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Docker-in-Docker (DinD) capabilities of public runners deactivated. More info

Commit b45413d6 authored by LANORE Vincent's avatar LANORE Vincent
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Auto indentation of everything + removed extra blank lines

parent 2d04fc2f
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Showing with 215 additions and 235 deletions
lib/bppsuite.ml
View file @ b45413d6
......@@ -21,8 +21,6 @@ let bash_script args code =
in
seq ~sep:"\n" [ prelude ; string code ]
let conf_file_bppseqgen ~tree ~out ~nb_sites ~config =
seq ~sep:"\n" (
[
......@@ -42,14 +40,12 @@ let bppseqgen ?(descr="") ~nb_sites ~tree ~config : nucleotide_fasta workflow =
mkdir_p dest;
cmd "cat" ~stdout:config_f [(file_dump (conf_file_bppseqgen ~tree ~out ~nb_sites ~config))];
cmd "bppseqgen" [
assign "param" config_f;
]
assign "param" config_f;
]
]
)
] / selector ["seq.fa"]
let conf_file_bppseqgen_multi_profiles ~tree ~profile_f ~ne_c ~config ~nb_sites_per_profile =
seq ~sep:"\n" (
[
......@@ -63,8 +59,6 @@ let conf_file_bppseqgen_multi_profiles ~tree ~profile_f ~ne_c ~config ~nb_sites_
@ config
)
let bppseqgen_multi_profiles_script ~config ~nb_combis ~out ~profile_f =
let vars = [
"FINAL_OUT", ident out ;
......@@ -145,9 +139,9 @@ let conf_file_bppseqman_fa2phy ~fna =
assign "output.sequence.file" dest ;
assign "output.sequence.format" (string "Phylip") ;
string {| input.alignment = true
input.sequence.remove_stop_codons = no
input.sequence.sites_to_use = all
sequence.manip =
input.sequence.remove_stop_codons = no
input.sequence.sites_to_use = all
sequence.manip =
|}
]
......@@ -162,7 +156,7 @@ let fa2phy ~(fna: nucleotide_fasta workflow) : nucleotide_phylip workflow =
let paste_fna ~(fna_l: nucleotide_fasta workflow list) : nucleotide_fasta workflow =
workflow ~descr:"bppsuite.catfasta" [
cmd "catfasta2phyml.pl" ~stdout:dest ~env (List.concat [
[string "-f" ] ;
List.map fna_l ~f:(fun fna -> dep fna) ;
])
[string "-f" ] ;
List.map fna_l ~f:(fun fna -> dep fna) ;
])
]
lib/convergence_detection.ml
View file @ b45413d6
......@@ -75,49 +75,48 @@ let merge_results ~res_by_tools : text_file workflow =
in
workflow ~descr:"convergence_detection.merge_results" [
cmd "python" ~env [
file_dump (string Scripts.merge_det_results) ;
opt "-o" ident dest ;
seq ~sep:" " command ;
] ;
file_dump (string Scripts.merge_det_results) ;
opt "-o" ident dest ;
seq ~sep:" " command ;
] ;
]
let plot_merge_results ~plot_all_sites ~(res_by_tools:result list) ~tree ~faa ~tsv : svg workflow =
