Commit 5598b501 authored by LANORE Vincent's avatar LANORE Vincent
Browse files

Added a realata command

parent d3e25255
......@@ -4,6 +4,7 @@ open Reviewphiltrans
let () =
Command.group ~summary:"Reviewphiltrans" [
"validation", Pipeline.validation_command ;
"realdata", Pipeline.realdata_command ;
"alistats", Alistats.command ;
]
|> Command.run
......@@ -108,17 +108,17 @@ let plot_merge_results ?t_choices ~plot_all_sites ~(res_by_tools:result list) ~t
in
let default_t = List.map res_by_tools ~f:(fun res ->
let opt = match res with
| `Pcoc _ -> "PCOC:1,PC:1,OC:1"
| `Pcoc_gamma _ -> "PCOC_gamma:1,PC_gamma:1,OC_gamma:1"
| `Pcoc_C60 _ -> "PCOC_C60:1,PC_C60:1,OC_C60:1"
| `Diffsel _ -> "Diffsel_mean:0.11,Diffsel_max:1"
| `Identical_LG _ -> "Identical_LG08:1"
| `Identical_WAG _ -> "Identical_WAG01:1"
| `Topological_LG _ -> "Topological_LG08:1"
| `Topological_WAG _ -> "Topological_WAG01:1"
| `Tdg09 _ -> "Tdg09_1MinusFDR:1,Tdg09_prob_post:1,Tdg09_1MinusLRT:1"
| `Multinomial _ -> "Mutinomial_1MinusLRT:1"
| `Msd _ -> "Msd_0.05_1MinusP:1"
| `Pcoc _ -> "PCOC:0,PC:0,OC:0"
| `Pcoc_gamma _ -> "PCOC_gamma:0,PC_gamma:0,OC_gamma:0"
| `Pcoc_C60 _ -> "PCOC_C60:0,PC_C60:0,OC_C60:0"
| `Diffsel _ -> "Diffsel_mean:0,Diffsel_max:0"
| `Identical_LG _ -> "Identical_LG08:0"
| `Identical_WAG _ -> "Identical_WAG01:0"
| `Topological_LG _ -> "Topological_LG08:0"
| `Topological_WAG _ -> "Topological_WAG01:0"
| `Tdg09 _ -> "Tdg09_1MinusFDR:0,Tdg09_prob_post:0,Tdg09_1MinusLRT:0"
| `Multinomial _ -> "Mutinomial_1MinusLRT:0"
| `Msd _ -> "Msd_0.05_1MinusP:0"
in
string opt
......
......@@ -16,7 +16,7 @@ let repo ~preview dataset_l =
let repo_ready_data = Ready_dataset.repo dataset.dataset in
let repo_raw_data = Raw_dataset.repo ~prefix:model_prefix (Ready_dataset.to_raw dataset.dataset) in
List.concat [
Repo.shift "minimal" (Repo.shift (tree_prefix ^"_"^model_prefix) repo_raw_data);
Repo.shift "minimal" (Repo.shift (tree_prefix ^ "_" ^ model_prefix) repo_raw_data);
Repo.shift "debug" repo_ready_data;
]
|> Repo.shift "dataset"
......
......@@ -205,13 +205,13 @@ let derive_from_dataset ~dataset ~preview ~use_diffsel ~use_c60=
`Pcoc;
] @ List.map [0.05] (fun x -> `Msd x)) ;
(* if preview then *)
[`Tdg09;]
[`Tdg09;]
(* else
[ `Tdg09;
[ `Tdg09;
`Pcoc_gamma;
`Identical_WAG;
`Topological_WAG;
] *)
] *)
;
if use_diffsel then
[`Diffsel]
......@@ -369,3 +369,46 @@ let validation_command =
in
validation_main ~outdir ?indir ?ns ?np ?mem ~preview ~use_diffsel ~use_c60 ~no_Ne ~ne_test ~no_HaPC ~tree_dir ~profile_fn ~use_concat ~only_simu ~add_indels ?seed
]
let realdata_main ~outdir ~indir ~preview ~use_diffsel ~use_c60 ?(np = 2) ?(mem = 2) ?(seed = Random.int Int.max_value) () =
(* seed-related stuff *)
printf "Global seed: %i\n" seed;
Out_channel.write_all "global.seed" ~data:(string_of_int seed);
Random.init seed ;
(* real trees *)
let dataset_l = parse_input_data ~seed indir in
let dataset_results_l = derive_det ~dataset_l ~preview ~use_diffsel ~use_c60 in
let repo_real_trees = [
Dataset.repo dataset_l ~preview ;
repo_of_dataset_results_l ~dataset_results_l ;
] |> List.concat (* list of repos *)
in
let repo = Repo.shift "Real_datasets" repo_real_trees in
Repo.build ~outdir ~np ~mem:(`GB mem) ~logger repo
(* time_logger#report sim_repo_l#dataset_results (Filename.concat outdir ("elapsed_time_" ^ (Unix.time () |> int_of_float |> string_of_int) ^ ".tsv")) *)
let realdata_command =
let open Command.Let_syntax in
Command.basic
~summary:"Run simulation pipeline on real data only"
[%map_open
let outdir =
flag "--outdir" (required string) ~doc:"PATH Output directory"
and indir =
flag "--indir" (required string) ~doc:"PATH Input directory"
and preview =
flag "--preview-mode" no_arg ~doc:" Preview mode"
and use_diffsel =
flag "--diffsel" no_arg ~doc:" use the diffsel method (very slow)."
and use_c60 =
flag "--c60" no_arg ~doc:" use the pcoc c60 method (slow)."
and np =
flag "--np" (optional int) ~doc:"INT Number of available processors"
and mem =
flag "--mem" (optional int) ~doc:"INT Available memory (in GB)"
and seed =
flag "--seed" (optional int) ~doc:"INT Global seed"
in
realdata_main ~outdir ~indir ?np ?mem ~preview ~use_diffsel ~use_c60 ?seed
]
\ No newline at end of file
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