Merge pull request #326 from veg/new-analysis-options

veg/datamonkey-js#752 -- adding new fel options
veg · Dec 10, 2024 · a2f8388 · a2f8388
2 parents 4f9c490 + 7d4c671
commit a2f8388
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Showing 4 changed files with 77 additions and 57 deletions.
diff --git a/app/fel/fel.js b/app/fel/fel.js
@@ -5,14 +5,19 @@ var config = require("../../config.json"),
   fs = require("fs"),
   path = require("path");
 
-var fel = function(socket, stream, params) {
+var fel = function (socket, stream, params) {
   var self = this;
   self.socket = socket;
   self.stream = stream;
   self.params = params;
 
   // object specific attributes
   self.type = "fel";
+
+  // New attributes for multiple hits and site multihit
+  self.multiple_hits = self.params.analysis.multiple_hits || "None"; // e.g., [Double, Double+Triple, None]
+  self.site_multihit = self.params.analysis.site_multihit || "Estimate"; // e.g., [Estimate, Global]
+
   self.qsub_script_name = "fel.sh";
   self.qsub_script = __dirname + "/" + self.qsub_script_name;
 
@@ -38,52 +43,56 @@ var fel = function(socket, stream, params) {
   self.tree_fn = self.fn + ".tre";
 
   self.qsub_params = [
-    "-l walltime=" + 
-    config.fel_walltime + 
-    ",nodes=1:ppn=" + 
+    "-l walltime=" +
+    config.fel_walltime +
+    ",nodes=1:ppn=" +
     config.fel_procs,
     "-q",
     config.qsub_queue,
     "-v",
     "fn=" +
-      self.fn +
-      ",tree_fn=" +
-      self.tree_fn +
-      ",sfn=" +
-      self.status_fn +
-      ",pfn=" +
-      self.progress_fn +
-      ",rfn=" +
-      self.results_short_fn +
-      ",treemode=" +
-      self.treemode +
-      ",bootstrap=" +
-      self.bootstrap +
-      ",resample=" +
-      self.resample+
-      ",genetic_code=" +
-      self.genetic_code +
-      ",analysis_type=" +
-      self.type +
-      ",rate_variation=" +
-      self.rate_variation +
-      ",ci=" +
-      self.ci +
-      ",cwd=" +
-      __dirname +
-      ",msaid=" +
-      self.msaid +
-      ",procs=" +
-      config.fel_procs,
+    self.fn +
+    ",tree_fn=" +
+    self.tree_fn +
+    ",sfn=" +
+    self.status_fn +
+    ",pfn=" +
+    self.progress_fn +
+    ",rfn=" +
+    self.results_short_fn +
+    ",treemode=" +
+    self.treemode +
+    ",bootstrap=" +
+    self.bootstrap +
+    ",resample=" +
+    self.resample +
+    ",genetic_code=" +
+    self.genetic_code +
+    ",analysis_type=" +
+    self.type +
+    ",rate_variation=" +
+    self.rate_variation +
+    ",ci=" +
+    self.ci +
+    ",cwd=" +
+    __dirname +
+    ",msaid=" +
+    self.msaid +
+    ",procs=" +
+    config.fel_procs +
+    ",multiple_hits=" +
+    self.multiple_hits +
+    ",site_multihit=" +
+    self.site_multihit,
     "-o",
     self.output_dir,
     "-e",
     self.output_dir,
-    self.qsub_script
+    self.qsub_script,
   ];
 
   // Write tree to a file
-  fs.writeFile(self.tree_fn, self.nwk_tree, function(err) {
+  fs.writeFile(self.tree_fn, self.nwk_tree, function (err) {
     if (err) throw err;
   });
 

diff --git a/app/fel/fel.sh b/app/fel/fel.sh
@@ -17,6 +17,8 @@ RESAMPLE=$resample
 RESULTS_FN=$rfn
 GENETIC_CODE=$genetic_code
 RATE_VARIATION=$rate_variation
+MULTIPLE_HITS=$multiple_hits
+SITE_MULTIHIT=$site_multihit
 PROCS=$procs
 
