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https://github.com/KevinMidboe/linguist.git
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add better HyPhy samples
This commit is contained in:
Mike Doud
252
samples/HyPhy/AAModelComparison.bf
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252
samples/HyPhy/AAModelComparison.bf
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@@ -0,0 +1,252 @@
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if (Rows (modelMatrixList) == 0)
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{
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modelMatrixList =
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{
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{"Equal Input", "EIAA.mdl", "19"}
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{"Dayhoff","Dayhoff.mdl","0"}
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{"Dayhoff+F","Dayhoff_F.mdl","19"}
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{"JTT", "Jones.mdl", "0"}
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{"JTT+F", "Jones_F.mdl", "19"}
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{"WAG", "WAG.mdl", "0"}
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{"WAG+F", "WAG_F.mdl", "19"}
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{"rtREV", "rtREV.mdl", "0"}
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{"rtREV+F", "rtREV_F.mdl", "19"}
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{"mtMAM", "mtMAM.mdl", "0"}
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{"mtMAM+F", "mtMAM_F.mdl", "19"}
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{"mtREV 24", "mtREV_24.mdl", "0"}
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{"mtREV 24+F", "mtREV_24_F.mdl", "19"}
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{"HIV within", "HIVwithin.mdl", "0"}
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{"HIV within+F", "HIVwithin+F.mdl", "19"}
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{"HIV between", "HIVbetween.mdl", "0"}
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{"HIV between+F", "HIVbetween+F.mdl", "19"}
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{"REV-1 step", "reducedREV.mdl", "19"}
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{"REV", "mtREV.mdl", "19"}
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};
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}
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/*___________________________________________________________________________________________________________*/
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function runAModel (modelID, fileName, xtraP, midx)
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{
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ExecuteCommands ("#include \"TemplateModels/"+fileName+"\";");
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Tree givenTree = treeString;
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LikelihoodFunction lf = (filteredData,givenTree);
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GetString (lf_info, lf, -1);
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locals = lf_info["Local Independent"];
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if (Columns (branchLengthStash))
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{
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USE_LAST_RESULTS = 1;
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for (_iv = 0; _iv < Columns (locals); _iv = _iv+1)
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{
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ExecuteCommands (locals[_iv] + "=1;\n");
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}
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currentBL = BranchLength (givenTree,0);
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currentBN = BranchName (givenTree,-1);
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for (_iv = 0; _iv < Columns (currentBN); _iv = _iv+1)
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{
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ExecuteCommands ("givenTree."+currentBN[_iv]+".t="+branchLengthStash[_iv]/currentBL+";");
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}
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}
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else
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{
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for (_iv = 0; _iv < Columns (locals); _iv = _iv+1)
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{
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ExecuteCommands (locals[_iv] + "=0.1;\n");
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}
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USE_LAST_RESULTS = 1;
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}
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Optimize (res,lf);
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fprintf (stdout, "| ", modelID);
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for (k=0; k<maxModelWidth-Abs(modelID)-1; k=k+1)
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{
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fprintf (stdout, " ");
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}
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params = res[1][1]+xtraP;
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AIC = 2(-res[1][0]+params);
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if (filteredData.sites-params>1)
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{
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cAIC = 2(-res[1][0]+params*(filteredData.sites/(filteredData.sites-params-1)));
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}
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else
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{
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cAIC = 0;
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}
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branchLengths = BranchLength (givenTree,-1);
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TL = 0;
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for (k=Rows(branchLengths)*Columns(branchLengths)-1; k>=0; k=k-1)
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{
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TL = TL + branchLengths[k];
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}
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fprintf (stdout, "| ", Format (res[1][0],14,3), " | ", Format (params,5,0), " | ",
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Format (AIC, 9,3), " | ",);
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if (cAIC > 0)
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{
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fprintf (stdout, Format (cAIC,11,3), " | ");
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}
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else
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{
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fprintf (stdout, " N/A | ");
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}
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fprintf (stdout, Format (TL,11,3), " |\n", sepString);
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resultMatrix[midx][0] = res[1][0];
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resultMatrix[midx][1] = params;
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resultMatrix[midx][2] = AIC;
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resultMatrix[midx][3] = cAIC;
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resultMatrix[midx][4] = TL;
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if (AIC < bestAIC)
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{
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bestAIC = AIC;
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bestAICidx = midx;
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branchLengthStash = BranchLength (givenTree,-1);
