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VEBER Philippe
codepi
Commits
aa74ed23
Commit
aa74ed23
authored
Aug 24, 2018
by
Philippe Veber
Browse files
started adding seed control
parent
d93a3737
Changes
3
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3 changed files
with
16 additions
and
8 deletions
+16
-8
lib/diffsel.ml
lib/diffsel.ml
+2
-1
lib/diffsel.mli
lib/diffsel.mli
+2
-0
lib/pipeline.ml
lib/pipeline.ml
+12
-7
No files found.
lib/diffsel.ml
View file @
aa74ed23
...
...
@@ -62,7 +62,7 @@ echo end_it=$end_it
|
}
let
diffsel
~
(
phy_n
:
nucleotide_phylip
workflow
)
~
(
tree
:
_
workflow
)
~
(
w_every
:
int
)
~
(
n_cycles
:
int
)
~
(
id
:
int
)
~
tag
:
[
`diffsel
]
directory
workflow
=
let
diffsel
~
(
phy_n
:
nucleotide_phylip
workflow
)
~
(
tree
:
_
workflow
)
~
(
w_every
:
int
)
~
(
n_cycles
:
int
)
~
(
id
:
int
)
~
tag
?
seed
()
:
[
`diffsel
]
directory
workflow
=
let
env
=
docker_image
~
account
:
"vlanore"
~
name
:
"diffsel"
~
tag
()
in
let
tmp_tree
=
tmp
//
"myrun.tree"
in
let
tmp_ali
=
tmp
//
"myrun.ali"
in
...
...
@@ -89,6 +89,7 @@ let diffsel ~(phy_n:nucleotide_phylip workflow) ~(tree: _ workflow) ~(w_every:in
opt
"-d"
ident
tmp_ali
;
opt
"-ncond"
int
2
;
opt
"-x"
seq
[
int
w_every
;
string
" "
;
int
n_cycles
];
option
(
opt
"-seed"
int
)
seed
;
ident
chainname_tmp
;
];
cmd
"bash"
[(
file_dump
(
diffsel_add_iterations_script
~
chainname
~
ali
:
tmp_ali
~
tree
:
tmp_tree
))];
...
...
lib/diffsel.mli
View file @
aa74ed23
...
...
@@ -8,6 +8,8 @@ val diffsel :
n_cycles
:
int
->
id
:
int
->
tag
:
string
->
?
seed
:
int
->
unit
->
[
`diffsel
]
directory
workflow
val
selector
:
...
...
lib/pipeline.ml
View file @
aa74ed23
...
...
@@ -243,7 +243,7 @@ let derive_from_det_meth ~det_meth ~(dataset : Dataset.t) ~preview =
|
`Pcoc_gamma
->
`Pcoc_gamma
(
Pcoc
.
pcoc
~
catx_est
:
10
~
plot_complete
:
true
~
gamma
:
true
~
faa
~
tree
:
tree_sc
)
|
`Pcoc_C60
->
`Pcoc_C60
(
Pcoc
.
pcoc
~
catx_est
:
60
~
plot_complete
:
true
~
gamma
:
false
~
faa
~
tree
:
tree_sc
)
|
`Tdg09
->
`Tdg09
(
Tamuri
.
tdg09
~
faa
~
tree
:
tree_sc
)
|
`Diffsel
->
`Diffsel
(
Diffsel
.
diffsel
~
phy_n
~
tree
:
diffsel_tree
~
w_every
~
n_cycles
~
id
:
1
~
tag
:
"master_a4b5"
)
|
`Diffsel
->
`Diffsel
(
Diffsel
.
diffsel
~
phy_n
~
tree
:
diffsel_tree
~
w_every
~
n_cycles
~
id
:
1
~
tag
:
"master_a4b5"
~
seed
:
(
Random
.
int
Int
.
max_value
)
()
)
|
`Identical_LG
->
`Identical_LG
(
Identical
.
identical
~
faa
~
tree_id
~
tree_sc
~
prot_model
:
"LG08"
)
|
`Identical_WAG
->
`Identical_WAG
(
Identical
.
identical
~
faa
~
tree_id
~
tree_sc
~
prot_model
:
"WAG01"
)
|
`Topological_LG
->
`Topological_LG
(
Topological
.
topological
~
faa
~
tree
:
tree_id
~
tree_conv
~
prot_model
:
"LG08"
)
...
...
