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Commit 92bcfe14 authored by Louis Duchemin's avatar Louis Duchemin

RER converge start up handle from orthomam

parent d79f5bbb
......@@ -595,3 +595,29 @@ let draw_site q pos =
| Error msg -> failwith msg
in
Workflow.path_plugin ~descr:"orthomam." f
let rer_converge ?max_read ?transform ?weighted ?scale ?continuous ~db
~phenotypes =
let open Bistro_bio in
let module RER = Rer_converge in
let species_tree = estimated_codon_tree db in
let model = Iqtree.model_spec ~freq_type:`F `ECMK07 in
let queries =
alignments_of_db db
|> List.map ~f:(query ~convergent_species:phenotypes)
in
let gene_ids = List.map ~f:family_id queries in
let ali_files = List.map ~f:Q.alignment queries in
let gene_trees =
List.map
~f:(fun q ->
Iqtree.iqtree ~te:species_tree ~m:model ~st:(`CODON 1) (`phylip q)
|> Iqtree.treefile)
ali_files
|> List.zip_exn gene_ids
in
let gene_tree_set = RER.gene_tree_file gene_trees in
let phenotype = RER.phenotypes_of_convergent_species phenotypes in
RER.rer_converge ?max_read ?transform ?weighted ?scale ?continuous
~gene_tree_set ~phenotype
......@@ -85,3 +85,13 @@ val site_ranking :
Candidate_site.t list workflow
val draw_site : query -> int -> pdf file
val rer_converge :
?max_read:int ->
?transform:[ `none | `sqrt | `log ] ->
?weighted:bool ->
?scale:bool ->
?continuous:bool ->
db:Orthomam_db.t ->
phenotypes:string list workflow ->
tsv file
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