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VEBER Philippe
codepi
Commits
87b4f2e6
Commit
87b4f2e6
authored
Nov 22, 2020
by
Philippe Veber
Browse files
renaming
parent
c3de289d
Changes
6
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6 changed files
with
13 additions
and
13 deletions
+13
-13
lib/mutsel_simulator.ml
lib/mutsel_simulator.ml
+3
-3
lib/mutsel_simulator.mli
lib/mutsel_simulator.mli
+3
-3
lib/simulation_pipeline.ml
lib/simulation_pipeline.ml
+4
-4
lib/simulation_pipeline.mli
lib/simulation_pipeline.mli
+1
-1
lib/tk/mutsel_simulator.ml
lib/tk/mutsel_simulator.ml
+1
-1
lib/tk/mutsel_simulator.mli
lib/tk/mutsel_simulator.mli
+1
-1
No files found.
lib/simulator.ml
→
lib/
mutsel_
simulator.ml
View file @
87b4f2e6
...
...
@@ -22,7 +22,7 @@ let simulation ?branch_scale ?seed ~n_h0 ~n_ha ~ne_s:(ne_s0, ne_s1) ~gBGC:(gBGC0
|>
to_fitness
|>
Array
.
map
~
f
:
Amino_acid
.
Vector
.
of_array_exn
)
in
Codepitk
.
S
imulator
.
Site_independent
_mutsel
.
simulation
Codepitk
.
Mutsel_s
imulator
.
Site_independent
.
simulation
?
branch_scale
?
seed
~
n_h0
~
n_ha
~
gBGC
:
(
gBGC0
,
gBGC1
)
~
ne_s
:
(
ne_s0
,
ne_s1
)
~
tree
~
fitness_profiles
()
in
...
...
@@ -30,7 +30,7 @@ let simulation ?branch_scale ?seed ~n_h0 ~n_ha ~ne_s:(ne_s0, ne_s1) ~gBGC:(gBGC0
let
alignment_of_simulation
sim
=
let
f
=
fun
%
workflow
dest
->
let
sim
:
Codepitk
.
S
imulator
.
Site_independent
_mutsel
.
simulation
=
let
sim
:
Codepitk
.
Mutsel_s
imulator
.
Site_independent
.
simulation
=
[
%
eval
sim
]
in
let
species_name
=
Phylogenetics
.
Tree
.
leaves
sim
.
tree
in
...
...
@@ -45,7 +45,7 @@ let alignment_of_simulation sim =
let
fitness_histogram
sim
=
let
f
=
fun
%
workflow
dest
->
let
open
Phylogenetics
in
let
sim
:
Codepitk
.
S
imulator
.
Site_independent
_mutsel
.
simulation
=
let
sim
:
Codepitk
.
Mutsel_s
imulator
.
Site_independent
.
simulation
=
[
%
eval
sim
]
in
let
params
=
Array
.
append
sim
.
h0_params
sim
.
ha_params
in
...
...
lib/simulator.mli
→
lib/
mutsel_
simulator.mli
View file @
87b4f2e6
...
...
@@ -12,14 +12,14 @@ val simulation :
tree
:
nhx
file
->
fitness_profiles
:#
text
file
->
unit
->
S
imulator
.
Site_independent
_mutsel
.
simulation
workflow
Mutsel_s
imulator
.
Site_independent
.
simulation
workflow
val
alignment_of_simulation
:
S
imulator
.
Site_independent
_mutsel
.
simulation
workflow
->
Mutsel_s
imulator
.
Site_independent
.
simulation
workflow
->
nucleotide_fasta
file
val
fitness_histogram
:
S
imulator
.
Site_independent
_mutsel
.
simulation
workflow
->
Mutsel_s
imulator
.
Site_independent
.
simulation
workflow
->
pdf
file
val
pair_tree
:
...
...
lib/simulation_pipeline.ml
View file @
87b4f2e6
...
...
@@ -29,7 +29,7 @@ let tree_workflow = function
|
Pair_tree
{
branch_length1
;
branch_length2
;
npairs
}
->
S
imulator
.
pair_tree
~
branch_length1
~
branch_length2
~
npairs
Mutsel_s
imulator
.
pair_tree
~
branch_length1
~
branch_length2
~
npairs
module
Make
(
Q
:
Detection_pipeline
.
Query
)
=
struct
include
Detection_pipeline
.
Make
(
Q
)
...
...
@@ -68,11 +68,11 @@ module Mutsel_query = struct
let
simulation
{
n_h0
;
n_ha
;
profiles
;
ne_s
;
gBGC
;
branch_scale
;
seed
;
tree
;
_
}
=
let
tree
=
tree_workflow
tree
in
let
fitness_profiles
=
Workflow
.
input
profiles
in
S
imulator
.
simulation
~
branch_scale
~
n_ha
~
n_h0
~
ne_s
~
gBGC
~
tree
~
seed
~
fitness_profiles
()
Mutsel_s
imulator
.
simulation
~
branch_scale
~
n_ha
~
n_h0
~
ne_s
~
gBGC
~
tree
~
seed
~
fitness_profiles
()
let
nucleotide_alignment
p
=
simulation
p
|>
S
imulator
.
alignment_of_simulation
|>
Mutsel_s
imulator
.
alignment_of_simulation
let
tree
~
branch_length_unit
:_
{
tree
;
_
}
=
tree_workflow
tree
end
...
...
@@ -103,7 +103,7 @@ module Mutsel = struct
let
f
=
fun
%
workflow
()
->
let
open
Phylogenetics
in
let
open
Codepitk
in
let
open
Codepitk
.
S
imulator
.
Site_independent
_mutsel
in
let
open
Codepitk
.
Mutsel_s
imulator
.
Site_independent
in
let
module
Codon
=
Codon
.
Universal_genetic_code
.
NS
in
let
sim
:
simulation
=
[
%
eval
simulation
q
]
in
let
result_paths
=
[
%
eval
Bistro
.
Workflow
.
path_list
(
List
.
map
methods
~
f
:
(
fun
f
->
f
q
))]
in
...
...
lib/simulation_pipeline.mli
View file @
87b4f2e6
...
...
@@ -34,7 +34,7 @@ module Mutsel : sig
val
simulation
:
query
->
Codepitk
.
S
imulator
.
Site_independent
_mutsel
.
simulation
workflow
Codepitk
.
Mutsel_s
imulator
.
Site_independent
.
simulation
workflow
type
benchmark
=
{
...
...
lib/tk/simulator.ml
→
lib/tk/
mutsel_
simulator.ml
View file @
87b4f2e6
...
...
@@ -8,7 +8,7 @@ let tree_rescale_branch_length t ~scale =
{
bi
with
length
=
bi
.
length
*.
scale
}
)
module
Site_independent
_mutsel
=
struct
module
Site_independent
=
struct
include
Simulator
.
Make
(
Mutsel
.
NSCodon
)(
Mutsel
)(
Branch_info
)
let
alignment
tree
~
root
param
=
...
...
lib/tk/simulator.mli
→
lib/tk/
mutsel_
simulator.mli
View file @
87b4f2e6
open
Phylogenetics
module
Site_independent
_mutsel
:
sig
module
Site_independent
:
sig
type
simulation
=
{
sequences
:
Dna
.
t
list
;
fitness_profiles
:
Amino_acid
.
vector
array
;
...
...
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