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}
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if (cAIC > 0)
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{
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if (bestCAIC > cAIC)
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{
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bestCAIC = cAIC;
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bestCAICidx = midx;
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}
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}
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return 0;
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}
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/*___________________________________________________________________________________________________________*/
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maxModelWidth = 7;
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skipCodeSelectionStep = 0;
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ChoiceList (doREV, "Include REV?", 1, SKIP_NONE, "Yes", "Include REV and reduced REV models. CAUTION: these models take a long time to fit.",
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"No", "Only use empirical models");
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if (doREV < 0)
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{
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return 0;
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}
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if (doREV == 0)
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{
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#include "TemplateModels/chooseGeneticCode.def";
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skipCodeSelectionStep = 1;
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}
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modelCount = Rows (modelMatrixList) - 2*doREV;
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for (k=0; k<modelCount; k=k+1)
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{
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maxModelWidth = Max(maxModelWidth,Abs (modelMatrixList[k][0])+2);
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}
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sepString = "";
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capString = "";
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sepString * 256;
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sepString * "+";
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capString * 256;
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capString * "| Model";
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for (k=0; k<maxModelWidth; k=k+1)
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{
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sepString * "-";
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}
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for (k=0; k<maxModelWidth-6; k=k+1)
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{
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capString * " ";
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}
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capString * "| Log Likelihood | #prms | AIC Score | c-AIC Score | Tree Length |\n";
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sepString * "+----------------+-------+-----------+-------------+-------------+\n";
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sepString * 0;
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capString * 0;
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branchLengthStash = 0;
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SKIP_MODEL_PARAMETER_LIST = 0;
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#include "TemplateModels/modelParameters2.mdl";
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if (modelType == 1)
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{
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#include "TemplateModels/defineGamma.mdl";
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}
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if (modelType == 2)
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{
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#include "TemplateModels/defineHM.mdl";
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}
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SKIP_MODEL_PARAMETER_LIST = 1;
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SetDialogPrompt ("Please load an amino-acid data file:");
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DataSet ds = ReadDataFile (PROMPT_FOR_FILE);
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DataSetFilter filteredData = CreateFilter (ds,1);
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fprintf (stdout,"\nRunning aminoacid model comparisons on ", LAST_FILE_PATH, "\n\nThe alignment has ",ds.species, " sequences and ", ds.sites, " sites\n");
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_DO_TREE_REBALANCE_ = 1;
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#include "queryTree.bf";
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resultMatrix = {modelCount, 5};
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fprintf (stdout, "\n",sepString,capString,sepString);
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bestAIC = 1e100;
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bestCAIC = 1e100;
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bestAICidx = 0;
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bestCAICidx = -1;
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for (mid=0; mid<modelCount; mid=mid+1)
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{
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runAModel (modelMatrixList[mid][0], modelMatrixList[mid][1], 0+modelMatrixList[mid][2], mid);
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}
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fprintf (stdout, "\n\nBest AIC model:\n\t", modelMatrixList[bestAICidx][0], " with the score of ", bestAIC);
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if (bestCAICidx>=0)
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{
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fprintf (stdout, "\n\nBest c-AIC model:\n\t", modelMatrixList[bestCAICidx][0], " with the score of ", bestCAIC);
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}
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labelMatrix = {{"Log-likelihood","Parameters","AIC","c-AIC","Total tree length",""}};
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aaString = "Model";
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for (fC = 0; fC < modelCount; fC = fC+1)
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{
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aaString = aaString + ";" + modelMatrixList[fC][0];
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}
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USE_LAST_RESULTS = 0;
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labelMatrix[5] = aaString;
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skipCodeSelectionStep = 0;
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OpenWindow (CHARTWINDOW,{{"Model Fits"}
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{"labelMatrix"},
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{"resultMatrix"},
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{"Bar Chart"},
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{"Index"},
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{"c-AIC"},
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{"Model Index"},
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{""},
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{"AIC"}
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},
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"SCREEN_WIDTH-60;SCREEN_HEIGHT-60;30;30");
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