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Commit 1fa08ee7 authored by Philippe Veber's avatar Philippe Veber
Browse files

Orthomam: tree output for the whole database

parent 2f0ee844
...@@ -69,7 +69,7 @@ let%pworkflow clip_tree_on_alignment tree ali = ...@@ -69,7 +69,7 @@ let%pworkflow clip_tree_on_alignment tree ali =
let omm_tree_of_db db = let omm_tree_of_db db =
Workflow.input (Orthomam_db.tree db) Workflow.input (Orthomam_db.tree db)
let annotate_convergent_species_in_tree (tree : newick file) species : newick file = let annotate_convergent_species_in_tree (tree : newick file) species : nhx file =
Workflow.path_plugin ~version:3 ~descr:"tree_of_convergent_species" ( Workflow.path_plugin ~version:3 ~descr:"tree_of_convergent_species" (
let open Phylogenetics in let open Phylogenetics in
let%pdeps species = species let%pdeps species = species
...@@ -359,14 +359,16 @@ module Q = struct ...@@ -359,14 +359,16 @@ module Q = struct
Workflow.input (q.alignment :> string) Workflow.input (q.alignment :> string)
|> remove_unobserved_sequences_from_alignment |> remove_unobserved_sequences_from_alignment
let omm_tree_with_branch_lengths ~branch_length_unit = match branch_length_unit with
| `Nucleotide -> estimated_nucleotide_tree
| `Amino_acid -> estimated_amino_acid_tree
| `Codon -> estimated_codon_tree
let tree ~branch_length_unit q = let tree ~branch_length_unit q =
let omm_tree_with_branch_lengths = match branch_length_unit with
| `Nucleotide -> estimated_nucleotide_tree q.db
| `Amino_acid -> estimated_amino_acid_tree q.db
| `Codon -> estimated_codon_tree q.db
in
clip_tree_on_alignment clip_tree_on_alignment
(annotate_convergent_species_in_tree omm_tree_with_branch_lengths q.convergent_species) (annotate_convergent_species_in_tree
(omm_tree_with_branch_lengths ~branch_length_unit q.db)
q.convergent_species)
(alignment q) (alignment q)
let nucleotide_alignment q = let nucleotide_alignment q =
...@@ -375,6 +377,11 @@ end ...@@ -375,6 +377,11 @@ end
include Q include Q
let tree_of_db db ~branch_length_unit ~convergent_species =
annotate_convergent_species_in_tree
(omm_tree_with_branch_lengths ~branch_length_unit db)
(Workflow.data convergent_species)
include Detection_pipeline.Make(Q) include Detection_pipeline.Make(Q)
let species_with_echolocation = [ let species_with_echolocation = [
......
...@@ -19,6 +19,12 @@ val alignment : query -> phylip file ...@@ -19,6 +19,12 @@ val alignment : query -> phylip file
val nucleotide_alignment : query -> nucleotide_fasta file val nucleotide_alignment : query -> nucleotide_fasta file
val tree_of_db :
Orthomam_db.t ->
branch_length_unit:[`Nucleotide | `Amino_acid | `Codon] ->
convergent_species:string list ->
nhx file
val tree : val tree :
branch_length_unit:[`Nucleotide | `Amino_acid | `Codon] -> branch_length_unit:[`Nucleotide | `Amino_acid | `Codon] ->
query -> query ->
......
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