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VEBER Philippe
codepi
Commits
5598b501
Commit
5598b501
authored
Dec 06, 2018
by
LANORE Vincent
Browse files
Added a realata command
parent
d3e25255
Changes
4
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4 changed files
with
59 additions
and
15 deletions
+59
-15
app/reviewphiltrans_app.ml
app/reviewphiltrans_app.ml
+1
-0
lib/convergence_detection.ml
lib/convergence_detection.ml
+11
-11
lib/dataset.ml
lib/dataset.ml
+1
-1
lib/pipeline.ml
lib/pipeline.ml
+46
-3
No files found.
app/reviewphiltrans_app.ml
View file @
5598b501
...
...
@@ -4,6 +4,7 @@ open Reviewphiltrans
let
()
=
Command
.
group
~
summary
:
"Reviewphiltrans"
[
"validation"
,
Pipeline
.
validation_command
;
"realdata"
,
Pipeline
.
realdata_command
;
"alistats"
,
Alistats
.
command
;
]
|>
Command
.
run
lib/convergence_detection.ml
View file @
5598b501
...
...
@@ -108,17 +108,17 @@ let plot_merge_results ?t_choices ~plot_all_sites ~(res_by_tools:result list) ~t
in
let
default_t
=
List
.
map
res_by_tools
~
f
:
(
fun
res
->
let
opt
=
match
res
with
|
`Pcoc
_
->
"PCOC:
1
,PC:
1
,OC:
1
"
|
`Pcoc_gamma
_
->
"PCOC_gamma:
1
,PC_gamma:
1
,OC_gamma:
1
"
|
`Pcoc_C60
_
->
"PCOC_C60:
1
,PC_C60:
1
,OC_C60:
1
"
|
`Diffsel
_
->
"Diffsel_mean:0
.11
,Diffsel_max:
1
"
|
`Identical_LG
_
->
"Identical_LG08:
1
"
|
`Identical_WAG
_
->
"Identical_WAG01:
1
"
|
`Topological_LG
_
->
"Topological_LG08:
1
"
|
`Topological_WAG
_
->
"Topological_WAG01:
1
"
|
`Tdg09
_
->
"Tdg09_1MinusFDR:
1
,Tdg09_prob_post:
1
,Tdg09_1MinusLRT:
1
"
|
`Multinomial
_
->
"Mutinomial_1MinusLRT:
1
"
|
`Msd
_
->
"Msd_0.05_1MinusP:
1
"
|
`Pcoc
_
->
"PCOC:
0
,PC:
0
,OC:
0
"
|
`Pcoc_gamma
_
->
"PCOC_gamma:
0
,PC_gamma:
0
,OC_gamma:
0
"
|
`Pcoc_C60
_
->
"PCOC_C60:
0
,PC_C60:
0
,OC_C60:
0
"
|
`Diffsel
_
->
"Diffsel_mean:0,Diffsel_max:
0
"
|
`Identical_LG
_
->
"Identical_LG08:
0
"
|
`Identical_WAG
_
->
"Identical_WAG01:
0
"
|
`Topological_LG
_
->
"Topological_LG08:
0
"
|
`Topological_WAG
_
->
"Topological_WAG01:
0
"
|
`Tdg09
_
->
"Tdg09_1MinusFDR:
0
,Tdg09_prob_post:
0
,Tdg09_1MinusLRT:
0
"
|
`Multinomial
_
->
"Mutinomial_1MinusLRT:
0
"
|
`Msd
_
->
"Msd_0.05_1MinusP:
0
"
in
string
opt
...
...
lib/dataset.ml
View file @
5598b501
...
...