let env = docker_image ~account:"carinerey" ~name:"pcoc" ~tag:"06212018" () in
(* use of pcoc env due to its working X server for dra plot with ete3 *)
let meths = List.map res_by_tools ~f:(fun res ->
let opt = match res with
| `Pcoc _ -> "PCOC,PC,OC"
| `Pcoc_gamma _ -> "PCOC_gamma,PC_gamma,OC_gamma,"
| `Pcoc_C60 _ -> "PCOC_C60,PC_C60,OC_C60,"
| `Diffsel _ -> "Diffsel_mean,Diffsel_max"
| `Diffsel_bis _ -> "Diffsel_bis_mean,Diffsel_bis_max"
| `Identical_LG _ -> "Identical_LG08"
| `Identical_WAG _ -> "Identical_WAG01"
| `Topological_LG _ -> "Topological_LG08"
| `Topological_WAG _ -> "Topological_WAG01"
| `Tdg09 _ -> "Tdg09_1-FDR,Tdg09_prob_post"
| `Multinomial _ -> "Mutinomial_LRT"
in
string opt
) |> seq ~sep:","
let opt = match res with
| `Pcoc _ -> "PCOC,PC,OC"
| `Pcoc_gamma _ -> "PCOC_gamma,PC_gamma,OC_gamma,"
| `Pcoc_C60 _ -> "PCOC_C60,PC_C60,OC_C60,"
| `Diffsel _ -> "Diffsel_mean,Diffsel_max"
| `Diffsel_bis _ -> "Diffsel_bis_mean,Diffsel_bis_max"
| `Identical_LG _ -> "Identical_LG08"
| `Identical_WAG _ -> "Identical_WAG01"
| `Topological_LG _ -> "Topological_LG08"
| `Topological_WAG _ -> "Topological_WAG01"
| `Tdg09 _ -> "Tdg09_1-FDR,Tdg09_prob_post"
| `Multinomial _ -> "Mutinomial_LRT"
in
string opt
) |> seq ~sep:","
in
let meths_t = List.map res_by_tools ~f:(fun res ->
let opt = match res with
| `Pcoc _ -> "PCOC:0.99,PC:0.99,OC:0.99"
| `Pcoc_gamma _ -> "PCOC_gamma:0.99,PC_gamma:0.99,OC_gamma:0.99"
| `Pcoc_C60 _ -> "PCOC_C60:0.99,PC_C60:0.99,OC_C60:0.99"
| `Diffsel _ -> "Diffsel_mean:0.11,Diffsel_max:0.9"
| `Diffsel_bis _ -> "Diffsel_bis_mean:0.11,Diffsel_bis_max:0.9"
| `Identical_LG _ -> "Identical_LG08:0.9"
| `Identical_WAG _ -> "Identical_WAG01:0.9"
| `Topological_LG _ -> "Topological_LG08:0.9"
| `Topological_WAG _ -> "Topological_WAG01:0.9"
| `Tdg09 _ -> "Tdg09_1-FDR:0.9,Tdg09_prob_post:0.9"
| `Multinomial _ -> "Mutinomial_LRT:0.9"
in
string opt
) |> seq ~sep:","
let opt = match res with
| `Pcoc _ -> "PCOC:0.99,PC:0.99,OC:0.99"
| `Pcoc_gamma _ -> "PCOC_gamma:0.99,PC_gamma:0.99,OC_gamma:0.99"
| `Pcoc_C60 _ -> "PCOC_C60:0.99,PC_C60:0.99,OC_C60:0.99"
| `Diffsel _ -> "Diffsel_mean:0.11,Diffsel_max:0.9"
| `Diffsel_bis _ -> "Diffsel_bis_mean:0.11,Diffsel_bis_max:0.9"
| `Identical_LG _ -> "Identical_LG08:0.9"
| `Identical_WAG _ -> "Identical_WAG01:0.9"
| `Topological_LG _ -> "Topological_LG08:0.9"
| `Topological_WAG _ -> "Topological_WAG01:0.9"
| `Tdg09 _ -> "Tdg09_1-FDR:0.9,Tdg09_prob_post:0.9"
| `Multinomial _ -> "Mutinomial_LRT:0.9"
in
string opt
) |> seq ~sep:","
in
let package_diffsel_script_utils = tmp // "diffsel_script_utils.py" in
let package_plot_data = tmp // "plot_data.py" in
......
