bppsuite: fixed random seed usage

lib/bppsuite.ml

@@ -56,16 +56,16 @@ let conf_file_bppseqgen_multi_profiles ~tree ~profile_f ~ne_c ~ne_a ~config ~nb_
       assign "NE_1"            (float ne_a) ;
       assign "NE_C"            (float ne_c) ;
       assign "NE_T"            (float ne_c) ;
-      assign "seed"            (int 1) ;
     ]
     @ config
   )
 
-let bppseqgen_multi_profiles_script ~config  ~out ~profile_c =
+let bppseqgen_multi_profiles_script ~config  ~out ~profile_c ~seed =
   let vars = [
     "FINAL_OUT", ident out ;
     "PARAM", config ;
     "PROFILE_C", ident profile_c ;
+    "RANDOM", int seed ;
   ]
   in
   bash_script vars {|
@@ -77,7 +77,9 @@ let bppseqgen_multi_profiles_script ~config  ~out ~profile_c =
     COL_M1=`echo $line | cut -f 1 -d " "`
     COL_M2=`echo $line | cut -f 2 -d " "`
     echo "i: $i" "COL_M1: $COL_M1" "COL_M2: $COL_M2"
-    bppseqgen param=$PARAM i=$i COL_M1=$COL_M1 COL_M2=$COL_M2 output.sequence.file=out_int_"$i".fa
+    SEED=${RANDOM}
+    echo seed=${SEED}
+    bppseqgen param=$PARAM i=$i COL_M1=$COL_M1 COL_M2=$COL_M2 output.sequence.file=out_int_"$i".fa seed=${SEED}
   done < "$PROFILE_C"
 
   cp $PROFILE_C $FINAL_OUT.info
@@ -88,7 +90,7 @@ let bppseqgen_multi_profiles_script ~config  ~out ~profile_c =
 |}
 
 
-let bppseqgen_multi_profiles ?(descr="") ~profile_f ~profile_c ~nb_sites ~tree ~config ~ne_c ~ne_a : bppseqgen_multi_profiles directory workflow =
+let bppseqgen_multi_profiles ?(descr="") ~profile_f ~profile_c ~nb_sites ~tree ~config ~ne_c ~ne_a ~seed : 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
@@ -106,7 +108,7 @@ let bppseqgen_multi_profiles ?(descr="") ~profile_f ~profile_c ~nb_sites ~tree ~
         dep profile_c
         ];*)
         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  ~out  ~profile_c:profile_c_ok))];
+        cmd "bash" [(file_dump (bppseqgen_multi_profiles_script ~config:config_f  ~out  ~profile_c:profile_c_ok ~seed))];
       ]
     )
   ]

lib/bppsuite.mli

@@ -20,6 +20,7 @@ val bppseqgen_multi_profiles :
   config:Bistro.Template.t list ->
   ne_c: float ->
   ne_a: float ->
+  seed:int ->
   bppseqgen_multi_profiles directory workflow
 
 val bppseqgen_multi_profiles_get_fa :

lib/pipeline.ml

@@ -110,7 +110,7 @@ let derive_from_model ~model ~input_tree ~tree_dataset ~tree_prefix ~profile ~pr
   in
   let profile_f = profile.profile_f in
   let profile_c = profile.profile_c in
-  let run_fna = Bppsuite.bppseqgen_multi_profiles ~descr ~nb_sites ~tree ~config:config_p ~profile_f ~profile_c ~ne_c ~ne_a in
+  let run_fna = Bppsuite.bppseqgen_multi_profiles ~descr ~nb_sites ~tree ~config:config_p ~profile_f ~profile_c ~ne_c ~ne_a ~seed:(Random.int Int.max_value) 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