Commit 93b3460e authored by Philippe Veber's avatar Philippe Veber
Browse files

File_format: nhx special case of newick

parent 1a09d0ef
...@@ -5,16 +5,16 @@ class type bimbam = object ...@@ -5,16 +5,16 @@ class type bimbam = object
method format : [`bimbam] method format : [`bimbam]
end end
class type nhx = object
inherit text
method format : [`nhx]
end
class type newick = object class type newick = object
inherit text inherit text
method format : [`newick] method format : [`newick]
end end
class type nhx = object
inherit newick
method newick_variant : [`nhx]
end
class type phylip = object class type phylip = object
inherit text inherit text
method format : [`phylip] method format : [`phylip]
......
...@@ -3,7 +3,7 @@ open Bistro ...@@ -3,7 +3,7 @@ open Bistro
open File_formats open File_formats
open Codepitk open Codepitk
let ensembl_tree : nhx file = let ensembl_tree : newick file =
Bistro_unix.wget "ftp://ftp.ensembl.org/pub/release-99/compara/species_trees/vertebrates_species-tree_Ensembl.nh" Bistro_unix.wget "ftp://ftp.ensembl.org/pub/release-99/compara/species_trees/vertebrates_species-tree_Ensembl.nh"
type alignment = Alignment of Orthomam_db.t * Orthomam_db.alignment type alignment = Alignment of Orthomam_db.t * Orthomam_db.alignment
...@@ -460,7 +460,7 @@ let%pworkflow convergence_species_tree_pdf ~convergent_species db = ...@@ -460,7 +460,7 @@ let%pworkflow convergence_species_tree_pdf ~convergent_species db =
|> Biotk_croquis.Croquis.Layout.simple |> Biotk_croquis.Croquis.Layout.simple
|> Fn.flip Biotk_croquis.Croquis.Layout.render_pdf [%dest] |> Fn.flip Biotk_croquis.Croquis.Layout.render_pdf [%dest]
let%workflow ranking_of_results ~alignment_ids ~convergent_species (alignments : aminoacid_fasta file list) (trees : newick file list) result_files ~column_label = let%workflow ranking_of_results ~alignment_ids ~convergent_species (alignments : aminoacid_fasta file list) (trees : #newick file list) result_files ~column_label =
let ranking_size = 1_000 in let ranking_size = 1_000 in
let column_label = [%param column_label] in let column_label = [%param column_label] in
let alignment_ids = Array.of_list [%param alignment_ids] in let alignment_ids = Array.of_list [%param alignment_ids] in
......
...@@ -36,11 +36,11 @@ val species_with_echolocation : string list ...@@ -36,11 +36,11 @@ val species_with_echolocation : string list
val prestin : Orthomam_db.t -> query val prestin : Orthomam_db.t -> query
val ensembl_tree : nhx file val ensembl_tree : newick file
val compare_tree_branch_lengths : val compare_tree_branch_lengths :
newick file -> nhx file ->
newick file -> nhx file ->
pdf file pdf file
val number_of_missing_sequences_repartition : val number_of_missing_sequences_repartition :
......
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