lib/convergence_detection.mli
View file @ b45413d6
......@@ -28,16 +28,16 @@ type dataset_res = {
res_by_tools: result list ;
merged_results : text_file workflow ;
plot_merged_results : svg workflow
}
}
val merge_results :
res_by_tools : result list ->
text_file workflow
val plot_merge_results :
plot_all_sites: bool ->
res_by_tools : result list ->
tree:nhx workflow ->
faa:aminoacid_fasta workflow ->
tsv:text_file workflow ->
svg workflow
plot_all_sites: bool ->
res_by_tools : result list ->
tree:nhx workflow ->
faa:aminoacid_fasta workflow ->
tsv:text_file workflow ->
svg workflow
lib/convergence_hypothesis.ml
View file @ b45413d6
......@@ -37,57 +37,56 @@ nonhomogeneous = general
rate_distribution=Constant()
|}
let bpp_config_H0_F= seq ~sep:"\n" [
seq [string "model1=Codon_AAFit(model=K80, fitness=Empirical(file=$(PROFILE_F), col=$(COL_M1)))" ] ;
seq [string "nonhomogeneous.root_freq=FromModel(model=$(model1))" ] ;
]
seq [string "model1=Codon_AAFit(model=K80, fitness=Empirical(file=$(PROFILE_F), col=$(COL_M1)))" ] ;
seq [string "nonhomogeneous.root_freq=FromModel(model=$(model1))" ] ;
]
let bpp_config_HaPCOC_F = seq ~sep:"\n" [
seq [string "model1=Codon_AAFit(model=K80, fitness=Empirical(file=$(PROFILE_F), col=$(COL_M1)))" ] ;
seq [string "modelT=OneChange(model=Codon_AAFit(model=K80, fitness=Empirical(file=$(PROFILE_F), col=$(COL_M2))), register=DnDs, numReg=2)" ] ;
seq [string "modelC=Codon_AAFit(model=K80, fitness=Empirical(file=$(PROFILE_F), col=$(COL_M2)))" ] ;
seq [string "nonhomogeneous.root_freq=FromModel(model=$(model1))" ] ;
]
seq [string "model1=Codon_AAFit(model=K80, fitness=Empirical(file=$(PROFILE_F), col=$(COL_M1)))" ] ;
seq [string "modelT=OneChange(model=Codon_AAFit(model=K80, fitness=Empirical(file=$(PROFILE_F), col=$(COL_M2))), register=DnDs, numReg=2)" ] ;
seq [string "modelC=Codon_AAFit(model=K80, fitness=Empirical(file=$(PROFILE_F), col=$(COL_M2)))" ] ;
seq [string "nonhomogeneous.root_freq=FromModel(model=$(model1))" ] ;
]
let bpp_config_HaPC_F = seq ~sep:"\n" [
seq [string "model1=Codon_AAFit(model=K80, fitness=Empirical(file=$(PROFILE_F), col=$(COL_M1)))" ] ;
seq [string "modelT=Codon_AAFit(model=K80, fitness=Empirical(file=$(PROFILE_F), col=$(COL_M2)))" ] ;
seq [string "modelC=Codon_AAFit(model=K80, fitness=Empirical(file=$(PROFILE_F), col=$(COL_M2)))" ] ;
seq [string "nonhomogeneous.root_freq=FromModel(model=$(model1))" ] ;
]
seq [string "model1=Codon_AAFit(model=K80, fitness=Empirical(file=$(PROFILE_F), col=$(COL_M1)))" ] ;