 HYPHY=$CWD/../../.hyphy/HYPHYMPI
@@ -30,12 +32,11 @@ 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 --ci $CI >> $PROGRESS_FILE"
-  mpirun -np $PROCS $HYPHY LIBPATH=$HYPHY_PATH ENV="TOLERATE_NUMERICAL_ERRORS=1;" $FEL --alignment $FN --tree $TREE_FN --code $GENETIC_CODE --branches FG --srv $RATE_VARIATION --output $RESULTS_FILE --resample $RESAMPLE --ci $CI >> $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 --multiple-hits $MULTIPLE_HITS --site-multihit $SITE_MULTIHIT >> $PROGRESS_FILE"
+  mpirun -np $PROCS $HYPHY LIBPATH=$HYPHY_PATH ENV="TOLERATE_NUMERICAL_ERRORS=1;" $FEL --alignment $FN --tree $TREE_FN --code $GENETIC_CODE --branches FG --srv $RATE_VARIATION --output $RESULTS_FILE --resample $RESAMPLE --ci $CI --multiple-hits $MULTIPLE_HITS --site-multihit $SITE_MULTIHIT >> $PROGRESS_FILE
 else
-  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 --ci $CI >> $PROGRESS_FILE"
-  mpirun -np $PROCS $HYPHY LIBPATH=$HYPHY_PATH ENV="TOLERATE_NUMERICAL_ERRORS=1;" $FEL --alignment $FN --tree $TREE_FN --code $GENETIC_CODE --branches FG --srv $RATE_VARIATION --output $RESULTS_FILE --ci $CI >> $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 --ci $CI --multiple-hits $MULTIPLE_HITS --site-multihit $SITE_MULTIHIT >> $PROGRESS_FILE"
+  mpirun -np $PROCS $HYPHY LIBPATH=$HYPHY_PATH ENV="TOLERATE_NUMERICAL_ERRORS=1;" $FEL --alignment $FN --tree $TREE_FN --code $GENETIC_CODE --branches FG --srv $RATE_VARIATION --output $RESULTS_FILE --ci $CI --multiple-hits $MULTIPLE_HITS --site-multihit $SITE_MULTIHIT >> $PROGRESS_FILE
 fi
 
 echo "Completed" > $STATUS_FILE
-
diff --git a/app/meme/meme.js b/app/meme/meme.js
@@ -5,7 +5,7 @@ var config = require("../../config.json"),
   fs = require("fs"),
   path = require("path");
 
-var meme = function(socket, stream, params) {
+var meme = function (socket, stream, params) {
   var self = this;
   self.socket = socket;
   self.stream = stream;
@@ -26,6 +26,12 @@ var meme = function(socket, stream, params) {
   self.bootstrap = self.params.analysis.bootstrap;
   self.resample = self.params.analysis.resample;
 
+  // New attributes for multiple hits and site multihit
+  self.multiple_hits = self.params.analysis.multiple_hits || "None"; // e.g., [Double, Double+Triple, None]
+  self.site_multihit = self.params.analysis.site_multihit || "Estimate"; // e.g., [Estimate, Global]
+  self.rates = self.params.analysis.rates || 2;
+  self.impute_states = self.params.analysis.impute_states || "No";
+
   // parameter-derived attributes
   self.fn = __dirname + "/output/" + self.id;
   self.output_dir = path.dirname(self.fn);
@@ -36,10 +42,7 @@ var meme = function(socket, stream, params) {
   self.tree_fn = self.fn + ".tre";
 
