Commit 5dae0406 authored by Philippe Veber's avatar Philippe Veber
Browse files

further refactoring bppseqgen

parent e96940c6
......@@ -130,13 +130,14 @@ rate_distribution=Constant()
|}
let multi_profiles ?(descr="") ~profile_f ~profile_c ~tree ~tree_dataset ~hypothesis ~ne_c ~ne_a ~seed =
let multi_profiles ?(descr="") ~profile_f ~profile_c ~tree_dataset ~hypothesis ~ne_c ~ne_a ~seed =
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
(* let profile_c_ok = tmp // "profiles_c.tsv" in *)
let profile_c_ok = dep profile_c in
let out = dest // "seq.fa" in
let tree = Tree_dataset.tree tree_dataset `Simulation in
let nodes = Tree_dataset.nodes tree_dataset hypothesis in
workflow ~descr:("bppsuite.bppseqgen" ^ descr) [
docker env (
......
......@@ -7,7 +7,6 @@ module Bppseqgen : sig
?descr : string ->
profile_f: text_file workflow ->
profile_c: text_file workflow ->
tree:nhx workflow ->
tree_dataset:[`tree_dataset] directory workflow ->
hypothesis:Convergence_hypothesis.t ->
ne_c: float ->
......
......@@ -53,7 +53,6 @@ let calc_fixed_seed ~(str:string) (seed:int) : int =
let derive_from_model ~model ~input_tree ~tree_dataset ~tree_prefix ~profile ~preview ~ns ~seed =
let model_prefix = Convergence_hypothesis.string_of_model model in
let tree = Tree_dataset.tree tree_dataset `Simulation in
let descr = "."^model_prefix^"."^tree_prefix in
(* only 1 profile or 1 couple of profiles*)
(*let config = Convergence_hypothesis.bpp_config nodes model in
......@@ -67,7 +66,7 @@ let derive_from_model ~model ~input_tree ~tree_dataset ~tree_prefix ~profile ~pr
let profile_c = profile.profile_c in
(*let seed = Random.int Int.max_value in*)
let seed = calc_fixed_seed ~str:descr seed in
let run_fna = Bppsuite.Bppseqgen.multi_profiles ~descr ~tree ~tree_dataset ~hypothesis:model ~profile_f ~profile_c ~ne_c ~ne_a ~seed in
let run_fna = Bppsuite.Bppseqgen.multi_profiles ~descr ~tree_dataset ~hypothesis:model ~profile_f ~profile_c ~ne_c ~ne_a ~seed in
let fna = Bppsuite.Bppseqgen.alignment run_fna in
let fna_infos = Some (Bppsuite.Bppseqgen.info run_fna) in
......
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