Commit e594f2a8 authored by Philippe Veber's avatar Philippe Veber
Browse files

removed buggy version of multinomial

parent 27217276
......@@ -31,8 +31,6 @@ module type S = sig
val topological : query -> cpt file
val multinomial : query -> cpt file
val multinomial_simulation_lrt : query -> cpt file
val multinomial_simulation_sparse : query -> cpt file
......@@ -121,11 +119,6 @@ module Make (Q : Query) = struct
Topological.topological ~faa ~tree ~tree_conv ~prot_model:"LG08" ()
|> Topological.results
let multinomial d =
Multinomial.multinomial
~tree_sc:(tree ~branch_length_unit:`Amino_acid d)
~faa:(amino_acid_alignment d) ()
let multinomial_asymptotic_lrt d =
Multinomial.multinomial_asymptotic_lrt
~tree_sc:(tree ~branch_length_unit:`Amino_acid d)
......
......@@ -31,8 +31,6 @@ module type S = sig
val topological : query -> cpt file
val multinomial : query -> cpt file
val multinomial_simulation_lrt : query -> cpt file
val multinomial_simulation_sparse : query -> cpt file
......
open Core
open Bistro
open Bistro.Shell_dsl
open File_formats
let multinomial ?(descr="") ~(tree_sc:_ file) ~(faa:aminoacid_fasta file) () : cpt file =
let img = Env.env_py in
Workflow.shell ~descr:("calc_multinomial."^descr) ~img [
cmd "python" [
file_dump (string Scripts.calc_multinomial) ;
opt "-t" dep tree_sc;
opt "-a" dep faa;
opt "-o" ident dest ;
]
]
let%pworkflow multinomial_ocaml_implementation ~meth ~(tree_sc:_ file) ~(faa:aminoacid_fasta file) (* : cpt file *) =
let open Phylogenetics in
let open Phylogenetics_convergence in
......
......@@ -218,7 +218,6 @@ let derive_from_det_meth ~det_meth ~(dataset : Dataset.t) ~preview =
| `Identical_WAG -> `Identical_WAG (Identical.identical ~descr ~faa ~tree_id ~tree_sc ~prot_model:"WAG01" ())
| `Topological_LG -> `Topological_LG (Topological.topological ~descr ~faa ~tree:tree_id ~tree_conv ~prot_model:"LG08" ())
| `Topological_WAG -> `Topological_WAG (Topological.topological ~descr ~faa ~tree:tree_id ~tree_conv ~prot_model:"WAG01" ())
| `Multinomial -> `Multinomial (Multinomial.multinomial ~descr ~faa ~tree_sc ())
| `Msd e -> `Msd (Msd.msd ~descr ~e ~faa ~tree_sc, e)
......
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