RER converge start up handle from orthomam

lib/orthomam.ml

@@ -595,3 +595,29 @@ let draw_site q pos =
     | Error msg -> failwith msg
   in
   Workflow.path_plugin ~descr:"orthomam." f
+
+
+let rer_converge ?max_read ?transform ?weighted ?scale ?continuous ~db
+    ~phenotypes =
+  let open Bistro_bio in
+  let module RER = Rer_converge in
+  let species_tree = estimated_codon_tree db in
+  let model = Iqtree.model_spec ~freq_type:`F `ECMK07 in
+  let queries =
+    alignments_of_db db
+    |> List.map ~f:(query ~convergent_species:phenotypes)
+  in
+  let gene_ids = List.map ~f:family_id queries in
+  let ali_files = List.map ~f:Q.alignment queries in
+  let gene_trees =
+    List.map
+      ~f:(fun q ->
+        Iqtree.iqtree ~te:species_tree ~m:model ~st:(`CODON 1) (`phylip q)
+        |> Iqtree.treefile)
+      ali_files
+    |> List.zip_exn gene_ids
+  in
+  let gene_tree_set = RER.gene_tree_file gene_trees in
+  let phenotype = RER.phenotypes_of_convergent_species phenotypes in
+  RER.rer_converge ?max_read ?transform ?weighted ?scale ?continuous
+    ~gene_tree_set ~phenotype

lib/orthomam.mli

@@ -85,3 +85,13 @@ val site_ranking :
   Candidate_site.t list workflow
 
 val draw_site : query -> int -> pdf file
+
+val rer_converge :
+  ?max_read:int ->
+  ?transform:[ `none | `sqrt | `log ] ->
+  ?weighted:bool ->
+  ?scale:bool ->
+  ?continuous:bool ->
+  db:Orthomam_db.t ->
+  phenotypes:string list workflow ->
+  tsv file