta)*alpha/beta,CONSTANT_ON_PARTITION);
}
else
{
global P1 = 1/3;
global P2 = .5;
P1:<1;
P2:<1;
global W1 = .25;
global R1 = 4;
global R2 = 3;
R1:>1;
R2:>1;
categFreqMatrix = {{P1,(1-P1)*P2, (1-P1)*(1-P2)}} ;
categRateMatrix = {{W1,W1*R1,W1*R1*R2}};
category c = (3, categFreqMatrix , MEAN, ,categRateMatrix, 0, 1e25, ,CONSTANT_ON_PARTITION);
}
}
}
}
}
}
}
}
}
}
}
}
}
}
}
return 0;
}
/* ____________________________________________________________________________________________________________________*/
function FrameText (frameChar,vertChar,parOff,theText)
{
h = Abs (theText)+4;
fprintf (stdout,"\n");
for (k=0; k<parOff; k=k+1)
{
fprintf (stdout," ");
}
for (k=0; k<h;k=k+1)
{
fprintf (stdout,frameChar);
}
fprintf (stdout,"\n");
for (k=0; k<parOff; k=k+1)
{
fprintf (stdout," ");
}
fprintf (stdout,vertChar," ",theText," ",vertChar,"\n");
for (k=0; k<parOff; k=k+1)
{
fprintf (stdout," ");
}
for (k=0; k<h;k=k+1)
{
fprintf (stdout,frameChar);
}
fprintf (stdout,"\n");
return 0;
}
/* ____________________________________________________________________________________________________________________*/
function BuildCodonFrequencies4 (obsF)
{
PIStop = 1.0;
result = {ModelMatrixDimension,1};
hshift = 0;
for (h=0; h<64; h=h+1)
{
first = h$16;
second = h%16$4;
third = h%4;
if (_Genetic_Code[h]==10)
{
hshift = hshift+1;
PIStop = PIStop-obsF[first][0]*obsF[second][0]*obsF[third][0];
continue;
}
result[h-hshift][0]=obsF[first][0]*obsF[second][0]*obsF[third][0];
}
return result*(1.0/PIStop);
}
/* ____________________________________________________________________________________________________________________*/
function BuildCodonFrequencies12 (obsF)
{
PIStop = 1.0;
result = {ModelMatrixDimension,1};
hshift = 0;
for (h=0; h<64; h=h+1)
{
first = h$16;
second = h%16$4;
third = h%4;
if (_Genetic_Code[h]==10)
{
hshift = hshift+1;
PIStop = PIStop-obsF[first][0]*obsF[second][1]*obsF[third][2];
continue;
}
result[h-hshift][0]=obsF[first][0]*obsF[second][1]*obsF[third][2];
}
return result*(1.0/PIStop);
}
/* ____________________________________________________________________________________________________________________*/
function GetDistributionParameters (sigLevel)
{
GetInformation (distrInfo,c);
D = Columns(distrInfo);
E = 0.0;
T = 0.0;
sampleVar = 0.0;
for (k=0; k<D; k=k+1)
{
T = distrInfo[0][k]*distrInfo[1][k];
E = E+T;
sampleVar = T*distrInfo[0][k]+sampleVar;
}
sampleVar = sampleVar-E*E;
fprintf (LAST_FILE_PATH,"\n\n------------------------------------------------\n\ndN/dS = ",E, " (sample variance = ",sampleVar,")\n");
for (k=0; k<D; k=k+1)
{
fprintf (LAST_FILE_PATH,"\nRate[",Format(k+1,0,0),"]=",
