Commit fde4e6e7 authored by Philippe Veber's avatar Philippe Veber
Browse files

Pipeline2.benchmark: added tdg09

parent 8ff45c6f
......@@ -78,12 +78,13 @@ let merge_results ?fna_infos ~(res_by_tools : result list) () : text_file pworkf
] ;
]
let merge_result_tables ?fna_infos ?oracle ?multinomial ?diffsel ?diffseldsparse () : text_file pworkflow =
let merge_result_tables ?fna_infos ?oracle ?multinomial ?tdg09 ?diffsel ?diffseldsparse () : text_file pworkflow =
Workflow.shell ~descr:"convergence_detection.merge_results" [
cmd "python" ~img:Env.env_py [
file_dump (string Scripts.merge_det_results) ;
opt "-o" ident dest ;
option (opt "--multinomial" dep) multinomial ;
option (opt "--tdg09" dep) tdg09 ;
option (opt "--diffsel" dep) diffsel ;
option (opt "--diffseldsparse" dep) diffseldsparse ;
option (opt "--oracle" dep) oracle ;
......
......@@ -36,6 +36,7 @@ val merge_result_tables :
?fna_infos:text_file pworkflow ->
?oracle:text_file pworkflow ->
?multinomial:text_file pworkflow ->
?tdg09:text_file pworkflow ->
?diffsel:text_file pworkflow ->
?diffseldsparse:text_file pworkflow ->
unit ->
......
......@@ -144,6 +144,12 @@ let diffsel d =
()
|> Diffsel.selector
let tdg09 d =
Tamuri.tdg09
~tree:(tree d)
~faa:(amino_acid_alignment d)
|> Tamuri.results
let multinomial d =
Multinomial.multinomial
~tree_sc:(tree d)
......@@ -211,11 +217,12 @@ let multinomial_benchmark d =
multinomial_simulation_sparse d ;
]
let benchmark d =
let benchmark ?(use_diffsel = false) d =
Convergence_detection.merge_result_tables
~multinomial:(multinomial d)
~diffsel:(diffsel d)
~diffseldsparse:(diffseldsparse ~eps:1e-3 ~pi:1. d)
~multinomial:(multinomial_asymptotic_lrt d)
~tdg09:(tdg09 d)
?diffsel:(if use_diffsel then Some (diffsel d) else None)
?diffseldsparse:(if use_diffsel then Some (diffseldsparse ~eps:1e-3 ~pi:1. d) else None)
~oracle:(oracle d)
()
|> Convergence_detection.recall_precision_curve
open Bistro
open File_formats
val simulator :
?branch_factor:float ->
?seed:int ->
......
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