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1047 lines
26 KiB
Beef
1047 lines
26 KiB
Beef
/*
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This file takes a nucleotide data set and a tree (either from the data file or from a separate file) and computes maximum likelihood estimates for every possible 4x4 reversible model on that data and tree.
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We use the string (v1,v2,v3,v4,v5,v6), where and v1..6 = 0..5
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to encode a 4x4 symmetric transition matrix with entries
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[* v1 v2 v3]
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[- * v4 v5]
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[- - * v6]
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[- - - * ]
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For instance: (010010) encodes HKY85.
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For each model the following information is reported:
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- Model string. (e.g. (012345) for the GRM)
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- Number of model parameters
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- Max ln-likelihood for the model
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- Likelihood ratio statistic (as a sub-model of the GRM)
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- AIC
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- P-Value for the Likelihood Ratio Test.
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Sergei L. Kosakovsky Pond, Summer 2002.
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*/
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function ReceiveJobs (sendOrNot)
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{
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if (MPI_NODE_COUNT>1)
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{
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MPIReceive (-1, fromNode, result_String);
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jobModelNum = MPINodeState[fromNode-1][1];
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vv1 = MPINodeState[fromNode-1][2];
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vv2 = MPINodeState[fromNode-1][3];
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vv3 = MPINodeState[fromNode-1][4];
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vv4 = MPINodeState[fromNode-1][5];
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vv5 = MPINodeState[fromNode-1][6];
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vv6 = MPINodeState[fromNode-1][7];
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if (sendOrNot)
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{
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MPISend (fromNode,lf);
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MPINodeState[fromNode-1][1] = modelNum;
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MPINodeState[fromNode-1][2] = v1;
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MPINodeState[fromNode-1][3] = v2;
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MPINodeState[fromNode-1][4] = v3;
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MPINodeState[fromNode-1][5] = v4;
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MPINodeState[fromNode-1][6] = v5;
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MPINodeState[fromNode-1][7] = v6;
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}
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else
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{
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MPINodeState[fromNode-1][0] = 0;
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MPINodeState[fromNode-1][1] = -1;
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}
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ExecuteCommands (result_String);
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}
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else
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{
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jobModelNum = modelNum;
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}
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if (jobModelNum == 0)
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{
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stdl = lf_MLES[1][0];
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fullnp = lf_MLES[1][1]+addOn;
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fprintf(stdout,"\n(012345) Full Model ln-lik = ",stdl,". Parameter Count=",Format(fullnp,0,0)," AIC = ", 2*(fullnp-stdl),"\n\n");
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resultCache [0][0] = 1;
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resultCache [0][1] = 2;
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resultCache [0][2] = 3;
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resultCache [0][3] = 4;
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resultCache [0][4] = 5;
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resultCache [0][5] = lf_MLES[1][0];
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resultCache [0][6] = lf_MLES[1][1]+addOn;
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resultCache [0][7] = 0;
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resultCache [0][8] = 0;
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fprintf (stdout,"\n# | Model | # prm | lnL | LRT | AIC | P-Value |");
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fprintf (stdout,"\n----|----------|-------|-----------|----------------|------------|------------------|");
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if (MPI_NODE_COUNT>1)