Format(distrInfo[0][k],12,8), " (weight=", Format(distrInfo[1][k],9,7),")");
}
for (k=0; k<D; k=k+1)
{
if (distrInfo[0][k]>1) break;
}
if (k<D)
/* have rates > 1 */
{
ConstructCategoryMatrix(marginals,lf,COMPLETE);
CC = Columns (marginals);
if (rateType>=13)
/* subset rate variation */
{
CC = CC/numberOfSubsets;
subsetMarginals = {D,numberOfSubsets};
for (v=0; v<numberOfSubsets; v=v+1)
{
for (l=0; l<D; l=l+1)
{
for (h=0; h<CC; h=h+1)
{
subsetMarginals[l][v] = subsetMarginals[l][v] + marginals[l][v*CC+h];
}
}
}
marginals = subsetMarginals;
subsetMarginals = 0;
fprintf (LAST_FILE_PATH,"\n\n------------------------------------------------\n\n Subsets with dN/dS>1 (Posterior cutoff = ",sigLevel,")\n\n");
for (v=0; v<numberOfSubsets; v=v+1)
{
sampleVar = 0;
for (h=0; h<D; h=h+1)
{
sampleVar = sampleVar+distrInfo[1][h]*marginals[h][v];
}
positiveProb = 0;
for (l=k; l<D; l=l+1)
{
positiveProb = positiveProb+distrInfo[1][l]*marginals[l][v];
}
positiveProb = positiveProb/sampleVar;
marginals[0][v] = positiveProb;
if (positiveProb>=sigLevel)
{
fprintf (LAST_FILE_PATH,Format (v+1,0,0)," (",positiveProb,")\n");
}
}
fprintf (LAST_FILE_PATH,"\n\n------------------------------------------------\n\n Subsets with dN/dS<=1 (Posterior cutoff = ",sigLevel,")\n\n");
for (v=0; v<numberOfSubsets; v=v+1)
{
if (marginals[0][v]<sigLevel)
{
fprintf (LAST_FILE_PATH,Format (v+1,0,0)," (",marginals[0][v],")\n");
}
}
}
else
{
fprintf (LAST_FILE_PATH,"\n\n------------------------------------------------\n\n Sites with dN/dS>1 (Posterior cutoff = ",sigLevel,")\n\n");
for (v=0; v<CC; v=v+1)
{
sampleVar = 0;
for (h=0; h<D; h=h+1)
{
sampleVar = sampleVar+distrInfo[1][h]*marginals[h][v];
}
positiveProb = 0;
for (l=k; l<D; l=l+1)
{
positiveProb = positiveProb+distrInfo[1][l]*marginals[l][v];
}
positiveProb = positiveProb/sampleVar;
marginals[0][v] = positiveProb;
if (positiveProb>=sigLevel)
{
fprintf (LAST_FILE_PATH,Format (v+1,0,0)," (",positiveProb,")\n");
}
}
fprintf (LAST_FILE_PATH,"\n\n------------------------------------------------\n\n Sites with dN/dS<=1 (Posterior cutoff = ",sigLevel,")\n\n");
for (v=0; v<CC; v=v+1)
{
if (marginals[0][v]<sigLevel)
{
fprintf (LAST_FILE_PATH,Format (v+1,0,0)," (",marginals[0][v],")\n");
}
}
}
marginals = 0;
}
else
{
fprintf (LAST_FILE_PATH,"\n\n------------------------------------------------\n\n No rate classes with dN/dS>1.");
}
fprintf (LAST_FILE_PATH,"\n\n------------------------------------------------\n\n");
return E;
}
/* ____________________________________________________________________________________________________________________*/
function PopulateModelMatrix (ModelMatrixName&, EFV)
{
