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

Commit 13812c9c authored by Philippe Veber's avatar Philippe Veber
Browse files

orthomam app

parent 1850b1c6
......@@ -13,3 +13,11 @@
(libraries reviewphiltrans)
(preprocess
(pps ppx_jane)))
(executable
(name orthomam_app)
(public_name orthomam_convergence)
(modules orthomam_app)
(libraries reviewphiltrans)
(preprocess
(pps ppx_jane)))
open Reviewphiltrans
module Top = Bistro_utils.Toplevel_eval.Make(struct let np = 8 let mem = 10 end)()
let () =
Reviewphiltrans_toolbox.Orthomam_db.make "/disk/data/omm"
|> Orthomam.(
site_ranking
~subset:5
~convergent_species:species_with_echolocation
~meth:`tdg09
)
|> Top.eval
|> List.length
|> print_int
......@@ -32,7 +32,7 @@ let query (Alignment (db, alignment)) ~convergent_species =
let family_id q =
Filename.basename q.alignment
|> Filename.chop_suffix "_NT.fasta.ali"
|> Fn.flip Filename.chop_suffix "_NT.fasta.ali"
|> String.chop_prefix_exn ~prefix:"all"
let%pworkflow remove_unobserved_sequences_from_alignment phylip : phylip file =
......@@ -581,13 +581,16 @@ let%workflow ranking_of_results ~alignment_ids ~convergent_species (alignments :
in
List.map top_sites ~f:annotate_site
let site_ranking ~meth ~convergent_species db =
let site_ranking ?subset ~meth ~convergent_species db =
let detection_method, column_label = match meth with
| `multinomial_asymptotic_lrt ->
multinomial_asymptotic_lrt, "1MinusLRT"
| `tdg09 ->
tdg09, "Tdg09_1MinusFDR"
in
let queries =
alignments_of_db db
|> (match subset with None -> Fn.id | Some n -> Fn.flip List.take n)
|> List.map ~f:(query ~convergent_species:(Workflow.data convergent_species))
in
let alignment_ids = List.map queries ~f:family_id in
......
......@@ -88,7 +88,8 @@ module Candidate_site : sig
end
val site_ranking :
meth:[`multinomial_asymptotic_lrt] ->
?subset:int ->
meth:[`multinomial_asymptotic_lrt | `tdg09] ->
convergent_species:string list ->
Orthomam_db.t ->
Candidate_site.t list workflow
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