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{
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for (h=1; h<203; h=h+1)
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{
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lnL = resultCache[h][5];
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if (lnL<0)
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{
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np = resultCache[h][6];
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LRT = -2*(lnL-stdl);
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if (LRT<0)
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{
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LRT = 0;
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}
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AIC = -2*lnL+2*np;
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PRINT_DIGITS = 3;
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fprintf (stdout,"\n",h);
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PRINT_DIGITS = 1;
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fprintf (stdout," | (",0, resultCache[h][0], resultCache[h][1], resultCache[h][2], resultCache[h][3], resultCache[h][4],") | ");
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fprintf (stdout,Format (np,5,0));
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PRINT_DIGITS = 8;
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fprintf (stdout, " | ",lnL," | ",Format(LRT,14,3), " | ", AIC, " | ", );
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PRINT_DIGITS = 15;
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if (LRT==0)
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{
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pValue = 1;
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}
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else
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{
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pValue = 1-CChi2(LRT,fullnp-np);
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}
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fprintf (stdout,pValue," |");
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resultCache [jobModelNum][7] = pValue;
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if (pValue<rejectAt)
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{
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rejectCount = rejectCount+1;
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resultCache [jobModelNum][8] = 0;
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}
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else
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{
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resultCache [jobModelNum][8] = 1;
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}
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if (pValue<rejectAt)
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{
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fprintf (stdout,"(*)");
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}
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}
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}
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}
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return fromNode-1;
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}
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else
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{
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if ((MPI_NODE_COUNT>1)&&(resultCache[0][5]>=0))
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{
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resultCache [jobModelNum][0] = vv2;
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resultCache [jobModelNum][1] = vv3;
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resultCache [jobModelNum][2] = vv4;
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resultCache [jobModelNum][3] = vv5;
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resultCache [jobModelNum][4] = vv6;
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resultCache [jobModelNum][5] = lf_MLES[1][0];
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resultCache [jobModelNum][6] = lf_MLES[1][1]+addOn;
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return fromNode - 1;
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}
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}
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np = lf_MLES[1][1]+addOn;
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lnL = lf_MLES[1][0];
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LRT = -2*(lnL-stdl);
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if (LRT<0)
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{
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LRT = 0;
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}
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AIC = -2*lnL+2*np;
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PRINT_DIGITS = 3;
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fprintf (stdout,"\n",jobModelNum);
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PRINT_DIGITS = 1;
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fprintf (stdout," | (",vv1,vv2,vv3,vv4,vv5,vv6,") | ");
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fprintf (stdout,Format (np,5,0));
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PRINT_DIGITS = 8;
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fprintf (stdout, " | ",lnL," | ",Format(LRT,14,3), " | ", AIC, " | ", );
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PRINT_DIGITS = 15;
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if (LRT==0)
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{
