Commit 93aba0ca authored by Philippe Veber's avatar Philippe Veber
Browse files

Pipeline2: added topological and identical methods

parent ad99038e
......@@ -78,13 +78,15 @@ let merge_results ?fna_infos ~(res_by_tools : result list) () : text_file pworkf
] ;
]
let merge_result_tables ?fna_infos ?oracle ?multinomial ?tdg09 ?diffsel ?diffseldsparse () : text_file pworkflow =
let merge_result_tables ?fna_infos ?oracle ?multinomial ?tdg09 ?identical ?topological ?diffsel ?diffseldsparse () : text_file pworkflow =
Workflow.shell ~descr:"convergence_detection.merge_results" [
cmd "python" ~img:Env.env_py [
file_dump (string Scripts.merge_det_results) ;
opt "-o" ident dest ;
option (opt "--multinomial" dep) multinomial ;
option (opt "--tdg09" dep) tdg09 ;
option (opt "--identical_LG" dep) identical ;
option (opt "--topological_LG" dep) topological ;
option (opt "--diffsel" dep) diffsel ;
option (opt "--diffseldsparse" dep) diffseldsparse ;
option (opt "--oracle" dep) oracle ;
......
......@@ -37,6 +37,8 @@ val merge_result_tables :
?oracle:text_file pworkflow ->
?multinomial:text_file pworkflow ->
?tdg09:text_file pworkflow ->
?identical:text_file pworkflow ->
?topological:text_file pworkflow ->
?diffsel:text_file pworkflow ->
?diffseldsparse:text_file pworkflow ->
unit ->
......
......@@ -150,6 +150,19 @@ let tdg09 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.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.results
let multinomial d =
Multinomial.multinomial
~tree_sc:(tree d)
......@@ -221,6 +234,8 @@ let result_table ?(use_diffsel = false) d =
Convergence_detection.merge_result_tables
~multinomial:(multinomial_asymptotic_lrt d)
~tdg09:(tdg09 d)
~identical:(identical d)
~topological:(topological d)
?diffsel:(if use_diffsel then Some (diffsel d) else None)
?diffseldsparse:(if use_diffsel then Some (diffseldsparse ~eps:1e-3 ~pi:1. d) else None)
~oracle:(oracle d)
......
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