define 2 different models

lib/bppsuite.ml

@@ -10,29 +10,18 @@ let assign k v =
   seq ~sep:"=" [ string k ; v ]
 
 
-let conf_file_bppseqgen ~tree ~nb_sites =
+let conf_file_bppseqgen ~tree ~nb_sites ~config =
   seq ~sep:"\n" [
     assign "input.tree.file" (dep tree) ;
     assign "output.sequence.file" dest ;
-    assign "model1" (string "Codon_AAFit(model=K80, fitness=FromModel(model=LGL08_CAT_C1(nbCat=10)))") ;
     assign "number_of_sites" (int nb_sites) ;
-    string {|alphabet=Codon(letter=DNA)
-             genetic_code = Standard
-             input.tree.format=Nhx
-             output.internal.sequences=no
-           |} ;
-    string {|nonhomogeneous = general
-             nonhomogeneous.number_of_models = 1
-             model1.nodes_id=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17
-             nonhomogeneous.root_freq=Fixed()
-             rate_distribution=Constant()
-           |};
+    string config ;
   ]
 
-let bppseqgen ~nb_sites ~tree : nucleotide_fasta workflow =
+let bppseqgen ~nb_sites ~tree ~config : nucleotide_fasta workflow =
   workflow ~descr:"bppsuite.bppseqgen" [
     cmd "bppseqgen" ~env [
-      assign "param" (file_dump (conf_file_bppseqgen ~tree ~nb_sites)) ;
+      assign "param" (file_dump (conf_file_bppseqgen ~tree ~nb_sites ~config)) ;
     ]
   ]
 

lib/bppsuite.mli

@@ -5,6 +5,7 @@ open File_formats
 val bppseqgen :
   nb_sites:int ->
   tree:nhx workflow ->
+  config: string ->
   nucleotide_fasta workflow
 
 val fna2faa :

lib/models_def.ml

+open Core
+open Bistro_utils
+open Bistro.EDSL
+open Bistro.Std
+open File_formats
+
+
+type model =
+  |H0
+  |Ha
+
+let string_of_model m = match m with
+  | H0 -> "H0"
+  | Ha -> "Ha" 
+
+let define_bpp_config_of_model ~parsed_tree m = match m with
+  | H0 -> {|alphabet=Codon(letter=DNA)
+             genetic_code = Standard
+             input.tree.format=Nhx
+             output.internal.sequences=no
+             nonhomogeneous = general
+             nonhomogeneous.number_of_models = 1
+             model1=Codon_AAFit(model=K80, fitness=FromModel(model=LGL08_CAT_C1(nbCat=10)))
+             model1.nodes_id=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17
+             nonhomogeneous.root_freq=Fixed()
+             rate_distribution=Constant()
+           |};
+  | Ha -> {|alphabet=Codon(letter=DNA)
+             genetic_code = Standard
+             input.tree.format=Nhx
+             output.internal.sequences=no
+             nonhomogeneous = general
+             nonhomogeneous.number_of_models = 2
+             model1=Codon_AAFit(model=K80, fitness=FromModel(model=LGL08_CAT_C1(nbCat=10)))
+             model1.nodes_id=15,1,13,14,4
+             model2=Codon_AAFit(model=K80, fitness=FromModel(model=LGL08_CAT_C7(nbCat=10)))
+             model2.nodes_id=0,2,3,5,6,7,8,9,10,11,12,16,17
+             nonhomogeneous.root_freq=Fixed()
+             rate_distribution=Constant()
+           |};

lib/pipeline.ml

@@ -3,7 +3,7 @@ open Bistro_utils
 open Bistro.EDSL
 open Bistro.Std
 open File_formats
-
+open Models_def
 
 let parse_input_tree ~tree : parsed_input_tree directory workflow =
     workflow ~descr:"utils.parse_input_tree" [
@@ -50,7 +50,8 @@ let repo_of_raw_dataset (raw_dataset:raw_dataset) =
 
 let derive_from_model ~model ~tree ~parsed_tree ~preview =
   let nb_sites = if preview then 10 else 100 in
-  let fna = Bppsuite.bppseqgen ~nb_sites ~tree:(select_out parsed_tree Tree4simu) in
+  let config = define_bpp_config_of_model model in
+  let fna = Bppsuite.bppseqgen ~nb_sites ~tree:(select_out parsed_tree Tree4simu) ~config in
   let faa = Bppsuite.fna2faa ~fna in
   let raw_dataset = { input_tree = tree ; fna} in
   let ready_dataset = { input_tree = tree ; parsed_tree; fna; faa} in
@@ -59,12 +60,13 @@ let derive_from_model ~model ~tree ~parsed_tree ~preview =
   else
     repo_of_raw_dataset raw_dataset
 
+
 let derive_from_tree ~tree_dir ~tree ~preview =
   let tree = input (Filename.concat tree_dir tree) in
   let parsed_tree = parse_input_tree ~tree in
-  let models = ["H0"] in
+  let models = [H0; Ha] in
   List.map models ~f:(fun model ->
-      Repo.shift model (derive_from_model ~model ~tree ~parsed_tree ~preview))
+      Repo.shift (string_of_model model) (derive_from_model ~model ~tree ~parsed_tree ~preview))
   |> List.concat
 
 let derive ~tree_dir ~trees ~preview =