Commit 86e2692e authored by Carine Rey's avatar Carine Rey
Browse files

try to connect simulations and detection pipelines

parent 978ce4ae
...@@ -27,11 +27,16 @@ push_docker: ...@@ -27,11 +27,16 @@ push_docker:
cd - ; \ cd - ; \
done done
test: test_simu:
cd example && \ cd example && \
reviewphiltrans pipeline --outdir outdir --tree-dir trees --profile-fn aa_fitness/tiragesBloomK30.tsv --preview --np 4 && \ reviewphiltrans pipeline simulation --outdir outdir --tree-dir trees --profile-fn aa_fitness/tiragesBloomK30.tsv --preview --np 4 && \
mv dag.dot dagtest.dot && \ mv dag.dot dagtest_sim.dot && \
dot -Tsvg dagtest.dot -o dagtest.svg dot -Tsvg dagtest_sim.dot -o dagtest_sim.svg
test_det:
cd example && \
reviewphiltrans pipeline detection --outdir outdir/detection --indir outdir/data --preview --np 4 && \
mv dag.dot dagtest_det.dot && \
dot -Tsvg dagtest_det.dot -o dagtest_det.svg
test_real: test_real:
cd example && \ cd example && \
......
...@@ -14,12 +14,11 @@ let repo ~preview dataset_l = ...@@ -14,12 +14,11 @@ let repo ~preview dataset_l =
List.map dataset_l ~f:(fun dataset -> List.map dataset_l ~f:(fun dataset ->
let model_prefix = dataset.model_prefix in let model_prefix = dataset.model_prefix in
let tree_prefix = dataset.tree_prefix in let tree_prefix = dataset.tree_prefix in
let repo = let repo_raw_data = Ready_dataset.repo dataset.dataset in
if preview then let repo_ready_data = if preview then Raw_dataset.repo ~prefix:model_prefix (Ready_dataset.to_raw dataset.dataset) else [] in
Ready_dataset.repo dataset.dataset [Repo.shift "data" (Repo.shift tree_prefix repo_ready_data);
else Repo.shift "debug_data" (Repo.shift tree_prefix (Repo.shift model_prefix repo_ready_data));
Raw_dataset.repo (Ready_dataset.to_raw dataset.dataset) ]
in
Repo.shift tree_prefix (Repo.shift model_prefix repo)
) )
|> List.concat |> List.concat
|> List.concat
...@@ -40,7 +40,7 @@ let parse_input_data indir = ...@@ -40,7 +40,7 @@ let parse_input_data indir =
} in } in
[dataset] [dataset]
else else
[] failwith ({|More than 2 files in |} ^ (Filename.concat indir dataset_prefix ))
) )
|> List.concat |> List.concat
...@@ -148,8 +148,10 @@ let repo_of_dataset_results_l ~dataset_results_l = ...@@ -148,8 +148,10 @@ let repo_of_dataset_results_l ~dataset_results_l =
let det_results_l = dataset_results.res_by_tools in let det_results_l = dataset_results.res_by_tools in
let merged_results = dataset_results.merged_results in let merged_results = dataset_results.merged_results in
let plot_merge_results = dataset_results.plot_merged_results in let plot_merge_results = dataset_results.plot_merged_results in
let merged_results_item = Repo.item ["merged_results.tsv"] merged_results in let model_prefix = dataset_results.model_prefix in
let plot_merged_results_item = Repo.item ["plot_merged_results"] plot_merge_results in let tree_prefix = dataset_results.tree_prefix in
let merged_results_item = Repo.item [tree_prefix ^"."^model_prefix^". merged_results.tsv"] merged_results in
let plot_merged_results_item = Repo.item [tree_prefix ^"."^model_prefix^".plot_merged_results"] plot_merge_results in
let repo = let repo =
merged_results_item :: merged_results_item ::
plot_merged_results_item :: plot_merged_results_item ::
......
...@@ -8,9 +8,8 @@ type t = { ...@@ -8,9 +8,8 @@ type t = {
fna_infos: text_file workflow option ; fna_infos: text_file workflow option ;
} }
let repo rd = let repo ~prefix rd =
Repo.[ Repo.[
item ["input_tree.nhx"] rd.input_tree ; item [prefix ^ ".nhx"] rd.input_tree ;
item ["simulated_sequences.fna"] rd.fna ; item [prefix ^ ".fna"] rd.fna ;
] ]
|> Repo.shift "raw_dataset"
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