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VEBER Philippe
codepi
Commits
93b3460e
Commit
93b3460e
authored
Nov 17, 2020
by
Philippe Veber
Browse files
File_format: nhx special case of newick
parent
1a09d0ef
Changes
3
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3 changed files
with
10 additions
and
10 deletions
+10
-10
lib/file_formats.ml
lib/file_formats.ml
+5
-5
lib/orthomam.ml
lib/orthomam.ml
+2
-2
lib/orthomam.mli
lib/orthomam.mli
+3
-3
No files found.
lib/file_formats.ml
View file @
93b3460e
...
...
@@ -5,16 +5,16 @@ class type bimbam = object
method
format
:
[
`bimbam
]
end
class
type
nhx
=
object
inherit
text
method
format
:
[
`nhx
]
end
class
type
newick
=
object
inherit
text
method
format
:
[
`newick
]
end
class
type
nhx
=
object
inherit
newick
method
newick_variant
:
[
`nhx
]
end
class
type
phylip
=
object
inherit
text
method
format
:
[
`phylip
]
...
...
lib/orthomam.ml
View file @
93b3460e
...
...
@@ -3,7 +3,7 @@ open Bistro
open
File_formats
open
Codepitk
let
ensembl_tree
:
n
hx
file
=
let
ensembl_tree
:
n
ewick
file
=
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
...
...
@@ -460,7 +460,7 @@ let%pworkflow convergence_species_tree_pdf ~convergent_species db =
|>
Biotk_croquis
.
Croquis
.
Layout
.
simple
|>
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
column_label
=
[
%
param
column_label
]
in
let
alignment_ids
=
Array
.
of_list
[
%
param
alignment_ids
]
in
...
...
lib/orthomam.mli
View file @
93b3460e
...
...
@@ -36,11 +36,11 @@ val species_with_echolocation : string list
val
prestin
:
Orthomam_db
.
t
->
query
val
ensembl_tree
:
n
hx
file
val
ensembl_tree
:
n
ewick
file
val
compare_tree_branch_lengths
:
n
ewick
file
->
n
ewick
file
->
n
hx
file
->
n
hx
file
->
pdf
file
val
number_of_missing_sequences_repartition
:
...
...
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