/usr/share/hyphy/TemplateBatchFiles/AnalyzeCodonData.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 | NICETY_LEVEL = 3;
#include "TemplateModels/chooseGeneticCode.def";
#include "simpleBootstrap.bf";
SetDialogPrompt ("Please specify a codon data file:");
COUNT_GAPS_IN_FREQUENCIES = 0;
VERBOSITY_LEVEL = 1;
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";
if (modelType)
{
ChoiceList (branchLengths, "Branch Lengths", 1, SKIP_NONE,
"Estimate", "Estimate branch lengths by ML",
"Proportional to input tree", "Branch lengths are proportional to those in input tree");
if (branchLengths < 0)
{
return;
}
if (branchLengths == 1)
{
global treeScaler = 1;
ReplicateConstraint ("this1.?.?:=treeScaler*this2.?.?__", givenTree, givenTree);
}
}
LikelihoodFunction lf = (filteredData,givenTree);
Optimize (res,lf);
fprintf (stdout, "\n______________RESULTS______________\n",lf);
/* compute syn and non-syn stencils for current genetic code */
#include "categoryEcho.bf";
GetString (sendMeBack,lf,-1);
sendMeBack["LogL"] = res[1][0];
sendMeBack["NP"] = res[1][1];
return sendMeBack;
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