Skip to content

GitLab

Commit 0972a129 authored by Carine Rey's avatar Carine Rey
Browse files

end add dataset with indels

parent df593f00
Hide whitespace changes
Inline Side-by-side
Showing with 37 additions and 9 deletions
lib/post_analyses.ml
View file @ 0972a129
......@@ -70,7 +70,9 @@ let make_t_choices ?(tree_prefix="") ~haPCOC_mr
~haPC_NeG5_NeC_div2_mr
~haPC_NeG5_NeC_x2_mr
~h0_NeG5_NeC_div2_mr
~h0_NeG5_NeC_x2_mr () : post_analyses_dir directory workflow =
~h0_NeG5_NeC_x2_mr
~h0_NeG5_indel_mr
~haPC_NeG5_indel_mr () : post_analyses_dir directory workflow =
let env = r_env in
let out = dest // "out" in
......@@ -89,6 +91,8 @@ let make_t_choices ?(tree_prefix="") ~haPCOC_mr
("--HaPC_NeG5_NeC_x2_res" , haPC_NeG5_NeC_x2_mr );
("--H0_NeG5_NeC_div2_res" , h0_NeG5_NeC_div2_mr );
("--H0_NeG5_NeC_x2_res" , h0_NeG5_NeC_x2_mr );
("--H0_NeG5_indel_res" , h0_NeG5_indel_mr);
("--HaPC_NeG5_indel_res" , haPC_NeG5_indel_mr );
("--HaPCOC" , haPCOC_mr );
] ~f:(fun (opt_name, mr_option) -> build_cmd_t_choices opt_name mr_option)
|> List.concat in
......@@ -190,6 +194,9 @@ type res_all_hyp = {
haPC_NeG5_NeC_x2_res : dataset_res option ;
h0_NeG5_NeC_div2_res : dataset_res option ;
h0_NeG5_NeC_x2_res : dataset_res option ;
h0_NeG5_indel_res : dataset_res option ;
haPC_NeG5_indel_res : dataset_res option ;
}
let make_t_choices_per_couple ~tree_prefix {ha_PCOC_res;
......@@ -203,6 +210,8 @@ let make_t_choices_per_couple ~tree_prefix {ha_PCOC_res;
haPC_NeG5_NeC_x2_res ;
h0_NeG5_NeC_div2_res ;
h0_NeG5_NeC_x2_res ;
h0_NeG5_indel_res;
haPC_NeG5_indel_res;
} =
let haPCOC_mr = get_merged_results_opt ha_PCOC_res in
......@@ -222,6 +231,9 @@ let make_t_choices_per_couple ~tree_prefix {ha_PCOC_res;
let haPC_NeG5_NeC_x2_mr = get_merged_results_opt haPC_NeG5_NeC_x2_res in
let h0_NeG5_NeC_div2_mr = get_merged_results_opt h0_NeG5_NeC_div2_res in
let h0_NeG5_NeC_x2_mr = get_merged_results_opt h0_NeG5_NeC_x2_res in
let h0_NeG5_indel_mr = get_merged_results_opt h0_NeG5_indel_res in
let haPC_NeG5_indel_mr = get_merged_results_opt haPC_NeG5_indel_res in
make_t_choices ~tree_prefix ~haPCOC_mr
~h0_NeG1_mr
......@@ -238,6 +250,8 @@ let make_t_choices_per_couple ~tree_prefix {ha_PCOC_res;
~haPC_NeG5_NeC_x2_mr
~h0_NeG5_NeC_div2_mr
~h0_NeG5_NeC_x2_mr
~h0_NeG5_indel_mr
~haPC_NeG5_indel_mr
()
......@@ -256,10 +270,13 @@ let get_t_choices ~tree_prefix ~(dataset_results_l: dataset_res list) : t_choice
let haPC_NeG4_res = List.find dataset_results_l (is_hyp ~hyp: "HaPC_NeG4" ) in
let haPC_NeG5_res = List.find dataset_results_l (is_hyp ~hyp: "HaPC_NeG5" ) in
let haPC_NeG5_NeC_div2_res = List.find dataset_results_l (is_hyp ~hyp: "HaPC_NeG5_NeC_div2" ) in
let haPC_NeG5_NeC_x2_res = List.find dataset_results_l (is_hyp ~hyp: "HaPC_NeG5_NeC_x2" ) in
let h0_NeG5_NeC_div2_res = List.find dataset_results_l (is_hyp ~hyp: "H0_NeG5_NeC_div2" ) in
let h0_NeG5_NeC_x2_res = List.find dataset_results_l (is_hyp ~hyp: "H0_NeG5_NeC_x2" ) in
let haPC_NeG5_NeC_div2_res = List.find dataset_results_l (is_hyp ~hyp: "HaPC_NeG5_NeC_div2" ) in
let haPC_NeG5_NeC_x2_res = List.find dataset_results_l (is_hyp ~hyp: "HaPC_NeG5_NeC_x2" ) in
let h0_NeG5_NeC_div2_res = List.find dataset_results_l (is_hyp ~hyp: "H0_NeG5_NeC_div2" ) in
let h0_NeG5_NeC_x2_res = List.find dataset_results_l (is_hyp ~hyp: "H0_NeG5_NeC_x2" ) in
let h0_NeG5_indel_res = List.find dataset_results_l (is_hyp ~hyp: "H0_NeG5_0.33_i" ) in
let haPC_NeG5_indel_res = List.find dataset_results_l (is_hyp ~hyp: "HaPC_NeG5_0.33_i" ) in
match (ha_PCOC_res) with