ModelMatrixName = {ModelMatrixDimension,ModelMatrixDimension};
hshift = 0;
if (modelType==0)
{
for (h=0; h<64; h=h+1)
{
if (_Genetic_Code[h]==10)
{
hshift = hshift+1;
continue;
}
vshift = hshift;
for (v = h+1; v<64; v=v+1)
{
diff = v-h;
if (_Genetic_Code[v]==10)
{
vshift = vshift+1;
continue;
}
if ((h$4==v$4)||((diff%4==0)&&(h$16==v$16))||(diff%16==0))
{
if (h$4==v$4)
{
transition = v%4;
transition2= h%4;
}
else
{
if(diff%16==0)
{
transition = v$16;
transition2= h$16;
}
else
{
transition = v%16$4;
transition2= h%16$4;
}
}
if (_Genetic_Code[0][h]==_Genetic_Code[0][v])
{
ModelMatrixName[h-hshift][v-vshift] := t*EFV__[transition__];
ModelMatrixName[v-vshift][h-hshift] := t*EFV__[transition2__];
}
else
{
ModelMatrixName[h-hshift][v-vshift] := c*t*EFV__[transition__];
ModelMatrixName[v-vshift][h-hshift] := c*t*EFV__[transition2__];
}
}
}
}
}
else
{
if (modelType==1)
{
for (h=0; h<64; h=h+1)
{
if (_Genetic_Code[h]==10)
{
hshift = hshift+1;
continue;
}
vshift = hshift;
for (v = h+1; v<64; v=v+1)
{
diff = v-h;
if (_Genetic_Code[v]==10)
{
vshift = vshift+1;
continue;
}
nucPosInCodon = 2;
if ((h$4==v$4)||((diff%4==0)&&(h$16==v$16))||(diff%16==0))
{
if (h$4==v$4)
{
transition = v%4;
transition2= h%4;
}
else
{
if(diff%16==0)
{
transition = v$16;
transition2= h$16;
nucPosInCodon = 0;
}
else
{
transition = v%16$4;
transition2= h%16$4;
nucPosInCodon = 1;
}
}
if (_Genetic_Code[0][h]==_Genetic_Code[0][v])
{
ModelMatrixName[h-hshift][v-vshift] := t*EFV__[transition__][nucPosInCodon__];
ModelMatrixName[v-vshift][h-hshift] := t*EFV__[transition2__][nucPosInCodon__];
}
else
{
ModelMatrixName[h-hshift][v-vshift] := c*t*EFV__[transition__][nucPosInCodon__];
ModelMatrixName[v-vshift][h-hshift] := c*t*EFV__[transition2__][nucPosInCodon__];
}
}
}
}
}
else
{
for (h=0; h<64; h=h+1)
{
if (_Genetic_Code[h]==10)
{
hshift = hshift+1;
continue;
}
vshift = hshift;
for (v = h+1; v<64; v=v+1)
{
diff = v-h;
if (_Genetic_Code[v]==10)
{
vshift = vshift+1;
continue;
}
if ((h$4==v$4)||((diff%4==0)&&(h$16==v$16))||(diff%16==0))
{
if (h$4==v$4)
{
transition = v%4;
transition2= h%4;
}
else
{
if(diff%16==0)
{
transition = v$16;
transition2= h$16;
}
else
{
transition = v%16$4;
transition2= h%16$4;
}
}
if (_Genetic_Code[0][h]==_Genetic_Code[0][v])
{
if (Abs(transition-transition2)%2)
{
ModelMatrixName[h-hshift][v-vshift] := kappa*t;
ModelMatrixName[v-vshift][h-hshift] := kappa*t;
}
else
{
ModelMatrixName[h-hshift][v-vshift] := t;
ModelMatrixName[v-vshift][h-hshift] := t;
}
}
else
{
if (Abs(transition-transition2)%2)
{
ModelMatrixName[h-hshift][v-vshift] := kappa*c*t;
ModelMatrixName[v-vshift][h-hshift] := kappa*c*t;
}
else
{
ModelMatrixName[h-hshift][v-vshift] := c*t;
ModelMatrixName[v-vshift][h-hshift] := c*t;
}
}
}
}
}
}
}
return (modelType>1);
}
/* ____________________________________________________________________________________________________________________*/
function PopulateModelMatrix2 (ModelMatrixName&, EFV)
{
ModelMatrixName = {ModelMatrixDimension,ModelMatrixDimension};
hshift = 0;
for (h=0; h<64; h=h+1)
{
if (_Genetic_Code[h]==10)
{
hshift = hshift+1;
continue;
}
vshift = hshift;
for (v = h+1; v<64; v=v+1)
{
diff = v-h;
if (_Genetic_Code[v]==10)
{
vshift = vshift+1;
continue;
}
if ((h$4==v$4)||((diff%4==0)&&(h$16==v$16))||(diff%16==0))
{
if (h$4==v$4)
{
transition = v%4;
transition2= h%4;
}
else
{
if(diff%16==0)
{
transition = v$16;
transition2= h$16;
}
else
{
transition = v%16$4;
transition2= h%16$4;
}
}
if (_Genetic_Code[0][h]==_Genetic_Code[0][v])
{
if (Abs(transition-transition2)%2)
{
ExecuteCommands ("ModelMatrixName[h-hshift][v-vshift] := kappa"+l+"*t;ModelMatrixName[v-vshift][h-hshift] := kappa"+l+"*t;");
}
else
{
ModelMatrixName[h-hshift][v-vshift] := t;
ModelMatrixName[v-vshift][h-hshift] := t;
}
}
else
{
if (Abs(transition-transition2)%2)
{
ExecuteCommands ("ModelMatrixName[h-hshift][v-vshift] := c*kappa"+l+"*t;ModelMatrixName[v-vshift][h-hshift] := c*kappa"+l+"*t;");
}
else
{
ModelMatrixName[h-hshift][v-vshift] := c*t;
ModelMatrixName[v-vshift][h-hshift] := c*t;
}
}
}
}
}
return 1;
}
/* ____________________________________________________________________________________________________________________*/
function spawnLikelihood (kappaSharedOrNot)
{
if (kappaSharedOrNot)
{
for (l=0; l<numberOfSubsets;l=l+1)
{
if (modelType<=1)
{
ExecuteCommands ("modelMatrix"+l+" = 0;MULTIPLY_BY_FREQS = PopulateModelMatrix (\"modelMatrix"+l+"\", observedFreq"+l+");");
}
else
{
ExecuteCommands ("modelMatrix"+l+" = 0;MULTIPLY_BY_FREQS = PopulateModelMatrix2 (\"modelMatrix"+l+"\", observedFreq"+l+");");
}
ExecuteCommands ("Model theModel"+l+" = (modelMatrix"+l+",vectorOfFrequencies"+l+",MULTIPLY_BY_FREQS);");
partitionTreeString=partitionTrees[l];
ExecuteCommands ("Tree subsetTree"+l+"=partitionTreeString;");
}
}
else
{
MULTIPLY_BY_FREQS = PopulateModelMatrix ("modelMatrix", observedFreq);
Model theModel = (modelMatrix,vectorOfFrequencies,MULTIPLY_BY_FREQS);
for (v=0; v<numberOfSubsets;v=v+1)
{
partitionTreeString=partitionTrees[v];
ExecuteCommands ("Tree subsetTree"+v+"=partitionTreeString;");
}
}
lfSpawnString = "LikelihoodFunction lf = (";
for (v=0; v<numberOfSubsets;v=v+1)
{
if (v)
{
lfSpawnString = lfSpawnString+",";
}
lfSpawnString = lfSpawnString+"subsetFilter"+v+",subsetTree"+v;
}
lfSpawnString = lfSpawnString+");";
ExecuteCommands (lfSpawnString);
return 0;
}