seq [string "modelT=Codon_AAFit(model=K80, fitness=Empirical(file=$(PROFILE_F), col=$(COL_M2)))" ] ;
seq [string "modelC=Codon_AAFit(model=K80, fitness=Empirical(file=$(PROFILE_F), col=$(COL_M2)))" ] ;
seq [string "nonhomogeneous.root_freq=FromModel(model=$(model1))" ] ;
]
let bpp_config_H0_F_Ne = seq ~sep:"\n" [
seq [string "model1=Codon_AAFit(model=K80, fitness=Empirical(file=$(PROFILE_F), col=$(COL_M1)), Ns=$(NE_1))" ] ;
seq [string "model2=Codon_AAFit(model=K80, fitness=Empirical(file=$(PROFILE_F), col=$(COL_M1)), Ns=$(NE_C))" ] ;
seq [string "nonhomogeneous.root_freq=FromModel(model=$(model1))" ] ;
]
seq [string "model1=Codon_AAFit(model=K80, fitness=Empirical(file=$(PROFILE_F), col=$(COL_M1)), Ns=$(NE_1))" ] ;
seq [string "model2=Codon_AAFit(model=K80, fitness=Empirical(file=$(PROFILE_F), col=$(COL_M1)), Ns=$(NE_C))" ] ;
seq [string "nonhomogeneous.root_freq=FromModel(model=$(model1))" ] ;
]
let bpp_config_HaPCOC_F_Ne = seq ~sep:"\n" [
seq [string "model1=Codon_AAFit(model=K80, fitness=Empirical(file=$(PROFILE_F), col=$(COL_M1)), Ns=$(NE_1))" ] ;
seq [string "modelT=OneChange(model=Codon_AAFit(model=K80, fitness=Empirical(file=$(PROFILE_F), col=$(COL_M2))), register=DnDs, numReg=2, Ns=$(NE_T))" ] ;
seq [string "modelC=Codon_AAFit(model=K80, fitness=Empirical(file=$(PROFILE_F), col=$(COL_M2)), Ns=$(NE_C))" ] ;
seq [string "nonhomogeneous.root_freq=FromModel(model=$(model1))" ] ;
]
seq [string "model1=Codon_AAFit(model=K80, fitness=Empirical(file=$(PROFILE_F), col=$(COL_M1)), Ns=$(NE_1))" ] ;
seq [string "modelT=OneChange(model=Codon_AAFit(model=K80, fitness=Empirical(file=$(PROFILE_F), col=$(COL_M2))), register=DnDs, numReg=2, Ns=$(NE_T))" ] ;
seq [string "modelC=Codon_AAFit(model=K80, fitness=Empirical(file=$(PROFILE_F), col=$(COL_M2)), Ns=$(NE_C))" ] ;
seq [string "nonhomogeneous.root_freq=FromModel(model=$(model1))" ] ;
]
let bpp_config_HaPC_F_Ne = seq ~sep:"\n" [
seq [string "model1=Codon_AAFit(model=K80, fitness=Empirical(file=$(PROFILE_F), col=$(COL_M1)), Ns=$(NE_1))" ] ;
seq [string "modelT=Codon_AAFit(model=K80, fitness=Empirical(file=$(PROFILE_F), col=$(COL_M2)))" ] ;
seq [string "modelC=Codon_AAFit(model=K80, fitness=Empirical(file=$(PROFILE_F), col=$(COL_M2)), Ns=$(NE_C))" ] ;
seq [string "nonhomogeneous.root_freq=FromModel(model=$(model1))" ] ;
]
seq [string "model1=Codon_AAFit(model=K80, fitness=Empirical(file=$(PROFILE_F), col=$(COL_M1)), Ns=$(NE_1))" ] ;
