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Commit 23cb6047 authored by Louis Duchemin's avatar Louis Duchemin

RERconverge : last fixes, enabling full run without errors

parent 30614834
......@@ -649,4 +649,4 @@ let rer_converge ?max_read ?transform ?weighted ?scale ?continuous ~db
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
~min_specs:10 ~gene_tree_set ~phenotype
~min_specs:10 ~master_tree:species_tree ~gene_tree_set ~phenotype
......@@ -48,7 +48,7 @@ let template_bool t = string (if t then "T" else "F")
let ropt f = Option.value_map ~f ~default:(string "NA")
let script ?max_read ?min_specs ~transform ~weighted ~scale ~continuous
~gene_tree_set ~phenotype (* ~master_tree *) =
~gene_tree_set ~phenotype ~master_tree =
let max_read = ropt int max_read in
let min_specs = ropt int min_specs in
[%script
......@@ -59,8 +59,8 @@ suppressPackageStartupMessages({
library(RERconverge)
})
#masterTree <- read.tree(file="{dep master_tree}")
gene_trees <- readTrees("{{dep gene_tree_set}}", max.read={{max_read}}, minSpecs={{min_specs}})
masterTree <- read.tree(file="{{dep master_tree}}")
gene_trees <- readTrees("{{dep gene_tree_set}}", max.read={{max_read}}, masterTree=masterTree, minSpecs={{min_specs}})
relative_rates <- getAllResiduals(
gene_trees,
......@@ -103,7 +103,7 @@ load_traits_paths <-
traits_paths <- load_traits_paths(
"{{dep phenotype}}",
"{{dep gene_tree_set}}",
gene_trees,
{{template_bool continuous}}
)
......@@ -119,15 +119,15 @@ res <- if ({{template_bool continuous}}) {
)
}
write_tsv("{{dest}}", res)
write_tsv(res, "{{dest}}")
|}]
let rer_converge ?max_read ?min_specs ?(transform = `sqrt)
?(weighted = true) ?(scale = true) ?(continuous = false)
~(* ~master_tree *) gene_tree_set ~phenotype =
~master_tree ~gene_tree_set ~phenotype =
Bistro_utils.R_script.workflow ~img ~descr:"rer_converge"
(script ?max_read ~transform ~weighted ~scale ~continuous ?min_specs
~gene_tree_set ~phenotype (* ~master_tree *))
~gene_tree_set ~phenotype ~master_tree)
let annotate_branches_with_tip_leaves (tree : tree) : annotated_tree =
let rec traverse_tree tree =
......
......@@ -13,7 +13,7 @@ val rer_converge :
?weighted:bool ->
?scale:bool ->
?continuous:bool ->
(* master_tree:newick file -> *)
master_tree:newick file ->
gene_tree_set:tsv file ->
phenotype:tsv file ->
tsv file
......
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