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VEBER Philippe
codepi
Commits
66dbf3dc
Commit
66dbf3dc
authored
Sep 04, 2018
by
LANORE Vincent
Browse files
Pipeline now passes seed to add_indel script (currently a random seed per fna; to be fixed).
parent
5b8de38b
Changes
3
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3 changed files
with
13 additions
and
12 deletions
+13
-12
lib/dataset.ml
lib/dataset.ml
+2
-2
lib/pipeline.ml
lib/pipeline.ml
+2
-2
lib/ready_dataset.ml
lib/ready_dataset.ml
+9
-8
No files found.
lib/dataset.ml
View file @
66dbf3dc
...
...
@@ -25,10 +25,10 @@ let repo ~preview dataset_l =
)
|>
List
.
concat
let
add_indels_to_dataset
d
=
let
add_indels_to_dataset
d
~
seed
=
let
p
=
0
.
33
in
let
model_prefix
=
sprintf
"%s_0.33_i"
d
.
model_prefix
in
let
tree_prefix
=
d
.
tree_prefix
in
let
is_real
=
d
.
is_real
in
let
dataset
=
Ready_dataset
.
add_indels_to_ready_dataset
~
p
d
.
dataset
in
let
dataset
=
Ready_dataset
.
add_indels_to_ready_dataset
~
p
~
seed
d
.
dataset
in
{
model_prefix
;
tree_prefix
;
is_real
;
dataset
;
seed
=
Hashtbl
.
hash
d
.
seed
}
lib/pipeline.ml
View file @
66dbf3dc
...
...
@@ -132,8 +132,8 @@ let derive_from_tree ~tree_dir ~tree ~profile ~preview ~use_concat ~ns ~no_Ne ~n
let
dataset_H0_NeG5
=
derive_from_model
~
model
:
H0_NeG5
~
input_tree
~
tree_dataset
~
tree_prefix
~
profile
~
preview
~
ns
~
seed
in
let
dataset_HaPCOC
=
derive_from_model
~
model
:
HaPCOC
~
input_tree
~
tree_dataset
~
tree_prefix
~
profile
~
preview
~
ns
~
seed
in
let
dataset_HaPC_NeG5
=
derive_from_model
~
model
:
HaPC_NeG5
~
input_tree
~
tree_dataset
~
tree_prefix
~
profile
~
preview
~
ns
~
seed
in
let
indel_H0_NeG5
=
Dataset
.
add_indels_to_dataset
dataset_H0_NeG5
in
let
indel_HaPC_NeG5
=
Dataset
.
add_indels_to_dataset
dataset_HaPC_NeG5
in
let
indel_H0_NeG5
=
Dataset
.
add_indels_to_dataset
dataset_H0_NeG5
~
seed
:
(
Random
.
int
Int
.
max_value
)
in
let
indel_HaPC_NeG5
=
Dataset
.
add_indels_to_dataset
dataset_HaPC_NeG5
~
seed
:
(
Random
.
int
Int
.
max_value
)
in
let
dataset_basis_hyps
=
[
dataset_H0_NeG5
;
dataset_HaPCOC
;
dataset_HaPC_NeG5
]
in
let
models
=
Convergence_hypothesis
.[
[
...
...
lib/ready_dataset.ml
View file @
66dbf3dc
...
...
@@ -68,24 +68,25 @@ let paste d1 d2 =
let
fna_infos
=
Some
(
paste_fna_infos
~
fna_infos_l
)
in
let
ready_dataset
=
of_raw
{
Raw_dataset
.
input_tree
=
r_d1
.
input_tree
;
fna
;
fna_infos
}
in
ready_dataset
let
add_indels_to_fna
~
(
p
:
float
)
(
fna
:
nucleotide_fasta
workflow
)
:
nucleotide_fasta
workflow
=
let
env
=
docker_image
~
account
:
"carinerey"
~
name
:
"python_basics"
~
tag
:
"07252018"
()
in
workflow
~
descr
:
(
"add_indels"
)
[
let
add_indels_to_fna
~
(
p
:
float
)
~
(
seed
:
int
)
(
fna
:
nucleotide_fasta
workflow
)
:
nucleotide_fasta
workflow
=
let
env
=
docker_image
~
account
:
"carinerey"
~
name
:
"python_basics"
~
tag
:
"07252018"
()
in
workflow
~
descr
:
(
"add_indels"
)
[
cmd
"python"
~
env
[
file_dump
(
string
Scripts
.
add_indels
)
;
opt
"-p"
float
p
;
opt
"-a"
dep
fna
;
opt
"-o"
ident
dest
;
opt
"-r"
int
seed
;
string
"-c"
;
]
]
let
add_indels_to_ready_dataset
~
p
d
=
let
add_indels_to_ready_dataset
~
p
~
seed
d
=
let
r_d
=
to_raw
d
in
let
fna
=
add_indels_to_fna
~
p
r_d
.
fna
in
(* VL: one seed per fna. FIXME:should be computed from global seed and task info instead *)
let
fna
=
add_indels_to_fna
~
p
~
seed
:
(
Random
.
int
Int
.
max_value
)
r_d
.
fna
in
let
fna_infos
=
r_d
.
fna_infos
in
let
ready_dataset
=
of_raw
{
Raw_dataset
.
input_tree
=
r_d
.
input_tree
;
fna
;
fna_infos
}
in
ready_dataset
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