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pValue = 1;
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}
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else
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{
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pValue = 1-CChi2(LRT,fullnp-np);
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}
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fprintf (stdout,pValue," |");
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resultCache [jobModelNum][0] = vv2;
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resultCache [jobModelNum][1] = vv3;
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resultCache [jobModelNum][2] = vv4;
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resultCache [jobModelNum][3] = vv5;
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resultCache [jobModelNum][4] = vv6;
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resultCache [jobModelNum][5] = lf_MLES[1][0];
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resultCache [jobModelNum][6] = lf_MLES[1][1]+addOn;
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resultCache [jobModelNum][7] = pValue;
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if (pValue<rejectAt)
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{
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rejectCount = rejectCount+1;
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resultCache [jobModelNum][8] = 0;
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}
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else
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{
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resultCache [jobModelNum][8] = 1;
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}
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if (pValue<rejectAt)
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{
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fprintf (stdout,"(*)");
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}
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return fromNode-1;
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}
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function PopulateModelMatrix (ModelMatrixName&, EFV)
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{
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if (!ModelMatrixDimension)
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{
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ModelMatrixDimension = 64;
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for (h = 0 ;h<64; h=h+1)
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{
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if (_Genetic_Code[h]==10)
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{
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ModelMatrixDimension = ModelMatrixDimension-1;
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}
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}
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}
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ModelMatrixName = {ModelMatrixDimension,ModelMatrixDimension};
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hshift = 0;
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if (modelType == 0)
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{
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for (h=0; h<64; h=h+1)
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{
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if (_Genetic_Code[h]==10)
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{
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hshift = hshift+1;
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continue;
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}
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vshift = hshift;
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for (v = h+1; v<64; v=v+1)
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{
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diff = v-h;
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if (_Genetic_Code[v]==10)
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{
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vshift = vshift+1;
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continue;
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}
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nucPosInCodon = 2;
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if ((h$4==v$4)||((diff%4==0)&&(h$16==v$16))||(diff%16==0))
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{
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if (h$4==v$4)
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{
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transition = v%4;
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transition2= h%4;
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}
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else
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{
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if(diff%16==0)
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{
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transition = v$16;
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transition2= h$16;
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nucPosInCodon = 0;
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}
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else
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{
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transition = v%16$4;
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transition2= h%16$4;
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nucPosInCodon = 1;