seq [string "modelT=Codon_AAFit(model=K80, fitness=Empirical(file=$(PROFILE_F), col=$(COL_M2)))" ] ;
seq [string "modelC=Codon_AAFit(model=K80, fitness=Empirical(file=$(PROFILE_F), col=$(COL_M2)), Ns=$(NE_C))" ] ;
seq [string "nonhomogeneous.root_freq=FromModel(model=$(model1))" ] ;
]
let bpp_config_F nodes hyp = [
string bpp_config_base ;
insert nodes ;
match hyp with
| H0 -> bpp_config_H0_F
| HaPC -> bpp_config_HaPC_F
| HaPCOC -> bpp_config_HaPCOC_F
| H0_NeSmall -> bpp_config_H0_F_Ne
| HaPC_NeSmall -> bpp_config_HaPC_F_Ne
| HaPCOC_NeSmall -> bpp_config_HaPCOC_F_Ne
| H0_NeBig -> bpp_config_H0_F_Ne
| HaPC_NeBig -> bpp_config_HaPC_F_Ne
| HaPCOC_NeBig -> bpp_config_HaPCOC_F_Ne
;
match hyp with
| H0 -> bpp_config_H0_F
| HaPC -> bpp_config_HaPC_F
| HaPCOC -> bpp_config_HaPCOC_F
| H0_NeSmall -> bpp_config_H0_F_Ne
| HaPC_NeSmall -> bpp_config_HaPC_F_Ne
| HaPCOC_NeSmall -> bpp_config_HaPCOC_F_Ne
| H0_NeBig -> bpp_config_H0_F_Ne
| HaPC_NeBig -> bpp_config_HaPC_F_Ne
| HaPCOC_NeBig -> bpp_config_HaPCOC_F_Ne
;
]
lib/dataset.ml
View file @ b45413d6
......@@ -14,9 +14,9 @@ let repo ~preview dataset_l =
let tree_prefix = dataset.tree_prefix in
let repo_ready_data = Ready_dataset.repo dataset.dataset in
let repo_raw_data = if preview then Raw_dataset.repo ~prefix:model_prefix (Ready_dataset.to_raw dataset.dataset) else [] in
List.concat [
Repo.shift "simulated_data" (Repo.shift (tree_prefix ^"_"^model_prefix) repo_raw_data);
Repo.shift "simulated_data_debug" (Repo.shift tree_prefix (Repo.shift model_prefix repo_ready_data));
]
List.concat [
Repo.shift "simulated_data" (Repo.shift (tree_prefix ^"_"^model_prefix) repo_raw_data);
Repo.shift "simulated_data_debug" (Repo.shift tree_prefix (Repo.shift model_prefix repo_ready_data));
]
)
|> List.concat
lib/defs.ml
View file @ b45413d6
......@@ -9,7 +9,3 @@ type output_parse_input_tree =
| Tree4detect
| Tree4simu
| Tree_diffsel
lib/diffsel.ml
View file @ b45413d6
......@@ -21,11 +21,11 @@ let diffsel ~(phy_n:nucleotide_phylip workflow) ~(tree: _ workflow) ~(w_every:in
cmd "cp" [dep phy_n; tmp_ali]; (* required dep to link the file in the env *)
cmd "cp" [dep tree; tmp_tree]; (* required dep to link the file in the env *)
cmd "/diffsel/_build/diffsel" [
opt "-t" ident tmp_tree;
opt "-d" ident tmp_ali ;
opt "-ncond" int 2 ;
opt "-x" seq [ int w_every; string " "; int n_cycles];
ident chainname ;
opt "-t" ident tmp_tree;
opt "-d" ident tmp_ali ;
opt "-ncond" int 2 ;
opt "-x" seq [ int w_every; string " "; int n_cycles];
ident chainname ;
];
]
)
......
