convergence_detection.mli 1.64 KB
Newer Older
Philippe Veber's avatar
Philippe Veber committed
1
open Bistro
2
open File_formats
Carine Rey's avatar
Carine Rey committed
3

Philippe Veber's avatar
Philippe Veber committed
4
type result = [
Philippe Veber's avatar
Philippe Veber committed
5 6 7 8 9 10 11 12 13
  | `Pcoc of [`pcoc] directory
  | `Pcoc_gamma of [`pcoc] directory
  | `Pcoc_C60 of [`pcoc] directory
  | `Diffsel of [`diffsel] directory
  | `Identical_LG of [`identical] directory
  | `Identical_WAG of [`identical] directory
  | `Topological_LG of [`topological] directory
  | `Topological_WAG of [`topological] directory
  | `Tdg09 of [`tdg09] directory
14
  | `Multinomial of cpt file
Philippe Veber's avatar
Philippe Veber committed
15
  | `Msd of [`msd] directory * float
Philippe Veber's avatar
Philippe Veber committed
16
]
Carine Rey's avatar
Carine Rey committed
17

Philippe Veber's avatar
Philippe Veber committed
18
val meth_string_of_result : result -> string
Carine Rey's avatar
Carine Rey committed
19 20 21 22

type dataset_res = {
  model_prefix : string ;
  tree_prefix : string ;
Carine Rey's avatar
Carine Rey committed
23
  dataset : Dataset.t ;
Philippe Veber's avatar
Philippe Veber committed
24
  res_by_tools: result list ;
25
  merged_results : cpt file ;
Philippe Veber's avatar
Philippe Veber committed
26
  plot_merged_results : svg file
27
}
Carine Rey's avatar
Carine Rey committed
28 29

val merge_results :
Philippe Veber's avatar
Philippe Veber committed
30
  ?fna_infos:text file ->
Philippe Veber's avatar
Philippe Veber committed
31
  res_by_tools : result list ->
Carine Rey's avatar
Carine Rey committed
32
  unit ->
33
  cpt file
Carine Rey's avatar
Carine Rey committed
34

35
val merge_result_tables :
Philippe Veber's avatar
Philippe Veber committed
36
  ?fna_infos:text file ->
37 38 39 40 41 42 43 44 45 46
  ?oracle:cpt file ->
  ?multinomial:cpt file ->
  ?tdg09:cpt file ->
  ?identical:cpt file ->
  ?topological:cpt file ->
  ?pcoc:cpt file ->
  ?pcoc_v2:cpt file ->
  ?pcoc_pcp:cpt file ->
  ?diffsel:cpt file ->
  ?diffseldsparse:cpt file ->
47
  unit ->
48
  cpt file
49

Carine Rey's avatar
Carine Rey committed
50
val plot_merge_results :
Philippe Veber's avatar
Philippe Veber committed
51
  ? t_choices : text file ->
52 53
  plot_all_sites: bool ->
  res_by_tools : result list ->
Philippe Veber's avatar
Philippe Veber committed
54 55
  tree:nhx file ->
  faa:aminoacid_fasta file ->
56
  tsv:cpt file ->
57
  unit ->
Philippe Veber's avatar
Philippe Veber committed
58
  svg file
59 60 61

val plot_convergent_sites :
  ?plot_all_sites:bool ->
Philippe Veber's avatar
Philippe Veber committed
62
  alignment:aminoacid_fasta file ->
63
  detection_results:cpt file ->
Philippe Veber's avatar
Philippe Veber committed
64
  tree:nhx file ->
65
  unit ->
Philippe Veber's avatar
Philippe Veber committed
66
  svg file
Philippe Veber's avatar
Philippe Veber committed
67 68

val recall_precision_curve :
69
  cpt file ->
Philippe Veber's avatar
Philippe Veber committed
70
  svg file
Philippe Veber's avatar
Philippe Veber committed
71 72 73 74

val oracle :
  n_h0:int ->
  n_ha:int ->
75
  cpt file
76 77

val recall_precision_auc_table :
78
  cpt file ->
79
  (string * float) list workflow