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}
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}
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rateType = mSpecMatrix[transition][transition2];
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if (rateType == 1)
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{
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if (_Genetic_Code[0][h]==_Genetic_Code[0][v])
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{
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ModelMatrixName[h-hshift][v-vshift] := AC*synRate*EFV__[transition__][nucPosInCodon__];
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ModelMatrixName[v-vshift][h-hshift] := AC*synRate*EFV__[transition2__][nucPosInCodon__];
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}
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else
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{
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ModelMatrixName[h-hshift][v-vshift] := AC*R*synRate*EFV__[transition__][nucPosInCodon__];
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ModelMatrixName[v-vshift][h-hshift] := AC*R*synRate*EFV__[transition2__][nucPosInCodon__];
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}
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}
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else
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{
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if (rateType == 2)
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{
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if (_Genetic_Code[0][h]==_Genetic_Code[0][v])
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{
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ModelMatrixName[h-hshift][v-vshift] := synRate*EFV__[transition__][nucPosInCodon__];
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ModelMatrixName[v-vshift][h-hshift] := synRate*EFV__[transition2__][nucPosInCodon__];
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}
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else
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{
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ModelMatrixName[h-hshift][v-vshift] := R*synRate*EFV__[transition__][nucPosInCodon__];
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ModelMatrixName[v-vshift][h-hshift] := R*synRate*EFV__[transition2__][nucPosInCodon__];
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}
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}
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else
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{
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if (rateType == 3)
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{
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if (_Genetic_Code[0][h]==_Genetic_Code[0][v])
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{
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ModelMatrixName[h-hshift][v-vshift] := AT*synRate*EFV__[transition__][nucPosInCodon__];
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ModelMatrixName[v-vshift][h-hshift] := AT*synRate*EFV__[transition2__][nucPosInCodon__];
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}
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else
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{
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ModelMatrixName[h-hshift][v-vshift] := AT*R*synRate*EFV__[transition__][nucPosInCodon__];
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ModelMatrixName[v-vshift][h-hshift] := AT*R*synRate*EFV__[transition2__][nucPosInCodon__];
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}
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}
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else
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{
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if (rateType == 4)
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{
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if (_Genetic_Code[0][h]==_Genetic_Code[0][v])
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{
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ModelMatrixName[h-hshift][v-vshift] := CG*synRate*EFV__[transition__][nucPosInCodon__];
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ModelMatrixName[v-vshift][h-hshift] := CG*synRate*EFV__[transition2__][nucPosInCodon__];
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}
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else
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{
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ModelMatrixName[h-hshift][v-vshift] := CG*R*synRate*EFV__[transition__][nucPosInCodon__];
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ModelMatrixName[v-vshift][h-hshift] := CG*R*synRate*EFV__[transition2__][nucPosInCodon__];
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}
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}
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else
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{
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if (rateType == 5)
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{
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if (_Genetic_Code[0][h]==_Genetic_Code[0][v])
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{
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ModelMatrixName[h-hshift][v-vshift] := CT*synRate*EFV__[transition__][nucPosInCodon__];
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ModelMatrixName[v-vshift][h-hshift] := CT*synRate*EFV__[transition2__][nucPosInCodon__];
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}
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else
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{