lib/diffsel.mli
View file @ b45413d6
......@@ -11,5 +11,5 @@ val diffsel :
[`diffsel] directory workflow
val selector :
[`diffsel] directory workflow ->
text_file workflow
[`diffsel] directory workflow ->
text_file workflow
lib/file_formats.ml
View file @ b45413d6
......@@ -25,4 +25,3 @@ class type nucleotide_phylip = object
inherit text_file
method format : [`Nucleotide]
end
lib/multinomial.ml
View file @ b45413d6
......@@ -9,13 +9,12 @@ let multinomial ~(tree_id:_ workflow) ~(tree_sc:_ workflow) ~(faa:aminoacid_fast
workflow ~descr:("calc_multinomial") [
mkdir_p dest;
cmd "python" ~env [
file_dump (string Scripts.calc_multinomial) ;
opt "-t" dep tree_sc;
opt "-a" dep faa;
opt "-o" ident (dest // "out.tsv") ;
file_dump (string Scripts.calc_multinomial) ;
opt "-t" dep tree_sc;
opt "-a" dep faa;
opt "-o" ident (dest // "out.tsv") ;
]
]
let results w =
w / selector ["out.tsv"]
lib/pcoc.ml
View file @ b45413d6
......@@ -8,13 +8,13 @@ let pcoc ?plot_complete ?gamma ?catx_est ~(faa:aminoacid_fasta workflow) ~(tree
let env = docker_image ~account:"carinerey" ~name:"pcoc" ~tag:"07022018" () in
workflow ~descr:"convergence_detection.pcoc" [
cmd "pcoc_det.py" ~env [
opt "-t" dep tree;
opt "-m" string "-";
opt "-aa" dep faa ;
opt "-o" ident dest ;
option ( flag string "--gamma" ) gamma;
option ( opt "-CATX_est" int) catx_est;
option ( flag string "--plot --plot_complete_ali" ) plot_complete;
opt "-t" dep tree;
opt "-m" string "-";
opt "-aa" dep faa ;
opt "-o" ident dest ;
option ( flag string "--gamma" ) gamma;
option ( opt "-CATX_est" int) catx_est;
option ( flag string "--plot --plot_complete_ali" ) plot_complete;
]
]
......
lib/pipeline.ml
View file @ b45413d6
......@@ -40,7 +40,7 @@ let parse_input_data indir =
} in
[dataset]
else
failwith ({|More than 2 files in |} ^ (Filename.concat indir dataset_prefix ))
failwith ({|More than 2 files in |} ^ (Filename.concat indir dataset_prefix ))
)
|> List.concat
......@@ -249,23 +249,23 @@ let simulation_main ~outdir ?(ns = 0) ?(np = 2) ?(mem = 2) ~tree_dir ~profile_fn
let validation_main ~outdir ?(indir = "") ?(ns = 0) ?(np = 2) ?(mem = 2) ~preview ~fast_mode ~tree_dir ~profile_fn ~use_concat () =
let trees = Array.to_list @@ Sys.readdir tree_dir in
let repo = List.map trees ~f:(fun tree ->
let trees = [tree] in
let tree_prefix = Filename.chop_extension tree in
let indir_dataset_l = if indir = "" then [] else parse_input_data indir in
let dataset_l =
derive_sim ~tree_dir ~trees ~profile_fn ~preview ~use_concat ~ns
@ indir_dataset_l in
let dataset_results_l = derive_det ~dataset_l ~preview ~fast_mode in
let post_analyses = Post_analyses.post_analyses_of_dataset_results_l ~dataset_results_l in
let repo_per_tree = [
Dataset.repo dataset_l ~preview ;
repo_of_dataset_results_l ~dataset_results_l ;
Repo.shift tree_prefix (Post_analyses.repo_of_post_analyses ~prefix:tree_prefix ~post_analyses);
] |> List.concat
in
repo_per_tree
)
|> List.concat
let trees = [tree] in
let tree_prefix = Filename.chop_extension tree in
let indir_dataset_l = if indir = "" then [] else parse_input_data indir in
let dataset_l =
derive_sim ~tree_dir ~trees ~profile_fn ~preview ~use_concat ~ns
@ indir_dataset_l in
let dataset_results_l = derive_det ~dataset_l ~preview ~fast_mode in
let post_analyses = Post_analyses.post_analyses_of_dataset_results_l ~dataset_results_l in
let repo_per_tree = [
Dataset.repo dataset_l ~preview ;
repo_of_dataset_results_l ~dataset_results_l ;
Repo.shift tree_prefix (Post_analyses.repo_of_post_analyses ~prefix:tree_prefix ~post_analyses);
] |> List.concat
in
repo_per_tree
)
|> List.concat
in
Repo.build ~outdir ~np ~mem:(`GB mem) ~logger repo
......
