Merge pull request #733 from veg/beta

2.3.9-rc
veg · Jan 11, 2018 · dd2474f · dd2474f
2 parents a9fb747 + ec4877d
commit dd2474f
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Showing 21 changed files with 524 additions and 24 deletions.
diff --git a/res/TemplateBatchFiles/LEISR.bf b/res/TemplateBatchFiles/LEISR.bf
@@ -77,7 +77,7 @@ leisr.analysis_type  = io.SelectAnOption ({{leisr.protein_type , "Infer relative
 
 if (leisr.analysis_type ==  leisr.protein_type) {
     leisr.baseline_model  = io.SelectAnOption (models.protein.empirical_models, "Select a protein model:");
-    leisr.generators = models.protein.empirical.default_generators;
+    leisr.generators = models.protein.empirical.plusF_generators;
 }
 else {
 

diff --git a/res/TemplateBatchFiles/SelectionAnalyses/MEME.bf b/res/TemplateBatchFiles/SelectionAnalyses/MEME.bf
@@ -149,6 +149,7 @@ meme.final_partitioned_mg_results = estimators.FitMGREV (meme.filter_names, meme
 }, meme.partitioned_mg_results);
 
 
+//meme.final_partitioned_mg_results = meme.partitioned_mg_results;
 
 
 io.ReportProgressMessageMD("MEME", "codon-refit", "* Log(L) = " + Format(meme.final_partitioned_mg_results[terms.fit.log_likelihood],8,2));
@@ -298,21 +299,20 @@ for (meme.partition_index = 0; meme.partition_index < meme.partition_count; meme
                      ));
 
     __make_filter ("meme.site_filter");
-
     LikelihoodFunction meme.site_likelihood = (meme.site_filter, meme.site_tree_fel);
 
-    __make_filter ("meme.site_filter_bsrel");
 
 
     estimators.ApplyExistingEstimates ("meme.site_likelihood", meme.site_model_mapping, meme.final_partitioned_mg_results,
                                         terms.globals_only);
+
 
-
+    __make_filter ("meme.site_filter_bsrel");
     LikelihoodFunction meme.site_likelihood_bsrel = (meme.site_filter_bsrel, meme.site_tree_bsrel);
 
 
     estimators.ApplyExistingEstimates ("meme.site_likelihood_bsrel", meme.site_model_mapping, meme.final_partitioned_mg_results,
-                                        "globals only");
+                                        terms.globals_only);
 
     meme.queue = mpi.CreateQueue ({terms.mpi.LikelihoodFunctions: {{"meme.site_likelihood","meme.site_likelihood_bsrel"}},
                                    terms.mpi.Models : {{"meme.site.background_fel","meme.site.bsrel"}},
@@ -458,11 +458,15 @@ lfunction meme.handle_a_site (lf_fel, lf_bsrel, filter_data, partition_index, pa
     bsrel_tree_id = (lfInfo["Trees"])[0];
 
     utility.SetEnvVariable ("USE_LAST_RESULTS", TRUE);
+    utility.SetEnvVariable ("ASSUME_REVERSIBLE_MODELS", TRUE);
+    utility.SetEnvVariable ("VERBOSITY_LEVEL", 500);
 
     ^"meme.site_alpha" = 1;
     ^"meme.site_beta_plus"  = 1;
     ^"meme.site_beta_nuisance"  = 1;
 
+    console.log ("Optimizing FEL for pattern " + pattern_info);
+    io.SpoolLF (lf_fel, "/tmp/meme.debug", "FEL");    
     Optimize (results, ^lf_fel);
 
     fel = estimators.ExtractMLEs (lf_fel, model_mapping);
@@ -477,6 +481,8 @@ lfunction meme.handle_a_site (lf_fel, lf_bsrel, filter_data, partition_index, pa
          /* avoid 0/0 by making the denominator non-zero*/
      }
 
+    console.log ("Optimizing MEME for pattern " + pattern_info);
+    io.SpoolLF (lf_bsrel, "/tmp/meme.debug", "MEME");
     Optimize (results, ^lf_bsrel);
 
     alternative = estimators.ExtractMLEs (lf_bsrel, model_mapping);
@@ -554,6 +560,7 @@ lfunction meme.handle_a_site (lf_fel, lf_bsrel, filter_data, partition_index, pa
 
 //----------------------------------------------------------------------------------------
 function meme.report.echo (meme.report.site, meme.report.partition, meme.report.row) {
+
     meme.print_row = None;
     if (meme.report.row [6] <= meme.pvalue) {
         meme.print_row = meme.report.positive_site;

diff --git a/res/TemplateBatchFiles/SelectionAnalyses/RELAX.bf b/res/TemplateBatchFiles/SelectionAnalyses/RELAX.bf
@@ -641,8 +641,7 @@ lfunction relax.select_branches(partition_info) {
 
     tree_for_analysis = (partition_info[0])[utility.getGlobalValue("terms.data.tree")];
     utility.ForEach (tree_for_analysis[utility.getGlobalValue("terms.trees.model_map")], "_value_", "`&available_models`[_value_] += 1");
-    list_models   = utility.Keys   (available_models); // get keys
-    branch_counts = utility.Values (available_models);
+    list_models   = utility.sortStrings(utility.Keys(available_models)); // get keys
     option_count  = Abs (available_models);
 
     io.CheckAssertion("`&option_count` >= 2", "RELAX requires at least one designated set of branches in the tree.");

diff --git a/res/TemplateBatchFiles/libv3/IOFunctions.bf b/res/TemplateBatchFiles/libv3/IOFunctions.bf
@@ -663,6 +663,7 @@ lfunction io.ReadDelimitedFile  (path, separator, has_header) {
         fscanf (path, REWIND, "Lines", data);
    } else {
         fscanf (PROMPT_FOR_FILE, REWIND, "Lines", data);
+        path = utility.getGlobalValue("LAST_FILE_PATH");
    }
    result = {utility.getGlobalValue("terms.io.rows") : {}};
    index = 0;
@@ -674,6 +675,7 @@ lfunction io.ReadDelimitedFile  (path, separator, has_header) {
    for (k = index; k < row_count; k+=1) {
         result [utility.getGlobalValue("terms.io.rows")] + regexp.Split (data[k], separator);
    }
+   result[utility.getGlobalValue("terms.json.file")] = path;
    return result;
 }
 

diff --git a/res/TemplateBatchFiles/libv3/UtilityFunctions.bf b/res/TemplateBatchFiles/libv3/UtilityFunctions.bf
@@ -935,4 +935,28 @@ lfunction utility.CatersianProduct (arguments) {
     return product;
 }
 
+function _sortStringsAux (theKey, theValue)
+{
+	for (_gb_idx2 = 0; _gb_idx2 < theValue; _gb_idx2=_gb_idx2+1)
+	{
+		_gb_sortedStrings [_gb_idx] = theKey;
+		_gb_idx = _gb_idx + 1;
+	}
+	return 0;
+}
+
+function utility.sortStrings (_theList)
+{
+	_gb_dim = Rows (_theList)*Columns (_theList);
+	_toSort = {};
+	for (_gb_idx = 0; _gb_idx < _gb_dim; _gb_idx = _gb_idx + 1)
+	{
+		_toSort[_theList[_gb_idx]] = _toSort[_theList[_gb_idx]]+1;
+	}
+	_gb_sortedStrings = {_gb_dim,1};
+	_gb_idx = 0;
+	_toSort["_sortStringsAux"][""];
+	return _gb_sortedStrings;
+}
+