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ModelMatrixName[h-hshift][v-vshift] := CT*R*synRate*EFV__[transition__][nucPosInCodon__];
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ModelMatrixName[v-vshift][h-hshift] := CT*R*synRate*EFV__[transition2__][nucPosInCodon__];
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}
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}
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else
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{
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if (_Genetic_Code[0][h]==_Genetic_Code[0][v])
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{
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ModelMatrixName[h-hshift][v-vshift] := GT*synRate*EFV__[transition__][nucPosInCodon__];
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ModelMatrixName[v-vshift][h-hshift] := GT*synRate*EFV__[transition2__][nucPosInCodon__];
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}
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else
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{
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ModelMatrixName[h-hshift][v-vshift] := GT*R*synRate*EFV__[transition__][nucPosInCodon__];
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ModelMatrixName[v-vshift][h-hshift] := GT*R*synRate*EFV__[transition2__][nucPosInCodon__];
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}
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}
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}
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}
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}
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}
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}
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}
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}
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}
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else
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{
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for (h=0; h<64; h=h+1)
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{
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if (_Genetic_Code[h]==10)
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{
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hshift = hshift+1;
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continue;
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}
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vshift = hshift;
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for (v = h+1; v<64; v=v+1)
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{
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diff = v-h;
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if (_Genetic_Code[v]==10)
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{
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vshift = vshift+1;
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continue;
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}
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nucPosInCodon = 2;
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if ((h$4==v$4)||((diff%4==0)&&(h$16==v$16))||(diff%16==0))
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{
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if (h$4==v$4)
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{
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transition = v%4;
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transition2= h%4;
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}
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else
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{
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if(diff%16==0)
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{
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transition = v$16;
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transition2= h$16;
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nucPosInCodon = 0;
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}
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else
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{
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transition = v%16$4;
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transition2= h%16$4;
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nucPosInCodon = 1;
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}
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}
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rateType = mSpecMatrix[transition][transition2];
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if (rateType == 1)
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{
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if (_Genetic_Code[0][h]==_Genetic_Code[0][v])
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{
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ModelMatrixName[h-hshift][v-vshift] := c*AC*synRate*EFV__[transition__][nucPosInCodon__];
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ModelMatrixName[v-vshift][h-hshift] := c*AC*synRate*EFV__[transition2__][nucPosInCodon__];
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}
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else
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{
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ModelMatrixName[h-hshift][v-vshift] := c*AC*R*synRate*EFV__[transition__][nucPosInCodon__];
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ModelMatrixName[v-vshift][h-hshift] := c*AC*R*synRate*EFV__[transition2__][nucPosInCodon__];
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}
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}
