Merge pull request #229 from stevenweaver/master

adding confidence interval. fixes veg/hyphy#1414
veg · Oct 15, 2021 · 0a5bb91 · 0a5bb91
2 parents e8ceda4 + 2827f8d
commit 0a5bb91
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Showing 3 changed files with 10 additions and 6 deletions.
diff --git a/app/absrel/absrel.sh b/app/absrel/absrel.sh
@@ -18,5 +18,5 @@ HYPHY=$CWD/../../.hyphy/HYPHYMPI
 
 export HYPHY_PATH=$CWD/../../.hyphy/res/
 
-echo "mpirun -np $PROCS $HYPHY LIBPATH=$HYPHY_PATH absrel --alignment $FN --tree $TREE_FN --code $GENETIC_CODE --branches FG --output $RESULTS_FN >> $PROGRESS_FILE"
-mpirun -np $PROCS $HYPHY LIBPATH=$HYPHY_PATH absrel --alignment $FN --tree $TREE_FN --code $GENETIC_CODE --branches FG --output $RESULTS_FN >> $PROGRESS_FILE
+echo 'mpirun -np $PROCS $HYPHY LIBPATH=$HYPHY_PATH absrel --alignment $FN --tree $TREE_FN --code $GENETIC_CODE --branches FG --output $RESULTS_FN ENV="TOLERATE_NUMERICAL_ERRORS=1;" >> $PROGRESS_FILE'
+mpirun -np $PROCS $HYPHY LIBPATH=$HYPHY_PATH absrel --alignment $FN --tree $TREE_FN --code $GENETIC_CODE --branches FG --output $RESULTS_FN ENV="TOLERATE_NUMERICAL_ERRORS=1;" >> $PROGRESS_FILE
diff --git a/app/fel/fel.js b/app/fel/fel.js
@@ -26,6 +26,7 @@ var fel = function(socket, stream, params) {
   self.genetic_code = code[self.params.msa[0].gencodeid + 1];
   self.nwk_tree = self.params.analysis.tagged_nwk_tree;
   self.rate_variation = self.params.analysis.ds_variation == 1 ? "Yes" : "No";
+  self.ci = self.params.analysis.ci == true ? "Yes" : "No";
 
   // parameter-derived attributes
   self.fn = __dirname + "/output/" + self.id;
@@ -66,6 +67,8 @@ var fel = function(socket, stream, params) {
       self.type +
       ",rate_variation=" +
       self.rate_variation +
+      ",ci=" +
+      self.ci +
       ",cwd=" +
       __dirname +
       ",msaid=" +

diff --git a/app/fel/fel.sh b/app/fel/fel.sh
@@ -12,6 +12,7 @@ TREE_FN=$tree_fn
 STATUS_FILE=$sfn
 PROGRESS_FILE=$pfn
 BOOTSTRAP=$bootstrap
+CI=$ci
 RESAMPLE=$resample
 RESULTS_FN=$rfn
 GENETIC_CODE=$genetic_code
@@ -29,11 +30,11 @@ trap 'echo "Error" > $STATUS_FILE; exit 1' ERR
 
 if [ $BOOTSTRAP = "true" ]
 then
-  echo "mpirun -np $PROCS $HYPHY LIBPATH=$HYPHY_PATH $FEL --alignment $FN --tree $TREE_FN --code $GENETIC_CODE --branches FG --srv $RATE_VARIATION --output $RESULTS_FILE --resample $RESAMPLE >> $PROGRESS_FILE"
-  mpirun -np $PROCS $HYPHY LIBPATH=$HYPHY_PATH $FEL --alignment $FN --tree $TREE_FN --code $GENETIC_CODE --branches FG --srv $RATE_VARIATION --output $RESULTS_FILE --resample $RESAMPLE >> $PROGRESS_FILE
+  echo "mpirun -np $PROCS $HYPHY LIBPATH=$HYPHY_PATH $FEL --alignment $FN --tree $TREE_FN --code $GENETIC_CODE --branches FG --srv $RATE_VARIATION --output $RESULTS_FILE --resample $RESAMPLE --ci $CI >> $PROGRESS_FILE"
+  mpirun -np $PROCS $HYPHY LIBPATH=$HYPHY_PATH $FEL --alignment $FN --tree $TREE_FN --code $GENETIC_CODE --branches FG --srv $RATE_VARIATION --output $RESULTS_FILE --resample $RESAMPLE --ci $CI >> $PROGRESS_FILE
 else
-  echo "$HYPHY LIBPATH=$HYPHY_PATH $BUSTED --code $GENETIC_CODE --alignment $FN --tree $TREE_FN --branches "All" --rates $omegaClasses --syn-rates $synRateClasses --srv $synRateVariation --grid-size $initialPointsInLikelihood --starting-points $initialGuesses --kill-zero-lengths $KZERO --output $RESULTS_FILE --save-fit /dev/null"
-  $HYPHY LIBPATH=$HYPHY_PATH $BUSTED --code $GENETIC_CODE --alignment $FN --tree $TREE_FN --branches "All" --rates $omegaClasses --syn-rates $synRateClasses --srv $synRateVariation --grid-size $initialPointsInLikelihood --starting-points $initialGuesses --kill-zero-lengths $KZERO --output $RESULTS_FILE --save-fit /dev/null > $PROGRESS_FILE
+  echo "$HYPHY LIBPATH=$HYPHY_PATH $BUSTED --code $GENETIC_CODE --alignment $FN --tree $TREE_FN --branches "All" --rates $omegaClasses --syn-rates $synRateClasses --srv $synRateVariation --grid-size $initialPointsInLikelihood --starting-points $initialGuesses --kill-zero-lengths $KZERO --output $RESULTS_FILE --save-fit /dev/null --ci $CI"
+  $HYPHY LIBPATH=$HYPHY_PATH $BUSTED --code $GENETIC_CODE --alignment $FN --tree $TREE_FN --branches "All" --rates $omegaClasses --syn-rates $synRateClasses --srv $synRateVariation --grid-size $initialPointsInLikelihood --starting-points $initialGuesses --kill-zero-lengths $KZERO --output $RESULTS_FILE --save-fit /dev/null --ci $CI > $PROGRESS_FILE
 fi
 
 echo "Completed" > $STATUS_FILE