Commit f962d9ce authored by Carine Rey's avatar Carine Rey
Browse files

add descr in diffsel

parent 17edfbb0
......@@ -63,7 +63,7 @@ echo end_it=$end_it
|}
let diffsel ~(phy_n:nucleotide_phylip workflow) ~(tree: _ workflow) ~(w_every:int) ~(n_cycles: int) ~(id: int) ?seed () : [`diffsel] directory workflow =
let diffsel ~(phy_n:nucleotide_phylip workflow) ~(tree: _ workflow) ~(w_every:int) ~(n_cycles: int) ~(id: int) ?(descr = "") ?seed () : [`diffsel] directory workflow =
let env = Env.env_diffsel in
let tmp_tree = tmp // "myrun.tree" in
let tmp_ali = tmp // "myrun.ali" in
......@@ -78,7 +78,7 @@ let diffsel ~(phy_n:nucleotide_phylip workflow) ~(tree: _ workflow) ~(w_every:in
let n_cycles = if (n_cycles > 200) then 20 else n_cycles in
let script_r = tmp // "DiffselMCMCConvergenceAnalysis.Rmd" in
(*_build/diffsel -t data/samhd1.tree -d data/samhd1.ali -ncond 3 -x 1 10000 myrun*)
workflow ~descr:("convergence_detection.run_diffsel." ^(string_of_int id)) [
workflow ~descr:("convergence_detection.run_diffsel." ^(string_of_int id) ^ "." ^ descr) [
docker env (
and_list [
mkdir_p dest;
......
......@@ -7,6 +7,7 @@ val diffsel :
w_every : int ->
n_cycles: int ->
id: int ->
?descr:string ->
?seed:int ->
unit ->
[`diffsel] directory workflow
......
......@@ -169,6 +169,9 @@ let repo_of_dataset_results_l ~dataset_results_l =
|> List.concat
let derive_from_det_meth ~det_meth ~(dataset : Dataset.t) ~preview =
let model_prefix = dataset.model_prefix in
let tree_prefix = dataset.tree_prefix in
let descr = model_prefix ^"." ^ tree_prefix in
let faa = dataset.dataset.faa in
let fna = dataset.dataset.fna in
let phy_n = Bppsuite.fna2phy ~fna in
......@@ -177,14 +180,14 @@ let derive_from_det_meth ~det_meth ~(dataset : Dataset.t) ~preview =
let diffsel_tree = Tree_dataset.diffsel_tree dataset.dataset.tree_dataset in
let tree_conv = Tree_dataset.topological_tree dataset.dataset.tree_dataset in
let w_every = if preview then 1 else 1 in
let n_cycles = if preview then 10 else 2000 in
let n_cycles = if preview then 2000 else 2000 in
let seed = Hashtbl.hash dataset.seed in
match det_meth with
| `Pcoc -> `Pcoc (Pcoc.pcoc ~catx_est:10 ~plot_complete:false ~gamma:false ~faa ~tree:tree_sc)
| `Pcoc_gamma -> `Pcoc_gamma (Pcoc.pcoc ~catx_est:10 ~plot_complete: false ~gamma:true ~faa ~tree:tree_sc)
| `Pcoc_C60 -> `Pcoc_C60 (Pcoc.pcoc ~catx_est:60 ~plot_complete: false ~gamma:false ~faa ~tree:tree_sc)
| `Tdg09 -> `Tdg09 (Tamuri.tdg09 ~faa ~tree:tree_sc)
| `Diffsel -> `Diffsel (Diffsel.diffsel ~phy_n ~tree:diffsel_tree ~w_every ~n_cycles ~id:1 ~seed ())
| `Diffsel -> `Diffsel (Diffsel.diffsel ~descr ~phy_n ~tree:diffsel_tree ~w_every ~n_cycles ~id:1 ~seed ())
| `Identical_LG -> `Identical_LG (Identical.identical ~faa ~tree_id ~tree_sc ~prot_model:"LG08")
| `Identical_WAG -> `Identical_WAG (Identical.identical ~faa ~tree_id ~tree_sc ~prot_model:"WAG01")
| `Topological_LG -> `Topological_LG (Topological.topological ~faa ~tree:tree_id ~tree_conv ~prot_model:"LG08")
......
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