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else
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{
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if (rateType == 2)
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{
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if (_Genetic_Code[0][h]==_Genetic_Code[0][v])
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{
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ModelMatrixName[h-hshift][v-vshift] := c*synRate*EFV__[transition__][nucPosInCodon__];
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ModelMatrixName[v-vshift][h-hshift] := c*synRate*EFV__[transition2__][nucPosInCodon__];
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}
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else
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{
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ModelMatrixName[h-hshift][v-vshift] := c*R*synRate*EFV__[transition__][nucPosInCodon__];
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ModelMatrixName[v-vshift][h-hshift] := c*R*synRate*EFV__[transition2__][nucPosInCodon__];
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}
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}
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else
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{
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if (rateType == 3)
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{
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if (_Genetic_Code[0][h]==_Genetic_Code[0][v])
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{
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ModelMatrixName[h-hshift][v-vshift] := c*AT*synRate*EFV__[transition__][nucPosInCodon__];
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ModelMatrixName[v-vshift][h-hshift] := c*AT*synRate*EFV__[transition2__][nucPosInCodon__];
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}
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else
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{
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ModelMatrixName[h-hshift][v-vshift] := c*AT*R*synRate*EFV__[transition__][nucPosInCodon__];
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ModelMatrixName[v-vshift][h-hshift] := c*AT*R*synRate*EFV__[transition2__][nucPosInCodon__];
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}
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}
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else
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{
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if (rateType == 4)
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{
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if (_Genetic_Code[0][h]==_Genetic_Code[0][v])
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{
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ModelMatrixName[h-hshift][v-vshift] := c*CG*synRate*EFV__[transition__][nucPosInCodon__];
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ModelMatrixName[v-vshift][h-hshift] := c*CG*synRate*EFV__[transition2__][nucPosInCodon__];
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}
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else
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{
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ModelMatrixName[h-hshift][v-vshift] := c*CG*R*synRate*EFV__[transition__][nucPosInCodon__];
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ModelMatrixName[v-vshift][h-hshift] := c*CG*R*synRate*EFV__[transition2__][nucPosInCodon__];
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}
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}
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else
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{
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if (rateType == 5)
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{
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if (_Genetic_Code[0][h]==_Genetic_Code[0][v])
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{
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ModelMatrixName[h-hshift][v-vshift] := c*CT*synRate*EFV__[transition__][nucPosInCodon__];
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ModelMatrixName[v-vshift][h-hshift] := c*CT*synRate*EFV__[transition2__][nucPosInCodon__];
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}
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else
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{
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ModelMatrixName[h-hshift][v-vshift] := c*CT*R*synRate*EFV__[transition__][nucPosInCodon__];
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ModelMatrixName[v-vshift][h-hshift] := c*CT*R*synRate*EFV__[transition2__][nucPosInCodon__];
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}
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}
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else
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{
|
|
if (_Genetic_Code[0][h]==_Genetic_Code[0][v])
|
|
{
|
|
ModelMatrixName[h-hshift][v-vshift] := c*GT*synRate*EFV__[transition__][nucPosInCodon__];
|
|
ModelMatrixName[v-vshift][h-hshift] := c*GT*synRate*EFV__[transition2__][nucPosInCodon__];
|
|
}
|
|
else
|
|
{
|
|
ModelMatrixName[h-hshift][v-vshift] := c*GT*R*synRate*EFV__[transition__][nucPosInCodon__];
|
|
ModelMatrixName[v-vshift][h-hshift] := c*GT*R*synRate*EFV__[transition2__][nucPosInCodon__];
|
|
}
|
|
}
|
|
}
|
|
}
|
|
}
|
|
}
|
|
}
|
|
}
|
|
}
|
|
}
|
|
return 0;
|
|
}
|
|
|
|
|
|
function BuildCodonFrequencies (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 setElement (h,v,cc)
|
|
{
|
|
mSpecMatrix[h][v]=cc+1;
|
|
mSpecMatrix[v][h]=cc+1;
|
|
return 1;
|
|
}
|
|
|
|
|
|