   self.qsub_params = [
-    "-l walltime=" + 
-    config.meme_walltime + 
-    ",nodes=1:ppn=" + 
-    config.meme_procs,
+    "-l walltime=" + config.meme_walltime + ",nodes=1:ppn=" + config.meme_procs,
     "-q",
     config.qsub_queue,
     "-v",
@@ -59,6 +62,16 @@ var meme = function(socket, stream, params) {
       self.bootstrap +
       ",resample=" +
       self.resample +
+      ",multiple_hits=" +
+      self.multiple_hits +
+      ",site_multihit=" +
+      self.site_multihit +
+      ",rates=" +
+      self.rates +
+      ",resample=" +
+      self.resample +
+      ",impute_states=" +
+      self.impute_states +
       ",genetic_code=" +
       self.genetic_code +
       ",analysis_type=" +
@@ -73,11 +86,11 @@ var meme = function(socket, stream, params) {
     self.output_dir,
     "-e",
     self.output_dir,
-    self.qsub_script
+    self.qsub_script,
   ];
 
   // Write tree to a file
-  fs.writeFile(self.tree_fn, self.nj, function(err) {
+  fs.writeFile(self.tree_fn, self.nj, function (err) {
     if (err) throw err;
   });
 

diff --git a/app/meme/meme.sh b/app/meme/meme.sh
@@ -11,8 +11,11 @@ CWD=$cwd
 TREE_FN=$tree_fn
 STATUS_FILE=$sfn
 PROGRESS_FILE=$pfn
-#BOOTSTRAP=$bootstrap
-#RESAMPLE=$resample
+MULTIPLE_HITS="$multiple_hits"
+SITE_MULTIHIT="$site_multihit"
+RATES="$rates"
+RESAMPLE="$resample"
+IMPUTE_STATES="$impute_states"
 RESULTS_FN=$fn.MEME.json
 GENETIC_CODE=$genetic_code
 PROCS=$procs
@@ -24,13 +27,7 @@ export HYPHY_PATH=$HYPHY_PATH
 
 trap 'echo "Error" > $STATUS_FILE; exit 1' ERR
 
-#if [ $BOOTSTRAP = "true" ]
-#then
-echo "mpirun -np $PROCS $HYPHY LIBPATH=$HYPHY_PATH   meme --alignment $FN --tree $TREE_FN --code $GENETIC_CODE >> $PROGRESS_FILE"
-mpirun -np $PROCS $HYPHY LIBPATH=$HYPHY_PATH ENV="TOLERATE_NUMERICAL_ERRORS=1;"  meme --alignment $FN --tree $TREE_FN --code $GENETIC_CODE >> $PROGRESS_FILE
-#else
-#  echo "mpirun -np $PROCS $HYPHY LIBPATH=$HYPHY_PATH   meme --alignment $FN --tree $TREE_FN --code $GENETIC_CODE >> $PROGRESS_FILE"
-#  mpirun -np $PROCS $HYPHY LIBPATH=$HYPHY_PATH ENV="TOLERATE_NUMERICAL_ERRORS=1;"  meme --alignment $FN --tree $TREE_FN --code $GENETIC_CODE >> $PROGRESS_FILE
-#fi
+echo "mpirun -np $PROCS $HYPHY LIBPATH=$HYPHY_PATH meme --alignment $FN --tree $TREE_FN --code $GENETIC_CODE --multiple-hits $MULTIPLE_HITS --site-multihit $SITE_MULTIHIT --rates $RATES --resample $RESAMPLE --impute-states $IMPUTE_STATES >> $PROGRESS_FILE"
+mpirun -np $PROCS $HYPHY LIBPATH=$HYPHY_PATH ENV="TOLERATE_NUMERICAL_ERRORS=1;" meme --alignment $FN --tree $TREE_FN --code $GENETIC_CODE --multiple-hits $MULTIPLE_HITS --site-multihit $SITE_MULTIHIT --rates $RATES --resample $RESAMPLE --impute-states $IMPUTE_STATES >> $PROGRESS_FILE
 
 echo "Completed" > $STATUS_FILE