Detection_pipeline: fixed mock tdg09

app/orthomam_app.ml

 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 () =
-  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
+  try
+    Reviewphiltrans_toolbox.Orthomam_db.make "/disk/data/omm"
+    |> Orthomam.(
+        site_ranking
+          ~convergent_species:species_with_echolocation
+          ~meth:`tdg09
+      )
+    |> Top.eval
+    |> Core.(Fn.flip List.take 10)
+    |> List.iter Reviewphiltrans.Orthomam.Candidate_site.(fun x -> print_endline x.alignment_id)
+  with
+  | Failure _ -> ()

lib/detection_pipeline.ml

@@ -111,7 +111,7 @@ module Make(Q : Query) = struct
     | Ok (_, item :: _) ->
       let open Core_kernel 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))
       |> Out_channel.write_lines [%dest]
     | _ -> failwith "couldn't read an item in fasta"