reviewphiltrans_app.ml

open Core
open Reviewphiltrans
open Bistro_utils


let first_nhx_in_dir dir =
  Sys.readdir dir
  |> Array.find_exn ~f:(String.is_suffix ~suffix:".nhx")

let sw b x = if b then Some x else None

let realdata_main ~use_diffsel
                  ~use_pcoc
                  ~use_pcoc_c60
                  ~use_pcoc_gamma
                  ~use_pcoc_v2 
                  ~use_pcoc_pcp
                  ~use_tdg09
                  ~use_topological
                  ~use_identical
                  ~no_use_multinomial
                  ~calc_dnds
                  ~calc_gene_trees
                  ~indir ~outdir ~np ~mem () =
  let loggers = [
      Console_logger.create () ;
  ] in
  let mem = Option.map mem ~f:(fun i -> `GB i) in
  let rd =
    Real_dataset.make
      ~alignment_dir_path:(Filename.concat indir "Alignments")
      ~tree_path:(Filename.concat indir (first_nhx_in_dir indir))
  in
  let use_multinomial = not no_use_multinomial in
  let meths = List.filter_opt [
      sw use_diffsel `Diffsel ;
      sw use_pcoc `Pcoc ;
      sw use_pcoc_c60 `Pcoc_C60 ;
      sw use_pcoc_gamma `Pcoc_gamma ;
      sw use_pcoc_v2   `PCOC_v2 ;
      sw use_pcoc_pcp `PCOC_pcp ;
      sw use_tdg09 `Tdg09 ;
      sw use_topological `Topological ;
      sw use_identical `Identical ;
      sw use_multinomial `Multinomial ;
    ]
  in
  let pal  = List.filter_opt [
    sw calc_dnds `DnDs;
    sw calc_gene_trees `GeneTree;
    ]
  in
  List.concat [
    Repo.shift "Merged_results" (Real_dataset.repo meths rd) ;
    Repo.shift "PreParsed_Dataset" (Real_dataset.repo_parsed_rd pal rd);
    ]
  |> Bistro_utils.Repo.build_main ~outdir ~loggers ?np ?mem

let realdata_command =
  let open Command.Let_syntax in
  Command.basic
    ~summary:"Run pipeline on real data"
    [%map_open
      let outdir =
        flag "--outdir" (required string) ~doc:"PATH Output directory"
      and indir =
        flag "--indir" (required string) ~doc:"PATH Input directory"
      and use_diffsel =
        flag "--diffsel" no_arg ~doc:" use the diffsel method (very slow)."
      and use_pcoc =
        flag "--pcoc" no_arg ~doc:" use the pcoc method (slow)."
      and use_pcoc_c60 =
        flag "--pcoc-c60" no_arg ~doc:" use the pcoc method with c60 profils (very_slow)."
      and use_pcoc_gamma =
        flag "--pcoc-gamma" no_arg ~doc:" use the pcoc method with the gamma option (very_slow)."
      and use_pcoc_v2 =
        flag "--pcoc-v2" no_arg ~doc:" use the pcoc v2 method with the C10 profiles (slow)."
      and use_pcoc_pcp =
        flag "--pcoc-pcp" no_arg ~doc:" use the pcoc v2 method with the physico-chemical profiles (slow)."
      and use_tdg09 =
        flag "--tdg09" no_arg ~doc:" use the tdg09 method (slow)."
      and use_topological =
        flag "--topological" no_arg ~doc:" use the topological method (fast)."
      and use_identical =
        flag "--identical" no_arg ~doc:" use the identical method (fast)."
      and no_use_multinomial =
        flag "--no-multinomial" no_arg ~doc:" not use the multinomial method (very fast so by default)."
      and calc_dnds =
          flag "--dnds" no_arg ~doc:" calculate dn ds dnds trees (slow)."
      and calc_gene_trees =
          flag "--gt" no_arg ~doc:" calculate gene trees (slow)."
      and np =
        flag "--np" (optional int) ~doc:"INT Number of available processors"
      and mem =
        flag "--mem" (optional int) ~doc:"INT Available memory (in GB)"
      in
      realdata_main ~use_diffsel
                    ~use_pcoc
                    ~use_pcoc_c60
                    ~use_pcoc_gamma
                    ~use_pcoc_v2 
                    ~use_pcoc_pcp
                    ~use_tdg09
                    ~use_topological
                    ~use_identical
                    ~no_use_multinomial
                    ~calc_dnds
                    ~calc_gene_trees
                    ~indir ~outdir ~np ~mem
    ]

let () =
  Command.group ~summary:"Reviewphiltrans" [
    "validation", Pipeline.validation_command ;
    "realdata", realdata_command ;
    "alistats", Alistats.command ;
  ]
  |> Command.run