Merge pull request #745 from veg/beta

2.3.11 - rc
veg · Feb 12, 2018 · edbca67 · edbca67
2 parents c5b6418 + 4bc8eae
commit edbca67
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Showing 12 changed files with 239 additions and 223 deletions.
diff --git a/res/TemplateBatchFiles/LEISR.bf b/res/TemplateBatchFiles/LEISR.bf
@@ -32,7 +32,7 @@ leisr.analysis_description = {
     terms.io.info: "LEISR (Likelihood Estimation of Individual Site Rates) infer relative amino-acid or nucleotide rates from a fixed nucleotide or amino-acid alignment and tree, with possibility for partitions. Relative site-specific substitution rates are
     inferred by first optimizing alignment-wide branch lengths, and then inferring a site-specific uniform tree scaler.",
     terms.io.version: "0.4",
-    terms.io.reference: "Spielman, S.J. and Kosakovsky Pond, S.L. Relative evolutionary rate inference in HyPhy with LEISR. bioRxiv. https://doi.org/10.1101/206011. (2017); Pupko, T., Bell, R. E., Mayrose, I., Glaser, F. & Ben-Tal, N. Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues. Bioinformatics 18, S71–S77 (2002).",
+    terms.io.reference: "Spielman, S.J. and Kosakovsky Pond, S.L. (2018). Relative evolutionary rate inference in HyPhy with PeerJ 6:e4339. DOI 10.7717/peerj.4339 ; Pupko, T., Bell, R. E., Mayrose, I., Glaser, F. & Ben-Tal, N. Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues. Bioinformatics 18, S71–S77 (2002).",
     terms.io.authors: "Sergei L Kosakovsky Pond and Stephanie J Spielman",
     terms.io.contact: "{spond,stephanie.spielman}@temple.edu"
 };

diff --git a/res/TemplateBatchFiles/SelectionAnalyses/MEME.bf b/res/TemplateBatchFiles/SelectionAnalyses/MEME.bf
@@ -459,13 +459,12 @@ lfunction meme.handle_a_site (lf_fel, lf_bsrel, filter_data, partition_index, pa
 
     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);
+    //console.log ("Optimizing FEL for pattern " + pattern_info);
     io.SpoolLF (lf_fel, "/tmp/meme.debug", "FEL");    
     Optimize (results, ^lf_fel);
 
@@ -481,7 +480,7 @@ 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);
+    //console.log ("Optimizing MEME for pattern " + pattern_info);
     io.SpoolLF (lf_bsrel, "/tmp/meme.debug", "MEME");
     Optimize (results, ^lf_bsrel);
 

diff --git a/res/TemplateBatchFiles/SelectionAnalyses/RELAX.bf b/res/TemplateBatchFiles/SelectionAnalyses/RELAX.bf
@@ -1,3 +1,4 @@
+
 RequireVersion("2.3.3");
 
 LoadFunctionLibrary("libv3/all-terms.bf"); // must be loaded before CF3x4
@@ -335,7 +336,7 @@ if (relax.has_unclassified) {
 
     relax.model_object_map ["relax.unclassified"] = relax.unclassified.bsrel_model;
     relax.model_map ["relax.unclassified"] = utility.Filter (relax.selected_branches[0], '_value_', '_value_ == relax.unclassified_branches_name');
-    models.BindGlobalParameters ({"0" : relax.unclassified.bsrel_model, "1" : relax.reference.bsrel_model}, terms.nucleotideRate("[ACGT]","[ACGT]"));
+    models.BindGlobalParameters ({"0" : relax.test.bsrel_model, "1" : relax.unclassified.bsrel_model}, terms.nucleotideRate("[ACGT]","[ACGT]"));
 }
 
 relax.alternative_model.fit =  estimators.FitLF (relax.filter_names, relax.trees, { "0" : relax.model_map}, relax.general_descriptive.fit, relax.model_object_map, {terms.run_options.retain_lf_object: TRUE});