use custom ocaml workflow for nucleotide sequence translation

instead of bppseqman, because it's slow to invoke a container for such
a fast operation.

lib/detection_pipeline.ml

@@ -44,7 +44,7 @@ module Make(Q : Query) = struct
   open Q
 
   let amino_acid_alignment d =
-    Bppsuite.fna2faa (nucleotide_alignment d)
+    Utils.amino_acid_fasta_of_nucleotide_fasta (nucleotide_alignment d)
 
   let phylip_nucleotide_alignment d =
     Bppsuite.fna2phy ~fna:(nucleotide_alignment d)

lib/utils.ml

 open Core_kernel
 open Bistro
 open Bistro.Shell_dsl
-open Biotope.Formats
+open File_formats
 
 let assign k v =
   seq ~sep:"=" [ string k ; v ]
@@ -68,3 +68,17 @@ let%pworkflow [@version 2] newick_of_nhx (t : nhx file) : newick file =
   let tree = Newick.from_file tree_file in
   let tree = Newick.map_inner_tree tree ~f:(Tree.map ~leaf:Fn.id ~node:Fn.id ~branch:(fun bi -> { bi with Newick.tags = [] })) in
   Newick.to_file tree [%dest]
+
+let%pworkflow amino_acid_fasta_of_nucleotide_fasta (fa : nucleotide_fasta file) =
+  let fa = [%path fa] in
+  match Biotk.Fasta.from_file fa with
+  | Error e -> failwith e
+  | Ok (_, items) ->
+    List.map items ~f:(fun it ->
+        let sequence =
+          it.sequence
+          |> Reviewphiltrans_toolbox.Utils.translate_nucleotide_sequence_whatever_it_takes
+        in
+        { it with Biotk.Fasta.sequence }
+      )
+    |> Biotk.Fasta.to_file [%dest]