/* ____________________________________________________________________________________________________________________*/
NICETY_LEVEL = 3;
#include "TemplateModels/chooseGeneticCode.def";
ModelMatrixDimension = 64;
for (h = 0 ;h<64; h=h+1)
{
if (_Genetic_Code[h]==10)
{
ModelMatrixDimension = ModelMatrixDimension-1;
}
}
#include "MFPSreader.def";
/* now spawn the dataset filters */
lowerSeqBound = 0;
for (modelType=0; modelType<numberOfSubsets; modelType = modelType+1)
{
ExecuteCommands ("DataSetFilter subsetFilter"+modelType+"= CreateFilter (ds,3,\"\",(speciesIndex>=lowerSeqBound)&&(speciesIndex<lowerSeqBound+partitionLengths[modelType]),GeneticCodeExclusions);");
lowerSeqBound = lowerSeqBound+partitionLengths[modelType];
}
chosenModelList = {17,1};
ChoiceList (modelType,"Distributions",1,SKIP_NONE,
"Run All","Run all available dN/dS distributions",
"Run Custom","Choose from available dN/dS distributions.");
if (modelType<0)
{
return;
}
if (modelType==0)
{
for (rateType = 0; rateType<17; rateType=rateType+1)
{
chosenModelList[rateType][0] = 1;
}
}
else
{
ChoiceList (modelTypes,"Distributions",0,SKIP_NONE,
"Single Rate","Single Rate",
"Neutral","Neutral",
"Selection","Selection",
"Discrete","Discrete",
"Freqs","Freqs",
"Gamma","Gamma",
"2 Gamma","2 Gamma",
"Beta","Beta",
"Beta & w","Beta & w",
"Beta & Gamma","Beta & Gamma",
"Beta & (Gamma+1)","Beta & (Gamma+1)",
"Beta & (Normal>1)","Beta & (Normal>1)",
"0 & 2 (Normal>1)","0 & 2 (Normal>1)",
"3 Normal","3 Normal",
"RE:Log normal","Random Effects: Log normal",
"RE:Gamma","Random Effects: Gamma",
"RE:Discrete","Random Effects: 3 bin Discrete");
if (modelTypes[0]<0)
{
return;
}
for (rateType = 0; rateType < Rows(modelTypes)*Columns(modelTypes); rateType = rateType + 1)
{
modelType = modelTypes[rateType];
chosenModelList[modelType] = 1;
}
}
ChoiceList (shareType,"Choose parameter sharing mode",1,SKIP_NONE,
"All","Share dN/dS, transversion/transition ratio (if applicable) and base frequencies for all subsets.",
"dN/dS Only","Share only dN/dS. Transversion/transition ratio (if applicable) and base frequencies are separate for each subset."
);
if (shareType<0)
{
return;
}
ChoiceList (modelType,"Choose a model",1,SKIP_NONE,
"MG94 1x4","Muse-Gaut 94 model with 4(-1) nucleotide frequency parameters (intra-codon position independent).",
"MG94 3x4","Muse-Gaut 94 model with 12(-3) nucleotide frequency parameters (intra-codon position specific).",
"GY94 1x4","Goldman-Yang 94 model with 4(-1) nucleotide frequency parameters (intra-codon position independent).",
"GY94 3x4","Goldman-Yang 94 model with 12(-3) nucleotide frequency parameters (intra-codon position specific)."
