Commit 2edb60ab authored by Philippe Veber's avatar Philippe Veber
Browse files

Detection_pipeline: fixed mock tdg09

parent 63e14e8c
open Reviewphiltrans open Reviewphiltrans
module Top = Bistro_utils.Toplevel_eval.Make(struct let np = 8 let mem = 10 end)() module Top = Bistro_utils.Toplevel_eval.Make(struct let np = 3 let mem = 10 end)()
let () = let () =
Reviewphiltrans_toolbox.Orthomam_db.make "/disk/data/omm" try
|> Orthomam.( Reviewphiltrans_toolbox.Orthomam_db.make "/disk/data/omm"
site_ranking |> Orthomam.(
~subset:5 site_ranking
~convergent_species:species_with_echolocation ~convergent_species:species_with_echolocation
~meth:`tdg09 ~meth:`tdg09
) )
|> Top.eval |> Top.eval
|> List.length |> Core.(Fn.flip List.take 10)
|> print_int |> List.iter Reviewphiltrans.Orthomam.Candidate_site.(fun x -> print_endline x.alignment_id)
with
| Failure _ -> ()
...@@ -111,7 +111,7 @@ module Make(Q : Query) = struct ...@@ -111,7 +111,7 @@ module Make(Q : Query) = struct
| Ok (_, item :: _) -> | Ok (_, item :: _) ->
let open Core_kernel in let open Core_kernel in
let n = String.length item.sequence in let n = String.length item.sequence in
"Sites Tdg09_1MinusFDR Tdg09_1MinusLRT Tdg09_prob_post" "Sites\tTdg09_1MinusFDR\tTdg09_1MinusLRT\tTdg09_prob_post"
:: List.init n ~f:(fun i -> sprintf "%d\t0.0\t0.0\tNA" (i + 1)) :: List.init n ~f:(fun i -> sprintf "%d\t0.0\t0.0\tNA" (i + 1))
|> Out_channel.write_lines [%dest] |> Out_channel.write_lines [%dest]
| _ -> failwith "couldn't read an item in fasta" | _ -> failwith "couldn't read an item in fasta"
......
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