Commit 98eaf13c authored by Philippe Veber's avatar Philippe Veber
Browse files

fix compilation errors due to merge with master

parent 7b42ed65
......@@ -37,9 +37,7 @@ eval "$(opam config env)"
## install dependencies
```
opam pin add -y owl-base https://github.com/pveber/owl.git#fix-multinomial
opam pin add -y owl https://github.com/pveber/owl.git#fix-multinomial
opam pin add -y biocaml --dev-repo
opam pin add -y croquis https://github.com/pveber/croquis.git
opam pin add -y bistro --dev-repo
opam pin add -y pipes https://github.com/pveber/pipes.git
opam pin add -y gzt https://github.com/pveber/gzt.git
......
......@@ -91,7 +91,7 @@ let bppancestor ?(descr="") ~faa ~tree ~config : _ workflow =
)
]
let identical ?(descr="") ~(tree_id:_ pworkflow) ~(tree_sc:_ pworkflow) ~(faa:aminoacid_fasta pworkflow) ~prot_model : [`identical] dworkflow =
let identical ?(descr="") ~(tree_id:_ pworkflow) ~(tree_sc:_ pworkflow) ~(faa:aminoacid_fasta pworkflow) ~prot_model () : [`identical] dworkflow =
let config = [assign "model" (string prot_model)] in
let out1 = dest // "out1.tsv" in
let out2 = dest // "out2.tsv" in
......
......@@ -3,7 +3,7 @@ open Bistro
open Bistro.Shell_dsl
open File_formats
let multinomial ?(descr="") ~(tree_sc:_ pworkflow) ~(faa:aminoacid_fasta pworkflow) : [`multinomial] dworkflow =
let multinomial ?(descr="") ~(tree_sc:_ pworkflow) ~(faa:aminoacid_fasta pworkflow) : text_file pworkflow =
let img = Env.env_py in
Workflow.shell ~descr:("calc_multinomial."^descr) [
mkdir_p dest;
......
......@@ -212,12 +212,12 @@ let derive_from_det_meth ~det_meth ~(dataset : Dataset.t) ~preview =
| `Pcoc -> `Pcoc (Pcoc.pcoc ~descr ~catx_est:10 ~max_gap_per_conv_leaf:25 ~max_gap_per_pos:25 ~plot_complete:false ~gamma:false ~faa ~tree:tree_sc ())
| `Pcoc_gamma -> `Pcoc_gamma (Pcoc.pcoc ~descr ~catx_est:10 ~max_gap_per_conv_leaf:25 ~max_gap_per_pos:25 ~plot_complete: false ~gamma:true ~faa ~tree:tree_sc ())
| `Pcoc_C60 -> `Pcoc_C60 (Pcoc.pcoc ~descr ~catx_est:60 ~plot_complete: false ~gamma:false ~faa ~tree:tree_sc ())
| `Tdg09 -> `Tdg09 (Tamuri.tdg09 ~descr ~faa ~tree:tree_sc)
| `Diffsel -> `Diffsel (Diffsel.diffsel ~descr ~phy_n ~tree:diffsel_tree ~w_every ~n_cycles ~id:1 ~seed ())
| `Identical_LG -> `Identical_LG (Identical.identical ~descr ~faa ~tree_id ~tree_sc ~prot_model:"LG08")
| `Identical_WAG -> `Identical_WAG (Identical.identical ~descr ~faa ~tree_id ~tree_sc ~prot_model:"WAG01")
| `Topological_LG -> `Topological_LG (Topological.topological ~descr ~faa ~tree:tree_id ~tree_conv ~prot_model:"LG08")
| `Topological_WAG -> `Topological_WAG (Topological.topological ~descr ~faa ~tree:tree_id ~tree_conv ~prot_model:"WAG01")
| `Tdg09 -> `Tdg09 (Tamuri.tdg09 ~descr ~faa ~tree:tree_sc ())
| `Diffsel -> `Diffsel (Diffsel.diffsel ~descr ~phy_n ~tree:diffsel_tree ~w_every ~n_cycles ~seed ())
| `Identical_LG -> `Identical_LG (Identical.identical ~descr ~faa ~tree_id ~tree_sc ~prot_model:"LG08" ())
| `Identical_WAG -> `Identical_WAG (Identical.identical ~descr ~faa ~tree_id ~tree_sc ~prot_model:"WAG01" ())
| `Topological_LG -> `Topological_LG (Topological.topological ~descr ~faa ~tree:tree_id ~tree_conv ~prot_model:"LG08" ())
| `Topological_WAG -> `Topological_WAG (Topological.topological ~descr ~faa ~tree:tree_id ~tree_conv ~prot_model:"WAG01" ())
| `Multinomial -> `Multinomial (Multinomial.multinomial ~descr ~faa ~tree_sc)
| `Msd e -> `Msd (Msd.msd ~descr ~e ~faa ~tree_sc, e)
......
