Commit b4a5fdfc authored by Philippe Veber's avatar Philippe Veber
Browse files

orthomam: direct access to prestin

parent bcc0415c
......@@ -11,6 +11,11 @@ type alignment = Alignment of Orthomam_db.t * Orthomam_db.alignment
let alignments_of_db db =
List.map (Orthomam_db.list_alignments db) ~f:(fun ali -> Alignment (db, ali))
let family_id_of_alignment (alignment : Orthomam_db.alignment) =
Filename.basename (alignment :> string)
|> Fn.flip Filename.chop_suffix "_NT.fasta.ali"
|> String.chop_prefix_exn ~prefix:"all"
let%pworkflow fasta_of_phylip ali =
let ali =
[%path ali]
......@@ -30,10 +35,7 @@ type query = {
let query (Alignment (db, alignment)) ~convergent_species =
{ db ; alignment ; convergent_species }
let family_id q =
Filename.basename (q.alignment :> string)
|> Fn.flip Filename.chop_suffix "_NT.fasta.ali"
|> String.chop_prefix_exn ~prefix:"all"
let family_id q = family_id_of_alignment q.alignment
let%pworkflow remove_unobserved_sequences_from_alignment phylip : phylip file =
let phylip = [%path phylip] in
......@@ -395,6 +397,15 @@ let species_with_echolocation = [
(* "Rhinolophus ferrumequinum" ; in ensembl but not in orthomam *)
]
let prestin db =
let alignments = alignments_of_db db in
let prestin_alignment = List.find_exn alignments ~f:(fun (Alignment (_, al)) ->
String.equal (family_id_of_alignment al) "ENSG00000170615_SLC26A5"
)
in
let convergent_species = Workflow.data species_with_echolocation in
query ~convergent_species prestin_alignment
let%pworkflow convergence_species_tree_pdf ~convergent_species db =
let convergent_species = [%param convergent_species] in
let tree_path = [%path estimated_amino_acid_tree db] in
......
......@@ -28,6 +28,8 @@ include Detection_pipeline.S with type query := query
val species_with_echolocation : string list
val prestin : Orthomam_db.t -> query
val ensembl_tree : nhx file
val compare_tree_branch_lengths :
......
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