Detection_pipeline: added failsafe version of tdg09

lib/detection_pipeline.ml

@@ -26,6 +26,7 @@ module type S = sig
   val multinomial_asymptotic_lrt : query -> text file
   val multinomial_asymptotic_sparse : query -> text file
   val tdg09 : query -> text file
+  val failsafe_tdg09 : query -> text file
   val pcoc : ?gamma:bool -> ?ncat:int -> query -> text file
   val pcoc_v2 :
     ?gamma:bool ->
@@ -105,6 +106,18 @@ module Make(Q : Query) = struct
       ()
     |> Tamuri.results
 
+  let%pworkflow mock_tdg09 d =
+    match Biotk.Fasta.from_file [%path amino_acid_alignment d] with
+    | Ok (_, item :: _) ->
+      let open Core_kernel in
+      let n = String.length item.sequence in
+      "Sites   Tdg09_1MinusFDR Tdg09_1MinusLRT Tdg09_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"
+
+  let failsafe_tdg09 d = Workflow.trywith (tdg09 d) (mock_tdg09 d)
+
   let diffseltree d =
     Tree_dataset.prepare_diffsel_tree (tree ~branch_length_unit:`Amino_acid d)
 

lib/detection_pipeline.mli

@@ -26,6 +26,7 @@ module type S = sig
   val multinomial_asymptotic_lrt : query -> text file
   val multinomial_asymptotic_sparse : query -> text file
   val tdg09 : query -> text file
+  val failsafe_tdg09 : query -> text file
   val pcoc : ?gamma:bool -> ?ncat:int -> query -> text file
   val pcoc_v2 :
     ?gamma:bool ->

lib/orthomam.ml

@@ -535,7 +535,7 @@ let site_ranking ?subset ~meth ~convergent_species db =
     | `multinomial_asymptotic_lrt ->
       multinomial_asymptotic_lrt, "1MinusLRT"
     | `tdg09 ->
-      tdg09, "Tdg09_1MinusFDR"
+      failsafe_tdg09, "Tdg09_1MinusFDR"
   in
   let queries =
     alignments_of_db db