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