add 2 hypothesis based on different Ne, H0_BigNeInSmallNe and H0_SmallNeInBigNe

lib/bppsuite.ml

@@ -46,13 +46,13 @@ let bppseqgen ?(descr="") ~nb_sites ~tree ~config : nucleotide_fasta workflow =
     )
   ] / selector ["seq.fa"]
 
-let conf_file_bppseqgen_multi_profiles ~tree ~profile_f ~ne_c ~config ~nb_sites_per_profile =
+let conf_file_bppseqgen_multi_profiles ~tree ~profile_f ~ne_c ~ne_a ~config ~nb_sites_per_profile =
   seq ~sep:"\n" (
     [
       assign "input.tree.file" (dep tree) ;
       assign "PROFILE_F" (dep profile_f) ;
       assign "number_of_sites" (int nb_sites_per_profile) ;
-      assign "NE_1"            (int 1     ) ;
+      assign "NE_1"            (float ne_a) ;
       assign "NE_C"            (float ne_c) ;
       assign "NE_T"            (float ne_c) ;
     ]
@@ -91,7 +91,7 @@ let bppseqgen_multi_profiles_script ~config ~nb_combis  ~out ~profile_f =
 |}
 
 
-let bppseqgen_multi_profiles ?(descr="") ~profile_f ~nb_sites ~tree ~config ~ne_c : bppseqgen_multi_profiles directory workflow =
+let bppseqgen_multi_profiles ?(descr="") ~profile_f ~nb_sites ~tree ~config ~ne_c ~ne_a : bppseqgen_multi_profiles directory workflow =
   let nb_sites_per_profile = 1 in
   let nb_combis = Pervasives.(nb_sites / nb_sites_per_profile) in
   let config_f = dest // "config.bpp" in
@@ -102,7 +102,7 @@ let bppseqgen_multi_profiles ?(descr="") ~profile_f ~nb_sites ~tree ~config ~ne_
         mkdir_p dest;
         mkdir_p tmp;
         cd tmp;
-        cmd "cat" ~stdout:config_f [(file_dump (conf_file_bppseqgen_multi_profiles ~tree ~profile_f ~config ~ne_c ~nb_sites_per_profile))];
+        cmd "cat" ~stdout:config_f [(file_dump (conf_file_bppseqgen_multi_profiles ~tree ~profile_f ~config ~ne_c ~ne_a ~nb_sites_per_profile))];
         cmd "bash" [(file_dump (bppseqgen_multi_profiles_script ~config:config_f ~nb_combis ~out ~profile_f))];
       ]
     )

lib/bppsuite.mli

@@ -18,6 +18,7 @@ val bppseqgen_multi_profiles :
   tree:nhx workflow ->
   config:Bistro.Template.t list ->
   ne_c: float ->
+  ne_a: float ->
   bppseqgen_multi_profiles directory workflow
 
 val bppseqgen_multi_profiles_get_fa :

lib/convergence_hypothesis.ml

@@ -8,6 +8,8 @@ type t =
   | HaPCOC
   | H0_NeSmall
   | H0_NeVerySmall
+  | H0_BigNeInSmallNe
+  | H0_SmallNeInBigNe
   | HaPCOC_NeSmall
   | HaPC_NeSmall
   | H0_NeBig
@@ -20,6 +22,8 @@ let string_of_model m = match m with
   | HaPCOC           -> "HaPCOC"
   | H0_NeSmall       -> "H0_NeSmall"
   | H0_NeVerySmall   -> "H0_NeVerySmall"
+  | H0_BigNeInSmallNe -> "H0_BigNeInSmallNe"
+  | H0_SmallNeInBigNe -> "H0_SmallNeInBigNe"
   | HaPCOC_NeSmall   -> "HaPCOC_NeSmall"
   | HaPC_NeSmall     -> "HaPC_NeSmall"
   | H0_NeBig         -> "H0_NeBig"
@@ -86,6 +90,8 @@ let bpp_config_F nodes hyp = [
   | HaPCOC              -> bpp_config_HaPCOC_F
   | H0_NeSmall          -> bpp_config_H0_F_Ne
   | H0_NeVerySmall      -> bpp_config_H0_F_Ne
+  | H0_BigNeInSmallNe   -> bpp_config_H0_F_Ne
+  | H0_SmallNeInBigNe   -> bpp_config_H0_F_Ne
   | HaPC_NeSmall        -> bpp_config_HaPC_F_Ne
   | HaPCOC_NeSmall      -> bpp_config_HaPCOC_F_Ne
   | H0_NeBig            -> bpp_config_H0_F_Ne

lib/pipeline.ml

@@ -64,9 +64,16 @@ let derive_from_model ~model ~input_tree ~tree_dataset ~tree_prefix ~profile_f ~
     | H0_NeBig -> 10.
     | HaPC_NeBig -> 10.
     | HaPCOC_NeBig -> 10.
+    | H0_BigNeInSmallNe -> 10.
+    | H0_SmallNeInBigNe -> 0.1
     | _ -> 1.
   in
-  let run_fna = Bppsuite.bppseqgen_multi_profiles ~descr ~nb_sites ~tree ~config:config_p ~profile_f ~ne_c in
+  let ne_a = match model with
+    | H0_BigNeInSmallNe -> 0.1
+    | H0_SmallNeInBigNe -> 10.
+    | _ -> 1.
+  in
+  let run_fna = Bppsuite.bppseqgen_multi_profiles ~descr ~nb_sites ~tree ~config:config_p ~profile_f ~ne_c ~ne_a in
   let fna = Bppsuite.bppseqgen_multi_profiles_get_fa run_fna in
   let fna_infos = Some (Bppsuite.bppseqgen_multi_profiles_get_info run_fna) in
 
@@ -101,6 +108,8 @@ let derive_from_tree ~tree_dir ~tree ~profile_f ~preview ~use_concat ~ns ~no_Ne
              HaPC_NeSmall    ;
              H0_NeBig        ;
              HaPC_NeBig      ;
+             H0_BigNeInSmallNe;
+             H0_SmallNeInBigNe;
             ]
          )
         ] |> List.concat

lib/tree_dataset.ml

@@ -27,6 +27,8 @@ let nodes dataset (model : Convergence_hypothesis.t) =
     |H0_NeSmall     -> [ "tree.H0_a.node_ids" ]
     |H0_NeVerySmall -> [ "tree.H0_a.node_ids" ]
     |H0_NeBig       -> [ "tree.H0_a.node_ids" ]
+    |H0_BigNeInSmallNe-> [ "tree.H0_a.node_ids" ]
+    |H0_SmallNeInBigNe-> [ "tree.H0_a.node_ids" ]
   )
 
 let tree dataset mode =