@@ -16,7 +16,7 @@ let repo ~preview dataset_l =
let
repo_ready_data
=
Ready_dataset
.
repo
dataset
.
dataset
in
let
repo_raw_data
=
Raw_dataset
.
repo
~
prefix
:
model_prefix
(
Ready_dataset
.
to_raw
dataset
.
dataset
)
in
List
.
concat
[
Repo
.
shift
"minimal"
(
Repo
.
shift
(
tree_prefix
^
"_"
^
model_prefix
)
repo_raw_data
);
Repo
.
shift
"minimal"
(
Repo
.
shift
(
tree_prefix
^
"_"
^
model_prefix
)
repo_raw_data
);
Repo
.
shift
"debug"
repo_ready_data
;
]
|>
Repo
.
shift
"dataset"
...
...
lib/pipeline.ml
View file @
5598b501
...
...
@@ -205,13 +205,13 @@ let derive_from_dataset ~dataset ~preview ~use_diffsel ~use_c60=
`Pcoc
;
]
@
List
.
map
[
0
.
05
]
(
fun
x
->
`Msd
x
))
;
(* if preview then *)
[
`Tdg09
;]
[
`Tdg09
;]
(* else
[ `Tdg09;
[ `Tdg09;
`Pcoc_gamma;
`Identical_WAG;
`Topological_WAG;
] *)
] *)
;
if
use_diffsel
then
[
`Diffsel
]
...
...
@@ -369,3 +369,46 @@ let validation_command =
in
validation_main
~
outdir
?
indir
?
ns
?
np
?
mem
~
preview
~
use_diffsel
~
use_c60
~
no_Ne
~
ne_test
~
no_HaPC
~
tree_dir
~
profile_fn
~
use_concat
~
only_simu
~
add_indels
?
seed
]
let
realdata_main
~
outdir
~
indir
~
preview
~
use_diffsel
~
use_c60
?
(
np
=
2
)
?
(
mem
=
2
)
?
(
seed
=
Random
.
int
Int
.
max_value
)
()
=
(* seed-related stuff *)
printf
"Global seed: %i
\n
"
seed
;
Out_channel
.
write_all
"global.seed"
~
data
:
(
string_of_int
seed
);
Random
.
init
seed
;
(* real trees *)
let
dataset_l
=
parse_input_data
~
seed
indir
in
let
dataset_results_l
=
derive_det
~
dataset_l
~
preview
~
use_diffsel
~
use_c60
in
let
repo_real_trees
=
[
Dataset
.
repo
dataset_l
~
preview
;
repo_of_dataset_results_l
~
dataset_results_l
;
]
|>
List
.
concat
(* list of repos *)
in
let
repo
=
Repo
.
shift
"Real_datasets"
repo_real_trees
in
Repo
.
build
~
outdir
~
np
~
mem
:
(
`GB
mem
)
~
logger
repo
(* time_logger#report sim_repo_l#dataset_results (Filename.concat outdir ("elapsed_time_" ^ (Unix.time () |> int_of_float |> string_of_int) ^ ".tsv")) *)
let
realdata_command
=
let
open
Command
.
Let_syntax
in
Command
.
basic
~
summary
:
"Run simulation pipeline on real data only"
[
%
map_open
let
outdir
=
flag
"--outdir"
(
required
string
)
~
doc
:
"PATH Output directory"
and
indir
=
flag
"--indir"
(
required
string
)
~
doc
:
"PATH Input directory"
and
preview
=
flag
"--preview-mode"
no_arg
~
doc
:
" Preview mode"
and
use_diffsel
=
flag
"--diffsel"
no_arg
~
doc
:
" use the diffsel method (very slow)."
and
use_c60
=
flag
"--c60"
no_arg
~
doc
:
" use the pcoc c60 method (slow)."
and
np
=
flag
"--np"
(
optional
int
)
~
doc
:
"INT Number of available processors"
and
mem
=
flag
"--mem"
(
optional
int
)
~
doc
:
"INT Available memory (in GB)"
and
seed
=
flag
"--seed"
(
optional
int
)
~
doc
:
"INT Global seed"
in
realdata_main
~
outdir
~
indir
?
np
?
mem
~
preview
~
use_diffsel
~
use_c60
?
seed
]
\ No newline at end of file
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