Commit 4c01f9c5 authored by Philippe Veber's avatar Philippe Veber
Browse files

Pipeline2: added pcoc

parent d06c4dbd
......@@ -78,7 +78,7 @@ let merge_results ?fna_infos ~(res_by_tools : result list) () : text_file pworkf
] ;
]
let merge_result_tables ?fna_infos ?oracle ?multinomial ?tdg09 ?identical ?topological ?diffsel ?diffseldsparse () : text_file pworkflow =
let merge_result_tables ?fna_infos ?oracle ?multinomial ?tdg09 ?identical ?topological ?pcoc ?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) ;
......@@ -87,6 +87,7 @@ let merge_result_tables ?fna_infos ?oracle ?multinomial ?tdg09 ?identical ?topol
option (opt "--tdg09" dep) tdg09 ;
option (opt "--identical_LG" dep) identical ;
option (opt "--topological_LG" dep) topological ;
option (opt "--pcoc" dep) pcoc ;
option (opt "--diffsel" dep) diffsel ;
option (opt "--diffseldsparse" dep) diffseldsparse ;
option (opt "--oracle" dep) oracle ;
......
......@@ -39,6 +39,7 @@ val merge_result_tables :
?tdg09:text_file pworkflow ->
?identical:text_file pworkflow ->
?topological:text_file pworkflow ->
?pcoc:text_file pworkflow ->
?diffsel:text_file pworkflow ->
?diffseldsparse:text_file pworkflow ->
unit ->
......
......@@ -199,6 +199,12 @@ let diffseldsparse ?pi ?shiftprob ?eps d =
|> Diffseldsparse.readdiffseldsparse
|> Diffseldsparse.results
let pcoc d =
let faa = amino_acid_alignment d in
let tree = tree d in
Pcoc.pcoc ~catx_est:10 ~plot_complete:false ~gamma:false ~faa ~tree
|> Pcoc.results
let alignment_plot d =
Convergence_detection.plot_convergent_sites
~tree:(tree d)
......@@ -236,8 +242,8 @@ let result_table ?(use_diffsel = false) d =
~tdg09:(tdg09 d)
~identical:(identical d)
~topological:(topological d)
~pcoc:(pcoc 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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