......@@ -151,19 +151,20 @@ let tdg09 d =
Tamuri.tdg09
~tree:(tree d)
~faa:(amino_acid_alignment d)
()
|> Tamuri.results
let identical d =
let tree_sc = Tree_dataset.tree (tree_dataset d) `Detection in
let tree_id = Tree_dataset.tree (tree_dataset d) `Simulation in
Identical.identical ~tree_id ~tree_sc ~prot_model:"LG08" ~faa:(amino_acid_alignment d)
Identical.identical ~tree_id ~tree_sc ~prot_model:"LG08" ~faa:(amino_acid_alignment d) ()
|> Identical.results
let topological d =
let faa = amino_acid_alignment d in
let tree = Tree_dataset.tree (tree_dataset d) `Simulation in
let tree_conv = Tree_dataset.topological_tree (tree_dataset d) in
Topological.topological ~faa ~tree ~tree_conv ~prot_model:"LG08"
Topological.topological ~faa ~tree ~tree_conv ~prot_model:"LG08" ()
|> Topological.results
let multinomial d =
......@@ -205,7 +206,7 @@ let diffseldsparse ?pi ?shiftprob ?eps d =
let pcoc ?(gamma = true) ?(ncat = 60) d =
let faa = amino_acid_alignment d in
let tree = tree d in
Pcoc.pcoc ~catx_est:ncat ~plot_complete:false ~gamma ~faa ~tree
Pcoc.pcoc ~catx_est:ncat ~plot_complete:false ~gamma ~faa ~tree ()
|> Pcoc.results
let alignment_plot d =
......@@ -366,4 +367,4 @@ let realistic_result (r: record_t) =
(* let v = g.gc_stat.gc_variance_among_sequences in
Float.(v >= 8.388e-05 && v <= 5.262e-02) *)
\ No newline at end of file
Float.(v >= 8.388e-05 && v <= 5.262e-02) *)
......@@ -5,7 +5,7 @@ open File_formats
let img = Env.env_tdg09
let tdg09 ?(descr="") ~(faa:aminoacid_fasta pworkflow) ~(tree:_ pworkflow) : [`tdg09] dworkflow =
let tdg09 ?(descr="") ~(faa:aminoacid_fasta pworkflow) ~(tree:_ pworkflow) () : [`tdg09] dworkflow =
let tdg09_out = dest // "tdg09.yaml" in
let tmp_ali_phy = dest // "tmp_ali.phy" in
let tmp_tree = dest // "tmp.nw" in
......
......@@ -48,7 +48,7 @@ let bppml ?(descr="") ~faa ~tree ~config : _ workflow =
)
]
let topological ?(descr="") ~(tree:_ pworkflow) ~(tree_conv:_ pworkflow) ~(faa:aminoacid_fasta pworkflow) ~prot_model : [`topological] dworkflow =
let topological ?(descr="") ~(tree:_ pworkflow) ~(tree_conv:_ pworkflow) ~(faa:aminoacid_fasta pworkflow) ~prot_model () : [`topological] dworkflow =
let config = [assign "model" (string prot_model)] in
let run_bppml = bppml ~descr:"" ~tree ~config ~faa in
let run_bppml_conv = bppml ~descr:".conv" ~tree:tree_conv ~config ~faa in
......
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