function printModelMatrix (modelString)
|
|
{
|
|
|
|
mstrConv = "1";
|
|
for (v2 = 1; v2 < 6; v2 = v2+1)
|
|
{
|
|
if (modelString[v2]=="0")
|
|
{
|
|
mstrConv = mstrConv+"1";
|
|
}
|
|
else
|
|
{
|
|
if (modelString[v2]=="1")
|
|
{
|
|
mstrConv = mstrConv+"B";
|
|
}
|
|
else
|
|
{
|
|
if (modelString[v2]=="2")
|
|
{
|
|
mstrConv = mstrConv+"C";
|
|
}
|
|
else
|
|
{
|
|
if (modelString[v2]=="3")
|
|
{
|
|
mstrConv = mstrConv+"D";
|
|
}
|
|
else
|
|
{
|
|
if (modelString[v2]=="4")
|
|
{
|
|
mstrConv = mstrConv+"E";
|
|
}
|
|
else
|
|
{
|
|
mstrConv = mstrConv+"F";
|
|
}
|
|
}
|
|
}
|
|
}
|
|
}
|
|
}
|
|
sep = "+---+-----+-----+-----+-----+\n";
|
|
fprintf (stdout, sep,
|
|
"| | A | C | G | T |\n",
|
|
sep,
|
|
"| A | * | ", mstrConv[0], "*t | ", mstrConv[1], "*t | ", mstrConv[2], "*t |\n",
|
|
sep,
|
|
"| C | ", mstrConv[0], "*t | * | ", mstrConv[3], "*t | ", mstrConv[4], "*t |\n",
|
|
sep,
|
|
"| G | ", mstrConv[1], "*t | " , mstrConv[3], "*t | * | ", mstrConv[5], "*t |\n",
|
|
sep,
|
|
"| T | ", mstrConv[2], "*t | " , mstrConv[4], "*t | ", mstrConv[5], "*t | * |\n",
|
|
sep, "\nt = synRate for synonymous substitutions, and t=R*synRate for non-synonumous ones.\n");
|
|
|
|
return 1;
|
|
}
|
|
|
|
#include "TemplateModels/chooseGeneticCode.def";
|
|
SetDialogPrompt ("Please specify a codon data file:");
|
|
|
|
DataSet ds = ReadDataFile (PROMPT_FOR_FILE);
|
|
DataSetFilter filteredData = CreateFilter (ds,3,"","",GeneticCodeExclusions);
|
|
|
|
fprintf (stdout,"\n______________READ THE FOLLOWING DATA______________\n",ds);
|
|
|
|
|
|
HarvestFrequencies (observedFreq,filteredData,3,1,1);
|
|
|
|
mSpecMatrix = {{*,1,1,1}{1,*,1,1}{1,1,*,1}{1,1,1,*}};
|
|
ModelMatrixDimension = 0;
|
|
|
|
_DO_TREE_REBALANCE_ = 1;
|
|
|
|
#include "queryTree.bf";
|
|
#include "TemplateModels/modelParameters5.mdl";
|
|
|
|
if (modelType > 0)
|
|
{
|
|
#include "TemplateModels/defineGamma.mdl";
|
|
}
|
|
|
|
ChoiceList (branchLengths,"Estimate Branch Lengths",1,SKIP_NONE,
|
|
"Every Time","Branch lengths are reestimated for every model.",
|
|
"Once","Branch lenghts obtained from the nucleotide GTR model and reused for subsequent models."
|
|
);
|
|
|
|
if (branchLengths<0)
|
|
{
|
|
return;
|
|
}
|
|
|
|
rejectAt = 0;
|
|
|
|
while ((rejectAt<=0)||(rejectAt>=1))
|
|
{
|
|
fprintf (stdout, "\nModel rejection level (e.g. 0.05):");
|
|
fscanf (stdin,"Number", rejectAt);
|
|
}
|
|
|
|
SetDialogPrompt ("Save results to:");
|
|
|
|
fprintf (PROMPT_FOR_FILE, CLEAR_FILE);
|
|
BASE_PATH = LAST_FILE_PATH;
|
|
|
|
KEEP_OPTIMAL_ORDER = 1;
|
|
MESSAGE_LOGGING = 0;
|
|
|
|
global AC=1;
|
|
global AT=1;
|
|
global CG=1;
|
|
global CT=1;
|
|
global GT=1;
|
|
global R=1;
|
|
|
|
|
|
r = setElement (0,2,1);
|
|
r = setElement (0,3,2);
|
|
r = setElement (1,2,3);
|
|
r = setElement (1,3,4);
|
|
r = setElement (2,3,5);
|
|
|
|
MG94custom = 0;
|
|
MULTIPLY_BY_FREQS = PopulateModelMatrix ("MG94custom", observedFreq);
|
|
vectorOfFrequencies = BuildCodonFrequencies (observedFreq);
|
|
Model MG94customModel = (MG94custom,vectorOfFrequencies,0);
|
|
|
|
USE_POSITION_SPECIFIC_FREQS = 1;
|
|
Tree tr = treeString;
|
|
|
|
addOn = 0;
|
|
|
|
if (branchLengths)
|
|
{
|
|
global TreeScaler = 1;
|
|
GTRMatrix = {{*,AC*nt,nt,AT*nt}{AC*nt,*,CG*nt,CT*nt}{nt,CG*nt,*,GT*nt}{AT*nt,CT*nt,GT*nt,*}};
|
|
DataSetFilter nucFilter = CreateFilter (filteredData,1);
|
|
HarvestFrequencies (nucFreq,nucFilter,1,1,1);
|
|
Model GTRModel = (GTRMatrix,nucFreq,1);
|
|
givenTreeString = Format (tr,0,0);
|
|
Tree nucTree = givenTreeString;
|
|
LikelihoodFunction lfn = (nucFilter, nucTree);
|
|
Optimize (nres,lfn);
|
|
ReplicateConstraint ("this1.?.synRate:=this2.?.nt__/TreeScaler",tr,nucTree);
|
|
addOn = nres[1][1]-nres[1][2]-1;
|
|
}
|
|
|
|
LikelihoodFunction lf = (filteredData, tr);
|
|
|
|
resultCache = {203,9};
|
|
|
|
modelNum = 0;
|
|
rejectCount = 0;
|
|
|
|
if (MPI_NODE_COUNT>1)
|
|
{
|
|
MPINodeState = {MPI_NODE_COUNT-1,8};
|
|
OPTIMIZE_SUMMATION_ORDER = 0;
|
|
MPISend (1,lf);
|
|
MPINodeState[0][0] = 1;
|
|
MPINodeState[0][1] = modelNum;
|
|
}
|
|
else
|
|
{
|
|
Optimize (lf_MLES,lf);
|
|
vv1 = 0;
|
|
vv2 = 0;
|
|
vv3 = 0;
|
|
vv4 = 0;
|
|
vv5 = 0;
|
|
vv6 = 0;
|
|
dummy = ReceiveJobs (0);
|
|
}
|
|
|
|
rateBiasTerms = {{"AC","1","AT","CG","CT","GT"}};
|
|
|
|
for (v2=0; v2<=1; v2=v2+1)
|
|
{
|
|
for (v3=0; v3<=v2+1; v3=v3+1)
|
|
{
|
|
if (v3>v2)
|
|
{
|
|
ub4 = v3;
|
|
}
|
|
else
|
|
{
|
|
ub4 = v2;
|
|
}
|
|
for (v4=0; v4<=ub4+1; v4=v4+1)
|
|
{
|
|
if (v4>=ub4)
|
|
{
|
|
ub5 = v4;
|
|
}
|
|
else
|
|
{
|
|
ub5 = ub4;
|
|
}
|
|
for (v5=0; v5<=ub5+1; v5=v5+1)
|
|
{
|
|
if (v5>ub5)
|
|
{
|
|
ub6 = v5;
|
|
}
|
|
else
|
|
{
|
|
ub6 = ub5;
|
|
}
|
|
for (v6=0; v6<=ub6+1; v6=v6+1)
|
|
{
|
|
if (v6==5)
|
|
{
|
|
break;
|
|
}
|
|
|
|
R = 1;
|
|
|
|
paramCount = 0;
|
|
|
|
modelDesc = "0"+Format(v2,1,0);
|
|
modelDesc = modelDesc+Format(v3,1,0);
|
|
modelDesc = modelDesc+Format(v4,1,0);
|
|
modelDesc = modelDesc+Format(v5,1,0);
|
|
modelDesc = modelDesc+Format(v6,1,0);
|
|
|
|
modelConstraintString = "";
|
|
|
|
AC = 1;
|
|
AT = 1;
|
|
CG = 1;
|
|
CT = 1;
|
|
GT = 1;
|
|
|
|
for (customLoopCounter2=1; customLoopCounter2<6; customLoopCounter2=customLoopCounter2+1)
|
|
{
|
|
for (customLoopCounter=0; customLoopCounter<customLoopCounter2; customLoopCounter=customLoopCounter+1)
|
|
{
|
|
if (modelDesc[customLoopCounter2]==modelDesc[customLoopCounter])
|
|
{
|
|
if (rateBiasTerms[customLoopCounter2] == "1")
|
|
{
|
|
modelConstraintString = modelConstraintString + rateBiasTerms[customLoopCounter]+":="+rateBiasTerms[customLoopCounter2]+";";
|
|
}
|
|
else
|
|
{
|
|
modelConstraintString = modelConstraintString + rateBiasTerms[customLoopCounter2]+":="+rateBiasTerms[customLoopCounter]+";";
|
|
}
|
|
break;
|
|
}
|
|
}
|
|
}
|
|
|
|
if (Abs(modelConstraintString))
|
|
{
|
|
ExecuteCommands (modelConstraintString);
|
|
}
|
|
|
|
|
|
modelNum = modelNum+1;
