Commit 45225422 authored by Philippe Veber's avatar Philippe Veber

Run: added tdg09

parent 4b01833c
......@@ -20,6 +20,13 @@ let multinomial_method = Detection_method {
f = Pipeline.multinomial_asymptotic_lrt ;
}
let tdg09_method = Detection_method {
id = "tdg09" ;
name = "TDG09" ;
cpt_column_label = "Tdg09_1MinusFDR" ;
f = Pipeline.tdg09 ;
}
let candidate_site_report dataset (Detection_method meth) =
let all_queries = Dataset.queries dataset in
let sites =
......@@ -113,11 +120,14 @@ type t = {
tree_file : string ;
alignment_dir : string ;
convergent_species_file : string ;
use_tdg09 : bool ;
}
let detection_methods _run = [
multinomial_method ;
]
let detection_methods run =
List.filter_opt [
Some multinomial_method ;
if run.use_tdg09 then Some tdg09_method else None ;
]
let convergent_species_workflow run =
[%workflow
......@@ -156,13 +166,17 @@ let repo run =
let main
~tree_file ~alignment_dir ~convergent_species_file
~outdir ~np ~mem () =
~outdir ~np ~mem
~use_tdg09 () =
let loggers = [
Console_logger.create () ;
] in
let mem = Option.map mem ~f:(fun i -> `GB i) in
let run = { tree_file ; alignment_dir ; convergent_species_file } in
let run = {
tree_file ; alignment_dir ; convergent_species_file ;
use_tdg09
} in
let repo = repo run in
Bistro_utils.Repo.build_main ~outdir ~loggers ?np ?mem repo
......@@ -183,6 +197,10 @@ let command =
flag "--np" (optional int) ~doc:"INT Number of available processors"
and mem =
flag "--mem" (optional int) ~doc:"INT Available memory (in GB)"
and use_tdg09 =
flag "--tdg09" no_arg ~doc:" Use TDG09 method"
in
main ~tree_file ~alignment_dir ~convergent_species_file ~outdir ~np ~mem
main
~tree_file ~alignment_dir ~convergent_species_file ~outdir ~np ~mem
~use_tdg09
]
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