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

Commit 9a03de8b authored by Philippe Veber's avatar Philippe Veber
Browse files

Simulation_dataset.benchmark_stats: fixed bug

parent 94013a1b
...@@ -15,7 +15,7 @@ let besnard2009 = { ...@@ -15,7 +15,7 @@ let besnard2009 = {
label = "besnard2009" ; label = "besnard2009" ;
tree = Bistro.Workflow.input "data/besnard2009/besnard2009.nhx" ; tree = Bistro.Workflow.input "data/besnard2009/besnard2009.nhx" ;
rooted = true ; rooted = true ;
branch_scale = 10. ; branch_scale = 1. ;
ne_s = 4., 4. ; ne_s = 4., 4. ;
} }
...@@ -23,7 +23,7 @@ let oneline_rodent = { ...@@ -23,7 +23,7 @@ let oneline_rodent = {
label = "online_rodent" ; label = "online_rodent" ;
tree = Bistro.Workflow.input "data/online_rodent/online_rodent.nhx" ; tree = Bistro.Workflow.input "data/online_rodent/online_rodent.nhx" ;
rooted = true ; rooted = true ;
branch_scale = 10. ; branch_scale = 1. ;
ne_s = 4., 4. ; ne_s = 4., 4. ;
} }
...@@ -31,7 +31,7 @@ let rubisco = { ...@@ -31,7 +31,7 @@ let rubisco = {
label = "rubisco" ; label = "rubisco" ;
tree = Rubisco_dataset.(Path "data/rubisco" |> Query.tree ~branch_length_unit:`Amino_acid) ; tree = Rubisco_dataset.(Path "data/rubisco" |> Query.tree ~branch_length_unit:`Amino_acid) ;
rooted = false ; rooted = false ;
branch_scale = 10. ; branch_scale = 1. ;
ne_s = 4., 4. ; ne_s = 4., 4. ;
} }
...@@ -44,7 +44,7 @@ let orthomam_echolocation = { ...@@ -44,7 +44,7 @@ let orthomam_echolocation = {
(Codepitk.Orthomam_db.make "omm") (Codepitk.Orthomam_db.make "omm")
) ; ) ;
rooted = false ; rooted = false ;
branch_scale = 10. ; branch_scale = 1. ;
ne_s = 4., 4. ; ne_s = 4., 4. ;
} }
......
...@@ -212,6 +212,7 @@ let%pworkflow benchmark_statistics simulation ~labels ~results = ...@@ -212,6 +212,7 @@ let%pworkflow benchmark_statistics simulation ~labels ~results =
let open Codepitk in let open Codepitk in
let open OCamlR_base in let open OCamlR_base in
let open Codepitk.Simulator.Site_independent_mutsel in let open Codepitk.Simulator.Site_independent_mutsel in
let module Codon = Codon.Universal_genetic_code.NS in
let load_results fn col = let load_results fn col =
let open Codepitk in let open Codepitk in
let df = Dataframe.from_file fn |> Rresult.R.failwith_error_msg in let df = Dataframe.from_file fn |> Rresult.R.failwith_error_msg in
...@@ -233,7 +234,6 @@ let%pworkflow benchmark_statistics simulation ~labels ~results = ...@@ -233,7 +234,6 @@ let%pworkflow benchmark_statistics simulation ~labels ~results =
l, `Numeric (Numeric.of_array_opt r) l, `Numeric (Numeric.of_array_opt r)
) in ) in
let amino_acid_vector_of_codon_vector xs = let amino_acid_vector_of_codon_vector xs =
let module Codon = Codon.Universal_genetic_code.NS in
Amino_acid.Vector.init (fun aa -> Amino_acid.Vector.init (fun aa ->
List.fold Codon.all ~init:0. ~f:(fun acc c -> List.fold Codon.all ~init:0. ~f:(fun acc c ->
if Amino_acid.equal aa (Codon.aa_of_codon c) then if Amino_acid.equal aa (Codon.aa_of_codon c) then
...@@ -258,7 +258,13 @@ let%pworkflow benchmark_statistics simulation ~labels ~results = ...@@ -258,7 +258,13 @@ let%pworkflow benchmark_statistics simulation ~labels ~results =
let t = let t =
Amino_acid.Table.init (fun aa -> Amino_acid.Table.init (fun aa ->
let aa = Amino_acid.to_char aa in let aa = Amino_acid.to_char aa in
List.count seqs ~f:(fun s -> Char.equal (s : Dna.t :> string).[i] aa) List.count seqs ~f:(fun s ->
let codon_str = String.sub (s : Dna.t :> string) ~pos:(i * 3) ~len:3 in
let codon = match Codon.of_string codon_str with
| Some c -> c
| None -> assert false
in
Char.equal (Amino_acid.to_char (Codon.aa_of_codon codon)) aa)
) )
in in
(t :> int array) (t :> int array)
......
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