......@@ -267,7 +284,8 @@ let get_t_choices ~tree_prefix ~(dataset_results_l: dataset_res list) : t_choice
let t_choices_dir = make_t_choices_per_couple ~tree_prefix {ha_PCOC_res;
h0_NeG1_res; h0_NeG2_res; h0_NeG3_res; h0_NeG4_res; h0_NeG5_res;
haPC_NeG1_res; haPC_NeG2_res;haPC_NeG3_res; haPC_NeG4_res; haPC_NeG5_res;
haPC_NeG5_NeC_div2_res; haPC_NeG5_NeC_x2_res; h0_NeG5_NeC_div2_res; h0_NeG5_NeC_x2_res} in
haPC_NeG5_NeC_div2_res; haPC_NeG5_NeC_x2_res; h0_NeG5_NeC_div2_res; h0_NeG5_NeC_x2_res;
h0_NeG5_indel_res;haPC_NeG5_indel_res} in
let t_choices_max = t_choices_dir / selector ["out.max_MCC_per_meth.tsv"] in
let t_choices_recall09 = t_choices_dir / selector ["out.recall09_per_meth.tsv"] in
let t_choices_complete = t_choices_dir / selector ["out.complete.tsv"] in
......
lib/scripts/calc_t_per_meth.R
View file @ 0972a129
......@@ -25,6 +25,8 @@ option_list = list(
make_option(c("--HaPC_NeG5_NeC_x2_res" ) , type="character", default=NA, help="merged_results HaPC_NeG5_NeC_x2_res" , metavar="character"),
make_option(c("--H0_NeG5_NeC_div2_res" ) , type="character", default=NA, help="merged_results H0_NeG5_NeC_div2_res" , metavar="character"),
make_option(c("--H0_NeG5_NeC_x2_res" ) , type="character", default=NA, help="merged_results H0_NeG5_NeC_x2_res" , metavar="character"),
make_option(c("--H0_NeG5_indel_res" ) , type="character", default=NA, help="merged_results H0_NeG5_indel_res" , metavar="character"),
make_option(c("--HaPC_NeG5_indel_res" ) , type="character", default=NA, help="merged_results HaPC_NeG5_indel_res" , metavar="character"),
make_option(c("--HaPCOC" ) , type="character", default=NA, help="merged_results HaPCOC" , metavar="character"),
make_option(c("--tree_prefix" ) , type="character", default="", help="tree_prefix" , metavar="character"),
......@@ -83,7 +85,8 @@ df_HaPC_NeG5_NeC_x2 = read_hyp(opt$HaPC_NeG5_NeC_x2 )
df_H0_NeG5_NeC_div2 = read_hyp(opt$H0_NeG5_NeC_div2 )
df_H0_NeG5_NeC_x2 = read_hyp(opt$H0_NeG5_NeC_x2 )
df_HaPC_NeG5_indel = read_hyp(opt$HaPC_NeG5_indel_res )
df_H0_NeG5_indel = read_hyp(opt$H0_NeG5_indel_res )
df_HaPCOC = read_hyp(opt$HaPCOC)
......@@ -120,6 +123,8 @@ df_d_H0HaPC_NeG5 = build_df_dist_couple(df_H0_NeG5, df_HaPC_NeG5, "H0/HaPC NeG
df_d_H0HaPC_NeG5_NeC_div2 = build_df_dist_couple(df_H0_NeG5_NeC_div2, df_HaPC_NeG5_NeC_div2, "H0/HaPC NeG5_NeC_div2")
df_d_H0HaPC_NeG5_NeC_x2 = build_df_dist_couple(df_H0_NeG5_NeC_x2, df_HaPC_NeG5_NeC_x2, "H0/HaPC NeG5_NeC_x2")
df_d_H0HaPC_NeG5_indel = build_df_dist_couple(df_H0_NeG5_indel, df_HaPC_NeG5_indel, "H0/HaPC NeG5_indel")
df_d = rbind.data.frame(
df_d_H0HaPCOC_NeG1,
df_d_H0HaPC_NeG1,
......@@ -128,7 +133,9 @@ df_d = rbind.data.frame(
df_d_H0HaPC_NeG4,
df_d_H0HaPC_NeG5,
df_d_H0HaPC_NeG5_NeC_div2,
df_d_H0HaPC_NeG5_NeC_x2)
df_d_H0HaPC_NeG5_NeC_x2,
df_d_H0HaPC_NeG5_indel
)
df_d = df_d[order(df_d$methode),]
......@@ -205,9 +212,12 @@ df_H0HaPC_NeG5 = build_df_couple(df_H0_NeG5, df_HaPC_NeG5, "H0/HaPC NeG5")
df_H0HaPC_NeG5_NeC_div2 = build_df_couple(df_H0_NeG5_NeC_div2, df_HaPC_NeG5_NeC_div2, "H0/HaPC NeG5_NeC_div2")
df_H0HaPC_NeG5_NeC_x2 = build_df_couple(df_H0_NeG5_NeC_x2, df_HaPC_NeG5_NeC_x2, "H0/HaPC NeG5_NeC_x2")
df_H0HaPC_NeG5_indel = build_df_couple(df_H0_NeG5_indel, df_HaPC_NeG5_indel, "H0/HaPC NeG5_indel")
df_l = list(df_H0HaPCOC_NeG1, df_H0HaPC_NeG1, df_H0HaPC_NeG2, df_H0HaPC_NeG3,
df_H0HaPC_NeG4, df_H0HaPC_NeG5, df_H0HaPC_NeG5_NeC_div2,
df_H0HaPC_NeG5_NeC_x2)
df_H0HaPC_NeG5_NeC_x2,df_H0HaPC_NeG5_indel)
df_l = df_l[-which(sapply(df_l, is.null))]
df = do.call("rbind",df_l)
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment