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Commit 88297304 authored by Louis Duchemin's avatar Louis Duchemin

Orthomam : adjusting pipeline upstream of rer_converge

parent 4a7cbafd
......@@ -602,17 +602,24 @@ let rer_converge ?max_read ?transform ?weighted ?scale ?continuous ~db
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)
|> Fn.flip List.take 10
in
let gene_ids = List.map ~f:family_id queries in
let ali_files = List.map ~f:Q.alignment queries in
(* let model = Iqtree.model_spec ~freq_type:`F `ECMK07 in *)
let gene_trees =
List.map
~f:(fun q ->
Iqtree.iqtree ~te:species_tree ~m:model ~st:(`CODON 1) (`phylip q)
let spp = iqtree_nexus_partition_file_of_alignment q in
let clipped_tree = clip_tree_on_alignment species_tree q in
Iqtree.iqtree ~te:clipped_tree (*~m:model*) ~st:`DNA ~spp
(`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
......
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