|
|
if (MPI_NODE_COUNT>1)
|
|
{
|
|
for (mpiNode = 0; mpiNode < MPI_NODE_COUNT-1; mpiNode = mpiNode+1)
|
|
{
|
|
if (MPINodeState[mpiNode][0]==0)
|
|
{
|
|
break;
|
|
}
|
|
}
|
|
|
|
if (mpiNode==MPI_NODE_COUNT-1)
|
|
/* all nodes busy */
|
|
{
|
|
mpiNode = ReceiveJobs (1);
|
|
}
|
|
else
|
|
{
|
|
MPISend (mpiNode+1,lf);
|
|
MPINodeState[mpiNode][0] = 1;
|
|
MPINodeState[mpiNode][1] = modelNum;
|
|
MPINodeState[mpiNode][2] = v1;
|
|
MPINodeState[mpiNode][3] = v2;
|
|
MPINodeState[mpiNode][4] = v3;
|
|
MPINodeState[mpiNode][5] = v4;
|
|
MPINodeState[mpiNode][6] = v5;
|
|
MPINodeState[mpiNode][7] = v6;
|
|
}
|
|
}
|
|
else
|
|
{
|
|
Optimize (lf_MLES,lf);
|
|
vv1 = v1;
|
|
vv2 = v2;
|
|
vv3 = v3;
|
|
vv4 = v4;
|
|
vv5 = v5;
|
|
vv6 = v6;
|
|
dummy = ReceiveJobs (0);
|
|
}
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
}
|
|
|
|
if (MPI_NODE_COUNT>1)
|
|
{
|
|
while (1)
|
|
{
|
|
for (nodeCounter = 0; nodeCounter < MPI_NODE_COUNT-1; nodeCounter = nodeCounter+1)
|
|
{
|
|
if (MPINodeState[nodeCounter][0]==1)
|
|
{
|
|
fromNode = ReceiveJobs (0);
|
|
break;
|
|
}
|
|
}
|
|
if (nodeCounter == MPI_NODE_COUNT-1)
|
|
{
|
|
break;
|
|
}
|
|
}
|
|
OPTIMIZE_SUMMATION_ORDER = 1;
|
|
}
|
|
|
|
function checkEmbedding (_m1, _m2)
|
|
{
|
|
for (r=0; r<6; r=r+1)
|
|
{
|
|
if (_m2[r]<_m1[r])
|
|
{
|
|
/*fprintf (stdout,_m1," ", _m2, " Reject 1 at position ",r,"\n");*/
|
|
return 0;
|
|
}
|
|
if (_m2[r]>_m1[r])
|
|
{
|
|
for (r2 = 0; r2 < 6; r2 = r2+1)
|
|
{
|
|
if ((_m2[r2]==_m2[r])&&(_m1[r2]!=_m1[r]))
|
|
{
|
|
/*fprintf (stdout,_m1," ", _m2, " Reject 2 at positions ",r,r2,"\n");*/
|
|
return 0;
|
|
}
|
|
}
|
|
}
|
|
}
|
|
return 1;
|
|
}
|
|
|
|
PRINT_DIGITS = 0;
|
|
|
|
fprintf (stdout, "\n\n--------------------------\n (*) => p-Value < ", rejectAt, "\nRejected ", rejectCount, " models.\n");
|
|
|
|
|
|
if (rejectCount<202)
|
|
{
|
|
|
|
fprintf (stdout, "\nPerforming nested tests on the remaining models...\n");
|
|
|
|
done = 0;
|
|
while (!done)
|
|
{
|
|
done = 1;
|
|
for (v2=1; v2<203; v2=v2+1)
|
|
{
|
|
if (resultCache[v2][8])
|
|
{
|
|
modelString = "0";
|
|
for (v3 = 0; v3<5; v3=v3+1)
|
|
{
|
|
modelString = modelString + resultCache [v2][v3];
|
|
}
|
|
for (v3 = v2+1; v3<203; v3 = v3+1)
|
|
{
|
|
if (resultCache[v3][8])
|
|
{
|
|
modelString2 = "0";
|
|
for (v4 = 0; v4<5; v4=v4+1)
|
|
{
|
|
modelString2 = modelString2 + resultCache [v3][v4];
|
|
}
|
|
if (checkEmbedding (modelString, modelString2))
|
|
{
|
|
fprintf (stdout,"H: (", modelString,") A: (", modelString2, "). ");
|
|
done = 0;
|
|
LRT = 2*(resultCache[v3][5]-resultCache[v2][5]);
|
|
npd = resultCache[v3][6]-resultCache[v2][6];
|
|
if (LRT<0)
|
|
{
|
|
pValue = 1;
|
|
}
|
|
else
|
|
{
|
|
pValue = 1-CChi2(LRT,npd);
|
|
}
|
|
fprintf (stdout," P-Value=", Format (pValue,10,3));
|
|
if (pValue<rejectAt)
|
|
{
|
|
fprintf (stdout,". Rejected H.\n");
|
|
resultCache[v2][8] = 0;
|
|
break;
|
|
}
|
|
else
|
|
{
|
|
fprintf (stdout,". Failed to reject H. Discarding A.\n");
|
|
resultCache[v3][8] = 0;
|
|
}
|
|
}
|
|
}
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
fprintf (stdout,"\n\nRemaining models:\n\n# | Model | # prm | lnL | LRT | AIC | P-Value |");
|
|
fprintf (stdout,"\n----|----------|-------|-----------|----------------|------------|------------------|");
|
|
fprintf (BASE_PATH,"\n\nRemaining models:\n\n# | Model | # prm | lnL | LRT | AIC | P-Value |");
|
|
fprintf (BASE_PATH,"\n----|----------|-------|-----------|----------------|------------|------------------|");
|
|
|
|
modelNum = 0;
|
|
v5 = 1e10;
|
|
v4 = 0;
|
|
|
|
for (v2=1; v2<203; v2=v2+1)
|
|
{
|
|
if (resultCache[v2][8])
|
|
{
|
|
modelNum = 0;
|
|
modelString = "0";
|
|
for (v3 = 0; v3<5; v3=v3+1)
|
|
{
|
|
modelString = modelString + resultCache [v2][v3];
|
|
}
|
|
np = resultCache[v2][6];
|
|
lnL = resultCache[v2][5];
|
|
LRT = -2*(lnL-stdl);
|
|
if (LRT<0)
|
|
{
|
|
LRT = 0;
|
|
}
|
|
AIC = -2*lnL+2*np;
|
|
modelNum = modelNum + 1;
|
|
PRINT_DIGITS = 3;
|
|
fprintf (stdout,"\n",v2);
|
|
fprintf (BASE_PATH,"\n",v2);
|
|
PRINT_DIGITS = 1;
|
|
fprintf (stdout," | (",0,resultCache[v2][0],resultCache[v2][1],resultCache[v2][2],resultCache[v2][3],resultCache[v2][4],") | ");
|
|
fprintf (stdout,Format (np,5,0));
|
|
fprintf (BASE_PATH," | (",0,resultCache[v2][0],resultCache[v2][1],resultCache[v2][2],resultCache[v2][3],resultCache[v2][4],") | ");
|
|
fprintf (BASE_PATH,Format (np,5,0));
|
|
PRINT_DIGITS = 8;
|
|
fprintf (stdout, " | ",lnL," | ",Format(LRT,14,3), " | ", AIC, " | ", );
|
|
fprintf (BASE_PATH, " | ",lnL," | ",Format(LRT,14,3), " | ", AIC, " | ", );
|
|
PRINT_DIGITS = 15;
|
|
if (LRT==0)
|
|
{
|
|
pValue = 1;
|
|
}
|
|
else
|
|
{
|
|
pValue = 1-CChi2(LRT,fullnp-np);
|
|
}
|
|
if (AIC<v5)
|
|
{
|
|
v5 = AIC;
|
|
v4 = v2;
|
|
}
|
|
fprintf (stdout,pValue," |");
|
|
fprintf (BASE_PATH,pValue," |");
|
|
|
|
}
|
|
}
|
|
|
|
PRINT_DIGITS = 0;
|
|
modelString = "0";
|
|
for (v3 = 0; v3<5; v3=v3+1)
|
|
{
|
|
modelString = modelString + Format(resultCache [v4][v3],0,0);
|
|
}
|
|
|
|
fprintf (stdout, "\n\nAIC based winner: (", modelString, ") with AIC = ", v5, "\n\n");
|
|
fprintf (BASE_PATH, "\n\nAIC based winner: (", modelString, ") with AIC = ", v5, "\n\n");
|
|
|
|
dummy = printModelMatrix (modelString);
|
|
|
|
modelString2 = "";
|
|
if (modelString == "000000")
|
|
{
|
|
modelString2 = "F81";
|
|
}
|
|
if (modelString == "010010")
|
|
{
|
|
modelString2 = "HKY85";
|
|
}
|
|
if (modelString == "010020")
|
|
{
|
|
modelString2 = "TrN";
|
|
}
|
|
if (Abs(modelString2))
|
|
{
|
|
fprintf (stdout, "\nThis model is better known as:", modelString2, "\n");
|
|
fprintf (BASE_PATH, "\nThis model is better known as:", modelString2, "\n");
|
|
}
|
|
|
|
}
|
|
else
|
|
{
|
|
fprintf (stdout, "\nGeneral Reversible Model is the winner!\n");
|
|
fprintf (BASE_PATH, "\nGeneral Reversible Model is the winner!\n");
|
|
}
|
|
|
|
|
|
|