/usr/share/hyphy/TemplateBatchFiles/AnalyzeCodonDataMPI.bf is in hyphy-common 2.2.6+dfsg-3build3.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 | #include "TemplateModels/chooseGeneticCode.def";
#include "simpleBootstrap.bf";
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);
SelectTemplateModel(filteredData);
_DO_TREE_REBALANCE_ = 1;
#include "queryTree.bf";
cs = 0;
lfString = "";
lfString * 128;
partCount = 10;
perProc = filteredData.sites$(partCount);
fprintf (stdout,"\n",perProc, " sites / processor\n");
for (k=0; k<partCount; k=k+1)
{
if (k < partCount-1)
{
upTo = cs+perProc;
}
else
{
upTo = filteredData.sites;
}
fc = "DataSetFilter filteredData_"+ k + "=CreateFilter (ds,3,\""+(cs*3)+"-"+(3*upTo-1)+"\",\"\",GeneticCodeExclusions);";
ExecuteCommands (fc);
ExecuteCommands ("Tree tree_"+ k + "=treeString;");
if (k)
{
ExecuteCommands ("ReplicateConstraint(\"this1.?.?:=this2.?.?\",tree_"+k+",tree_0);");
lfString * ",";
}
cs = cs+perProc;
lfString * ("filteredData_"+k+",tree_"+k);
}
lfString * 0;
ExecuteCommands ("LikelihoodFunction lf = ("+lfString+");");
mxF81 = {{*,t,t,t}{t,*,t,t}{t,t,*,t}{t,t,t,*}};
HarvestFrequencies (nucFreq,ds,1,1,1);
Model M81 = (mxF81,nucFreq,1);
Tree nucTree = treeString;
DataSetFilter nucData = CreateFilter (ds,1);
LikelihoodFunction nlf = (nucData,nucTree);
Optimize (nuc_ref,nlf);
ReplicateConstraint ("this1.?.synRate:=3*this2.?.t",tree_0,nucTree);
ClearConstraints (tree_0);
USE_LAST_RESULTS = 1;
Optimize (res,lf);
fprintf (stdout, "\n______________RESULTS______________\n",lf);
#include "categoryEcho.bf";
|