lib/post_analyses.ml
View file @ b45413d6
......@@ -12,19 +12,19 @@ type t_choices = {
t_choices_complete: text_file workflow ;
t_choices_max: text_file workflow ;
t_choices_plot: text_file workflow ;
}
}
type simu_infos = {
simu_infos: text_file workflow option ;
model_prefix: string ;
tree_prefix: string ;
}
}
type post_analyses = {
t_choices : t_choices option;
simu_infos_l : simu_infos list;
simu_infos_plot : text_file workflow ;
}
}
let is_hyp ~hyp (dataset_results :dataset_res) =
......@@ -35,7 +35,7 @@ let make_t_choices ~h0_merged_results ~ha_merged_results : post_analyses_dir dir
let env = docker_image ~account:"carinerey" ~name:"r_basics" ~tag:"07162018" () in
let out = dest // "out" in
workflow ~descr:"post_analyses.t_choices" [
docker env (
docker env (
and_list [
mkdir_p dest ;
cmd "Rscript" [
......@@ -43,60 +43,60 @@ let make_t_choices ~h0_merged_results ~ha_merged_results : post_analyses_dir dir
opt "--H0" dep h0_merged_results;
opt "--Ha" dep ha_merged_results;
opt "--out " ident out;
];
])
];
])
]
let make_simu_infos ?(descr="") ?(fna_infos) ~faa ~tree_sc : text_file workflow =
let env = docker_image ~account:"carinerey" ~name:"pcoc" ~tag:"07022018" () in
workflow ~descr:("post_analyses.simu_infos." ^ descr) [
cmd "python" ~env [
file_dump (string Scripts.calc_simu_infos) ;
opt "--faa" dep faa;
opt "--tree" dep tree_sc;
option ( opt "--fna_infos" dep) fna_infos;
opt "--output " ident dest;
file_dump (string Scripts.calc_simu_infos) ;
opt "--faa" dep faa;
opt "--tree" dep tree_sc;
option ( opt "--fna_infos" dep) fna_infos;
opt "--output " ident dest;
];
]
let group_simu_infos ~simu_infos_l : simu_infos directory workflow =
let env = docker_image ~account:"carinerey" ~name:"r_basics" ~tag:"07162018" () in
let cmd_cp_l = List.map simu_infos_l ~f:(fun s ->
match s.simu_infos with
match s.simu_infos with
| Some w -> [cmd "cp" [dep w ; tmp // (s.tree_prefix ^"."^ s.model_prefix ^ ".tsv")]]
| None -> []
) |> List.concat
in
let out = dest // "out" in
workflow ~descr:"post_analyses.plot_simu_infos" [
docker env (
docker env (
and_list ([
[mkdir_p dest];
[mkdir_p tmp ];
cmd_cp_l;
[cmd "Rscript" [
file_dump (string Scripts.plot_hyp_simu_validation) ;
opt "--input_dir" ident tmp;
opt "--out " ident out;
];]
]
|> List.concat)
)
[mkdir_p dest];
[mkdir_p tmp ];
cmd_cp_l;
[cmd "Rscript" [
file_dump (string Scripts.plot_hyp_simu_validation) ;
opt "--input_dir" ident tmp;
opt "--out " ident out;
];]
]
|> List.concat)
)
]
let get_t_choices ~(dataset_results_l: dataset_res list) : t_choices option =
let h0_res = List.find dataset_results_l (is_hyp ~hyp: "H0") in
let ha_res = List.find dataset_results_l (is_hyp ~hyp: "HaPCOC") in
match (h0_res, ha_res) with
| (Some h0, Some ha) ->
let h0_merged_results = h0.merged_results in
let ha_merged_results = ha.merged_results in
let t_choices_dir = make_t_choices ~h0_merged_results ~ha_merged_results in
let t_choices_max = t_choices_dir / selector ["out.max_per_meth.tsv"] in
let t_choices_complete = t_choices_dir / selector ["out.complete.tsv"] in