);
if (modelType<0)
{
return;
}
if ((modelType==0)||(modelType==2))
{
if (shareType==0)
{
HarvestFrequencies (observedFreq,filteredData,1,1,0);
vectorOfFrequencies = BuildCodonFrequencies4 (observedFreq);
}
else
{
for (v=0; v<numberOfSubsets;v=v+1)
{
ExecuteCommands ("global kappa"+v+"=2.;HarvestFrequencies (observedFreq"+v+",subsetFilter"+v+",1,1,0);vectorOfFrequencies"+v+"= BuildCodonFrequencies4 (observedFreq"+v+");");
}
}
}
else
{
if (shareType==0)
{
HarvestFrequencies (observedFreq,filteredData,3,1,1);
vectorOfFrequencies = BuildCodonFrequencies12 (observedFreq);
}
else
{
for (v=0; v<numberOfSubsets;v=v+1)
{
ExecuteCommands ("global kappa"+v+"=2.;HarvestFrequencies (observedFreq"+v+",subsetFilter"+v+",3,1,1);vectorOfFrequencies"+v+"= BuildCodonFrequencies12 (observedFreq"+v+");");
}
}
}
if (modelType>1)
{
global kappa = 2.;
}
fprintf (stdout, "\n\n\nChoose the cutoff (0 to 1) for posterior of dN/dS>1 for a site to be considered under selective pressure:");
fscanf (stdin, "Number",psigLevel);
if ((psigLevel <= 0)||(psigLevel>1))
{
psigLevel = .95;
}
fprintf (stdout, "\n>Using ", psigLevel , " cutoff\n");
fprintf (stdout, "\nChoose the number of categories in discretized distributions:");
fscanf (stdin, "Number",categCount);
categCount = categCount$1;
if (categCount<=0)
{
categCount = 8;
}
fprintf (stdout, "\n>Using ", Format (categCount,0,0), " categories.\n");
SetDialogPrompt ("Write detailed results to:");
fprintf (PROMPT_FOR_FILE,CLEAR_FILE);
global c = 1.;
dummyVar = FrameText ("-","|",2,"SUMMARY TABLE");
tableSeparator = "+-------------------------+----------------+---------------+-----+\n";
fprintf (stdout, "\n\"p\" is the number of parameters in addition to the branch lengths.\nDetailed results including sites with dN/dS>1 will be written to\n",LAST_FILE_PATH,"\n\n");
fprintf (stdout, tableSeparator,
"| MODEL (Number & Desc) | Log likelihood | dN/dS | p |\n",
tableSeparator);
cachedBranchLengths = {{-1,-1}};
if (chosenModelList[0]>0)
{
timer = Time(1);
fprintf (LAST_FILE_PATH,"\n*** RUNNING SINGLE RATE MODEL ***\n#################################\n");
dummy = spawnLikelihood (shareType);
Optimize (res,lf);
fprintf (LAST_FILE_PATH,"\n>Done in ", Time(1)-timer, " seconds \n\n");
fprintf (LAST_FILE_PATH,lf,"\n\n-----------------------------------\n\ndN/dS = ",c,"\n\n");
fprintf (stdout, "| 0. Single Rate Model | ",Format (res[1][0],14,6)," | ",Format (c,13,8)," | 0 |\n",
tableSeparator);
timer = res[1][1]-res[1][2];
cachedBranchLengths = {timer,1};
for (rateType = timer; rateType < Columns(cachedBranchLengths); rateType = rateType+1)
{
cachedBranchLengths[rateType-timer][0] = res [0][rateType];
}
}
for (rateType = 0; rateType < 16; rateType = rateType + 1)
{
if (chosenModelList[rateType+1]==0)
{
continue;
}
timer = Time(1);
dummy = SetWDistribution (categCount);
dummy = spawnLikelihood (shareType);
fprintf (LAST_FILE_PATH,"\n*** RUNNING MODEL ", Format(rateType+1,0,0), " (",ModelNames[rateType],") ***\n######################################\n");
/*if (cachedBranchLengths[0][0]>=0.0)
{
v = ParameterCount[rateType];
if (modelType>1)
{
v=v+1;
}
for (h=0; h<Rows(cachedBranchLengths); h=h+1)
{
SetParameter (lf,h+v,cachedBranchLengths[h][0]);
}
}*/
Optimize (res,lf);
fprintf (LAST_FILE_PATH,"\n>Done in ",Time(1)-timer, " seconds \n\n", lf);
fprintf (stdout, "| ");
if (rateType<9)
{
fprintf (stdout," ");
}
fprintf (stdout, Format (rateType+1,0,0), ". ", ModelNames[rateType]);
for (dummy = Abs(ModelNames[rateType])+5; dummy<25; dummy = dummy+1)
{
fprintf (stdout," ");
}
dummy = GetDistributionParameters(psigLevel);
fprintf (stdout,"| ",Format (res[1][0],14,6)," | ",Format (dummy,13,8)," | ",
Format(ParameterCount[rateType],0,0)," |\n",tableSeparator);
if (modelType>1)
{
kappa = 2.;
}
}
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