Orthomam: tree output for the whole database

lib/orthomam.ml

@@ -69,7 +69,7 @@ let%pworkflow clip_tree_on_alignment tree ali =
 let omm_tree_of_db db =
   Workflow.input (Orthomam_db.tree db)
 
-let annotate_convergent_species_in_tree (tree : newick file) species : newick file =
+let annotate_convergent_species_in_tree (tree : newick file) species : nhx file =
   Workflow.path_plugin ~version:3 ~descr:"tree_of_convergent_species" (
     let open Phylogenetics in
     let%pdeps species = species
@@ -359,14 +359,16 @@ module Q = struct
     Workflow.input (q.alignment :> string)
     |> remove_unobserved_sequences_from_alignment
 
+  let omm_tree_with_branch_lengths ~branch_length_unit = match branch_length_unit with
+    | `Nucleotide -> estimated_nucleotide_tree
+    | `Amino_acid -> estimated_amino_acid_tree
+    | `Codon -> estimated_codon_tree
+
   let tree ~branch_length_unit q =
-    let omm_tree_with_branch_lengths = match branch_length_unit with
-      | `Nucleotide -> estimated_nucleotide_tree q.db
-      | `Amino_acid -> estimated_amino_acid_tree q.db
-      | `Codon -> estimated_codon_tree q.db
-    in
     clip_tree_on_alignment
-      (annotate_convergent_species_in_tree omm_tree_with_branch_lengths q.convergent_species)
+      (annotate_convergent_species_in_tree
+         (omm_tree_with_branch_lengths ~branch_length_unit q.db)
+         q.convergent_species)
       (alignment q)
 
   let nucleotide_alignment q =
@@ -375,6 +377,11 @@ end
 
 include Q
 
+let tree_of_db db ~branch_length_unit ~convergent_species =
+  annotate_convergent_species_in_tree
+    (omm_tree_with_branch_lengths ~branch_length_unit db)
+    (Workflow.data convergent_species)
+
 include Detection_pipeline.Make(Q)
 
 let species_with_echolocation = [

lib/orthomam.mli

@@ -19,6 +19,12 @@ val alignment : query -> phylip file
 
 val nucleotide_alignment : query -> nucleotide_fasta file
 
+val tree_of_db :
+  Orthomam_db.t ->
+  branch_length_unit:[`Nucleotide | `Amino_acid | `Codon] ->
+  convergent_species:string list ->
+  nhx file
+
 val tree :
   branch_length_unit:[`Nucleotide | `Amino_acid | `Codon] ->
   query ->