let t_choices_plot = t_choices_dir / selector ["out.pdf"] in
Some {t_choices_max; t_choices_complete ; t_choices_plot}
| _ -> None
| (Some h0, Some ha) ->
let h0_merged_results = h0.merged_results in
let ha_merged_results = ha.merged_results in
let t_choices_dir = make_t_choices ~h0_merged_results ~ha_merged_results in
let t_choices_max = t_choices_dir / selector ["out.max_per_meth.tsv"] in
let t_choices_complete = t_choices_dir / selector ["out.complete.tsv"] in
let t_choices_plot = t_choices_dir / selector ["out.pdf"] in
Some {t_choices_max; t_choices_complete ; t_choices_plot}
| _ -> None
let get_simu_infos ~dataset_results =
let model_prefix = dataset_results.dataset.model_prefix in
......@@ -105,43 +105,43 @@ let get_simu_infos ~dataset_results =
let tree_sc = Tree_dataset.tree ready_dataset.tree_dataset `Detection in
let fna_infos = ready_dataset.fna_infos in
match fna_infos with
| Some w -> Some (make_simu_infos ~descr:model_prefix ~faa ~tree_sc ~fna_infos:w)
| None -> None (*make_simu_infos ~faa ~tree_sc*)
| Some w -> Some (make_simu_infos ~descr:model_prefix ~faa ~tree_sc ~fna_infos:w)
| None -> None (*make_simu_infos ~faa ~tree_sc*)
let post_analyses_of_dataset_results_l ~dataset_results_l =
let t_choices = get_t_choices ~dataset_results_l in
let simu_infos_l = List.map dataset_results_l ~f:(fun dataset_results ->
{simu_infos = (get_simu_infos ~dataset_results);
tree_prefix =dataset_results.tree_prefix ;
model_prefix = dataset_results.model_prefix
}
) in
{simu_infos = (get_simu_infos ~dataset_results);
tree_prefix =dataset_results.tree_prefix ;
model_prefix = dataset_results.model_prefix
}
) in
let simu_infos_plot = group_simu_infos ~simu_infos_l / selector ["out.pdf"] in
{t_choices ; simu_infos_l; simu_infos_plot}
let repo_of_post_analyses ~prefix ~post_analyses =
[
Repo.[
item [prefix ^ ".pdf"] post_analyses.simu_infos_plot
] |> Repo.shift "simu_infos"
;
(match post_analyses.t_choices with
| None -> []
| Some w ->
Repo.[
item [prefix ^ ".t_choices.max_mcc_per_meth.tsv"] w.t_choices_max ;
item [prefix ^ ".t_choices.complete.tsv"] w.t_choices_complete ;
item [prefix ^ ".t_choices.pdf"] w.t_choices_plot ;
] |> Repo.shift "t_choices"
);
(List.map post_analyses.simu_infos_l ~f:(fun simu_infos ->
match simu_infos.simu_infos with
| None -> []
| Some w ->
Repo.[
item [prefix ^ "." ^ simu_infos.model_prefix ^ ".tsv"] w
] |> Repo.shift "simu_infos"
) |> List.concat
);
Repo.[
item [prefix ^ ".pdf"] post_analyses.simu_infos_plot
] |> Repo.shift "simu_infos"
;
(match post_analyses.t_choices with
| None -> []
| Some w ->
Repo.[
item [prefix ^ ".t_choices.max_mcc_per_meth.tsv"] w.t_choices_max ;
item [prefix ^ ".t_choices.complete.tsv"] w.t_choices_complete ;
item [prefix ^ ".t_choices.pdf"] w.t_choices_plot ;
] |> Repo.shift "t_choices"
);
(List.map post_analyses.simu_infos_l ~f:(fun simu_infos ->
match simu_infos.simu_infos with
| None -> []
| Some w ->
Repo.[
item [prefix ^ "." ^ simu_infos.model_prefix ^ ".tsv"] w
] |> Repo.shift "simu_infos"