add option --dnds (calc dn ds dn/ds trees; add option --gt (calc gene trees)

app/reviewphiltrans_app.ml

@@ -16,6 +16,8 @@ let realdata_main ~use_diffsel
                   ~use_topological
                   ~use_identical
                   ~no_use_multinomial
+                  ~calc_dnds
+                  ~calc_gene_trees
                   ~indir ~outdir ~np ~mem () =
   let loggers = [
       Console_logger.create () ;
@@ -37,9 +39,14 @@ let realdata_main ~use_diffsel
       sw use_multinomial `Multinomial ;
     ]
   in
+  let pal  = List.filter_opt [
+    sw calc_dnds `DnDs;
+    sw calc_gene_trees `GeneTree;
+    ]
+  in
   List.concat [
     Repo.shift "Merged_results" (Real_dataset.repo meths rd) ;
-    Repo.shift "PreParsed_Dataset" (Real_dataset.repo_parsed_rd rd);
+    Repo.shift "PreParsed_Dataset" (Real_dataset.repo_parsed_rd pal rd);
     ]
   |> Bistro_utils.Repo.build_main ~outdir ~loggers ?np ?mem
 
@@ -66,10 +73,10 @@ let realdata_command =
         flag "--identical" no_arg ~doc:" use the identical method (fast)."
       and no_use_multinomial =
         flag "--no-multinomial" no_arg ~doc:" not use the multinomial method (very fast so by default)."
-      (* and preview =
-       *   flag "--preview-mode" no_arg ~doc:" Preview mode"
-       * and calc_dnds =
-       *   flag "--dnds" no_arg ~doc:" calculate dn ds dnds trees (slow)."*)
+      and calc_dnds =
+          flag "--dnds" no_arg ~doc:" calculate dn ds dnds trees (slow)."
+      and calc_gene_trees =
+          flag "--gt" no_arg ~doc:" calculate gene trees (slow)."
       and np =
         flag "--np" (optional int) ~doc:"INT Number of available processors"
       and mem =
@@ -82,6 +89,8 @@ let realdata_command =
                     ~use_topological
                     ~use_identical
                     ~no_use_multinomial
+                    ~calc_dnds
+                    ~calc_gene_trees
                     ~indir ~outdir ~np ~mem
     ]
 

lib/detection_pipeline.ml

@@ -17,6 +17,9 @@ module Make(D : Dataset) = struct
   let phylip_nucleotide_alignment d =
     Bppsuite.fna2phy ~fna:(nucleotide_alignment d)
 
+  let gene_tree d =
+    Tree_dataset.raxmlng_fna ~fna:(nucleotide_alignment d) ()
+
   let identical d =
     let tree_sc = Tree_dataset.prepare_sc_tree (tree d) in
     let tree_id = Tree_dataset.prepare_tree_with_node_id (tree d) in
@@ -90,4 +93,12 @@ module Make(D : Dataset) = struct
     let tree = tree d in
     Pcoc.pcoc ~catx_est:ncat ~plot_complete:false ~gamma ~faa ~tree ()
     |> Pcoc.results
+  
+  let dn_ds_dnds_trees d =
+    Testnh.dn_ds_trees_real_data ~fna:(nucleotide_alignment d) ~tree:(tree d) ()
+    
+  let dn_tree d   = (dn_ds_dnds_trees d).dn_tsv
+  let ds_tree d   = (dn_ds_dnds_trees d).ds_tsv
+  let dnds_tree d = (dn_ds_dnds_trees d).dnds_tsv
+    
 end

lib/real_dataset.ml

@@ -17,6 +17,10 @@ type meth =
    `Identical |
    `Diffsel]
 
+type pa =
+  [`DnDs |
+   `GeneTree]
+
 module Family : sig
   type dataset = t
   type t
@@ -92,6 +96,12 @@ let maybe_apply_method meths f m =
     Some (implementation f m)
   else None
 
+let maybe_apply_parralel_analyses pal p =
+  if List.mem pal p ~equal:Poly.equal then
+    true
+  else
+    false
+
 let result_table meths rd =
   let families = families rd in
   List.map families ~f:(fun f ->
@@ -113,13 +123,32 @@ let repo meths rd =
       Bistro_utils.Repo.item [name ^ ".tsv"] table
     )
 
-let repo_parsed_rd rd =
+let repo_parsed_rd pal rd =
   let families = families rd in
   List.map families ~f:(fun f ->
     [
-      Bistro_utils.Repo.item [(Family.name f) ^ ".faa"] (DP.amino_acid_alignment f);
-      Bistro_utils.Repo.item [(Family.name f) ^ ".species_tree.nhx"] (Family.tree f);
-      Bistro_utils.Repo.item [(Family.name f) ^ ".fna"] (Family.nucleotide_alignment f);
-      Bistro_utils.Repo.item [(Family.name f) ^ ".nw"] (DP.gene_tree f);
-    ] |> Repo.shift (Family.name f );
+      [
+          Bistro_utils.Repo.item [(Family.name f) ^ ".faa"] (DP.amino_acid_alignment f);
+          Bistro_utils.Repo.item [(Family.name f) ^ ".species_tree.nhx"] (Family.tree f);
+          Bistro_utils.Repo.item [(Family.name f) ^ ".fna"] (Family.nucleotide_alignment f);
+      ];
+          if (maybe_apply_parralel_analyses pal `GeneTree)
+          then
+          [
+            Bistro_utils.Repo.item [(Family.name f) ^ ".nw"] (DP.gene_tree f);
+          ]
+          else
+          [];
+          if (maybe_apply_parralel_analyses pal `DnDs)
+          then
+          [
+              [ Bistro_utils.Repo.item [(Family.name f) ^ ".dn.tsv"] (DP.dn_tree f);
+                Bistro_utils.Repo.item [(Family.name f) ^ ".ds.tsv"] (DP.ds_tree f);
+                Bistro_utils.Repo.item [(Family.name f) ^ ".dnds.tsv"] (DP.dnds_tree f);
+              ] |> Repo.shift "DnDs"
+          ] |> List.concat
+          else
+          [];
+    ] |> List.concat
+      |> Repo.shift (Family.name f )
   ) |> List.concat

lib/real_dataset.mli

@@ -13,6 +13,10 @@ type meth =
    `Identical |
    `Diffsel]
 
+type pa =
+  [`DnDs |
+   `GeneTree]
+
 val make :
   tree_path:string ->
   alignment_dir_path:string ->
@@ -28,6 +32,7 @@ val repo :
   t -> Bistro_utils.Repo.t
 
 val repo_parsed_rd :
+  pa list ->
   t -> Bistro_utils.Repo.t
 
 module Family : sig

lib/testnh.ml

@@ -236,7 +236,7 @@ let format_dn_ds ~ali_prefix ~(dn_tree:_ workflow) ~(ds_tree:_ workflow): direct
     ]
   ]
 
-let dn_ds_trees_real_data ~ali_prefix ~tree ~fna () : dnds_real=
+let dn_ds_trees_real_data ?(ali_prefix="gene") ~tree ~fna () : dnds_real=
   let run_bppml = bppml_mapnh ~descr:("."^ali_prefix) ~tree  ~fna in
   let dn_tree = Workflow.select run_bppml ["mapping_counts_per_type_dN.dnd"] in
   let ds_tree = Workflow.select run_bppml ["mapping_counts_per_type_dS.dnd"] in