Commit 91b4df22 authored by Carine Rey's avatar Carine Rey
Browse files

realdata: add a output repo with parsed input files

parent 5719e39f
......@@ -37,7 +37,10 @@ let realdata_main ~use_diffsel
sw use_multinomial `Multinomial ;
]
in
Real_dataset.repo meths rd
List.concat [
Repo.shift "Merged_results" (Real_dataset.repo meths rd) ;
Repo.shift "PreParsed_Dataset" (Real_dataset.repo_parsed_rd rd);
]
|> Bistro_utils.Repo.build_main ~outdir ~loggers ?np ?mem
let realdata_command =
......@@ -54,9 +57,9 @@ let realdata_command =
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)."
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)."
flag "--pcoc-gamma" no_arg ~doc:" use the pcoc method with the gamma option (very_slow)."
and use_topological =
flag "--topological" no_arg ~doc:" use the topological method (fast)."
and use_identical =
......
open Core_kernel
open Bistro
open Bistro_utils
type t = {
tree_path : string ;
......@@ -111,3 +112,13 @@ let repo meths rd =
List.map (result_table meths rd) ~f:(fun (name, table) ->
Bistro_utils.Repo.item [name ^ ".tsv"] table
)
let repo_parsed_rd rd =
let families = families rd in
List.map families ~f:(fun f ->
[
Bistro_utils.Repo.item [(Family.name f) ^ ".faa"] (DP.amino_acid_alignment f);
Bistro_utils.Repo.item [(Family.name f) ^ ".nhx"] (Family.tree f);
Bistro_utils.Repo.item [(Family.name f) ^ ".fna"] (Family.nucleotide_alignment f);
] |> Repo.shift (Family.name f );
) |> List.concat
......@@ -27,6 +27,9 @@ val repo :
meth list ->
t -> Bistro_utils.Repo.t
val repo_parsed_rd :
t -> Bistro_utils.Repo.t
module Family : sig
type t
val tree : t -> nhx pworkflow
......
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