Commit c82b037a authored by Philippe Veber's avatar Philippe Veber
Browse files

msd: added several values for e parameter

parent 4d6ddab5
......@@ -16,7 +16,7 @@ type result = [
| `Topological_WAG of [`topological] directory workflow
| `Tdg09 of [`tdg09] directory workflow
| `Multinomial of [`multinomial] directory workflow
| `Msd of [`msd] directory workflow
| `Msd of [`msd] directory workflow * float
]
let meth_string_of_result = function
......@@ -30,7 +30,7 @@ let meth_string_of_result = function
| `Topological_WAG _ -> "topological_WAG"
| `Tdg09 _ -> "tdg09"
| `Multinomial _ -> "multinomial"
| `Msd _ -> "msd"
| `Msd (_, e) -> sprintf "msd_%f" e
type dataset_res = {
model_prefix : string ;
......@@ -59,7 +59,7 @@ let merge_results ?fna_infos ~res_by_tools () : text_file workflow =
| `Topological_WAG d -> Topological.results d
| `Tdg09 d -> Tamuri.results d
| `Multinomial d -> Multinomial.results d
| `Msd d -> Msd.results d
| `Msd (d, e) -> Msd.results d
in
let opt = match res with
| `Pcoc _ -> string "--pcoc"
......
......@@ -16,7 +16,7 @@ type result = [
| `Topological_WAG of [`topological] directory workflow
| `Tdg09 of [`tdg09] directory workflow
| `Multinomial of [`multinomial] directory workflow
| `Msd of [`msd] directory workflow
| `Msd of [`msd] directory workflow * float
]
val meth_string_of_result : result -> string
......
......@@ -6,7 +6,7 @@ open File_formats
let env = docker_image ~account:"carinerey" ~name:"msd" ~tag:"08082018" ()
let msd ~(faa:aminoacid_fasta workflow) ~(tree_sc:_ workflow) : [`msd] directory workflow =
let msd ~e ~(faa:aminoacid_fasta workflow) ~(tree_sc:_ workflow) : [`msd] directory workflow =
let map_table = tmp // "map.tsv" in
let tree_nw = tmp // "tree.nw" in
let out = dest // "out.tsv" in
......@@ -22,7 +22,7 @@ let msd ~(faa:aminoacid_fasta workflow) ~(tree_sc:_ workflow) : [`msd] directory
cmd "msd" ~env [
opt "-t" int 1;
opt "-o" ident out ;
opt "-e" float 0.01 ;
opt "-e" float e ;
dep tree_sc;
ident map_table;
dep faa;
......
......@@ -161,7 +161,7 @@ let derive_from_tree ~tree_dir ~tree ~profile ~preview ~use_concat ~ns ~no_Ne ~n
let ready_dataset_H0 = (derive_from_model ~model:H0_NeG5 ~input_tree ~tree_dataset ~tree_prefix ~profile ~preview ~ns).dataset in
let ready_dataset_HaPCOC = (derive_from_model ~model:HaPCOC ~input_tree ~tree_dataset ~tree_prefix ~profile ~preview ~ns).dataset in
let ready_dataset_HaPC = (derive_from_model ~model:HaPC_NeG5 ~input_tree ~tree_dataset ~tree_prefix ~profile ~preview ~ns).dataset in
let concat_H0HaPCOC = {Dataset.model_prefix="H0_NeG5+HaPCOC"; tree_prefix; is_real = false; dataset = Ready_dataset.paste ready_dataset_H0 ready_dataset_HaPCOC} in
let _concat_H0HaPCOC = {Dataset.model_prefix="H0_NeG5+HaPCOC"; tree_prefix; is_real = false; dataset = Ready_dataset.paste ready_dataset_H0 ready_dataset_HaPCOC} in
let concat_H0HaPC = {Dataset.model_prefix="H0_NeG5+HaPC_NeG5"; tree_prefix; is_real = false; dataset = Ready_dataset.paste ready_dataset_H0 ready_dataset_HaPC} in
let dataset_concat_hypos = if use_concat then [concat_H0HaPC;] else [] in
List.concat [ dataset_per_hypo ; dataset_concat_hypos ]
......@@ -186,7 +186,7 @@ let repo_of_detection_result res =
| `Topological_WAG w -> item ["Topological_WAG.results.tsv"] (Topological.results w)
| `Tdg09 w -> item ["Tdg09.results.tsv"] (Tamuri.results w)
| `Multinomial w -> item ["Multinomial.results.tsv"] (Multinomial.results w)
| `Msd w -> item ["Msd.results.tsv"] (Msd.results w)
| `Msd (w, e) -> item [sprintf "Msd.%f.results.tsv" e] (Msd.results w)
] ;
[
match res with
......@@ -200,7 +200,7 @@ let repo_of_detection_result res =
| `Topological_WAG w -> item ["raw_results"] w
| `Tdg09 w -> item ["raw_results"] w
| `Multinomial w -> item ["raw_results"] w
| `Msd w -> item ["raw_results"] w
| `Msd (w, _) -> item ["raw_results"] w
] ;
match res with
| `Diffsel w -> [item ["chain_convergence_checking.html"] ((Diffsel.check_conv w) / selector ["out.html"])]
......@@ -249,7 +249,7 @@ let derive_from_det_meth ~det_meth ~(dataset : Dataset.t) ~preview =
| `Topological_LG -> `Topological_LG (Topological.topological ~faa ~tree:tree_id ~tree_conv ~prot_model:"LG08")
| `Topological_WAG -> `Topological_WAG (Topological.topological ~faa ~tree:tree_id ~tree_conv ~prot_model:"WAG01")
| `Multinomial -> `Multinomial (Multinomial.multinomial ~faa ~tree_id ~tree_sc)
| `Msd -> `Msd (Msd.msd ~faa ~tree_sc)
| `Msd e -> `Msd (Msd.msd ~e ~faa ~tree_sc, e)
let derive_from_dataset ~dataset ~preview ~fast_mode=
......@@ -273,7 +273,7 @@ let derive_from_dataset ~dataset ~preview ~fast_mode=
if fast_mode then
[]
else
[`Diffsel; `Pcoc_C60;`Msd;] ;
([`Diffsel; `Pcoc_C60] @ List.map [0.05;0.1;0.5;1.] (fun x -> `Msd x)) ;
]
|> List.concat in
let res_by_tools = List.map det_meths ~f:(fun det_meth ->
......
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