Commit 4fd11201 authored by Carine Rey's avatar Carine Rey Committed by Philippe Veber
Browse files

add input for diffsel in realdata dataset output

parent c0d4872d
......@@ -17,7 +17,7 @@ let repo dataset_l =
let model_prefix = dataset.model_prefix in
let tree_prefix = dataset.tree_prefix in
if dataset.is_real then
let repo_realdata = Raw_dataset.repo_realdata ~ali_prefix:model_prefix ~tree_prefix (Ready_dataset.to_raw dataset.dataset) in
let repo_realdata = Ready_dataset.repo_realdata ~ali_prefix:model_prefix ~tree_prefix dataset.dataset in
repo_realdata
|> Repo.shift "Dataset"
|> Repo.shift tree_prefix
......
......@@ -17,15 +17,7 @@ let repo ~prefix rd =
item [prefix ^ ".fna"] rd.fna ;
]
let repo_realdata ~tree_prefix ~ali_prefix rd =
let faa = Bppsuite.fna2faa ~fna:rd.fna in
Repo.[
item [ali_prefix ^ ".fna"] rd.fna ;
item [ali_prefix ^ ".faa"] faa ;
item [tree_prefix ^ "." ^ ali_prefix ^ ".nhx"] rd.input_tree ;
]
|> Repo.shift ali_prefix
|> Repo.shift "Alignments"
let filter_input_tree ?(descr="") ~(tree:_ workflow) ~(fna:nucleotide_fasta pworkflow) () : nhx pworkflow =
Workflow.shell ~descr:("filter_input_tree."^descr) [
......
......@@ -47,6 +47,22 @@ let repo rd =
]
|> List.concat
let repo_realdata ~tree_prefix ~ali_prefix rd =
let phy_nt = (Bppsuite.fna2phy ~fna:rd.fna) in
List.concat [
Repo.[
item [ali_prefix ^ ".fna"] rd.fna ;
item [ali_prefix ^ ".faa"] rd.faa ;
item [tree_prefix ^ "." ^ ali_prefix ^ ".nhx"] rd.input_tree ;
];
Repo.[
item [ali_prefix ^ ".nt.phy"] phy_nt ;
item [ali_prefix ^ ".tree.diffsel" ] (Tree_dataset.diffsel_tree rd.tree_dataset) ;
] |> Repo.shift "ForDiffsel";
]
|> Repo.shift ali_prefix
|> Repo.shift "Alignments"
let to_raw { input_tree ; fna ; fna_infos ; _ } =
{ Raw_dataset.input_tree ; fna ; fna_infos}
......
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