@@ -293,7 +293,7 @@ let derive_det ~dataset_l ~preview ~fast_mode =
List
.
map
dataset_l
~
f
:
(
fun
dataset
->
derive_from_dataset
~
preview
~
dataset
~
fast_mode
)
let
derive_profile
?
(
indir
=
""
)
?
(
ns
=
0
)
~
preview
~
fast_mode
~
no_Ne
~
ne_test
~
no_HaPC
~
tree_dir
~
profile
~
use_concat
~
only_simu
()
=
let
derive_profile
?
(
indir
=
""
)
?
(
ns
=
0
)
~
preview
~
fast_mode
~
no_Ne
~
ne_test
~
no_HaPC
~
tree_dir
~
profile
~
use_concat
~
only_simu
~
seed
()
=
let
trees
=
Array
.
to_list
@@
Sys
.
readdir
tree_dir
in
let
simu_dataset_l
=
derive_sim
~
tree_dir
~
trees
~
profile
~
preview
~
use_concat
~
ns
~
no_Ne
~
no_HaPC
~
ne_test
in
let
post_analyses_simu
=
Post_analyses
.
post_analyses_simu_of_simu_dataset_l
~
simu_dataset_l
in
...
...
@@ -357,7 +357,7 @@ let detection_main ~outdir ~indir ?(np = 2) ?(mem = 2) ~preview ~fast_mode () =
let
repo
=
repo_of_dataset_results_l
~
dataset_results_l
in
Repo
.
build
~
outdir
~
np
~
mem
:
(
`GB
mem
)
~
logger
repo
let
simulation_main
~
outdir
?
(
ns
=
0
)
?
(
np
=
2
)
?
(
mem
=
2
)
~
tree_dir
~
profile_fn
~
preview
~
use_concat
~
no_Ne
~
no_HaPC
()
=
let
simulation_main
~
outdir
?
(
ns
=
0
)
?
(
np
=
2
)
?
(
mem
=
2
)
~
tree_dir
~
profile_fn
~
preview
~
use_concat
~
no_Ne
~
no_HaPC
~
seed
()
=
let
nb_sites
=
if
ns
=
0
then
(
if
preview
then
20
else
50
)
else
ns
in
let
profile
=
Profile
.
profile_l_of_splitted_profile
~
nb_cat
:
1
~
nb_sites
profile_fn
in
let
trees
=
Array
.
to_list
@@
Sys
.
readdir
tree_dir
in
...
...
@@ -365,11 +365,12 @@ let simulation_main ~outdir ?(ns = 0) ?(np = 2) ?(mem = 2) ~tree_dir ~profile_fn
let
repo
=
Dataset
.
repo
dataset_l
~
preview
in
Repo
.
build
~
outdir
~
np
~
mem
:
(
`GB
mem
)
~
logger
repo
let
validation_main
~
outdir
?
(
indir
=
""
)
?
(
ns
=
0
)
?
(
np
=
2
)
?
(
mem
=
2
)
~
preview
~
fast_mode
~
no_Ne
~
ne_test
~
no_HaPC
~
tree_dir
~
profile_fn
~
use_concat
~
only_simu
()
=
let
validation_main
~
outdir
?
(
indir
=
""
)
?
(
ns
=
0
)
?
(
np
=
2
)
?
(
mem
=
2
)
~
preview
~
fast_mode
~
no_Ne
~
ne_test
~
no_HaPC
~
tree_dir
~
profile_fn
~
use_concat
~
only_simu
?
(
seed
=
Random
.
int
Int
.
max_value
)
()
=
(* simulated trees *)
Random
.
init
seed
;
let
nb_sites
=
if
ns
=
0
then
(
if
preview
then
20
else
50
)
else
ns
in
let
profile
=
Profile
.
profile_l_of_splitted_profile
~
nb_cat
:
3
~
nb_sites
profile_fn
in
let
sim_repo_l
=
derive_profile
~
indir
~
ns
~
preview
~
fast_mode
~
no_Ne
~
ne_test
~
no_HaPC
~
tree_dir
~
profile
~
use_concat
~
only_simu
()
in
let
sim_repo_l
=
derive_profile
~
indir
~
ns
~
preview
~
fast_mode
~
no_Ne
~
ne_test
~
no_HaPC
~
tree_dir
~
profile
~
use_concat
~
only_simu
~
seed
()
in
(* real trees *)
let
indir_dataset_l
=
if
indir
=
""
then
[]
else
parse_input_data
indir
in
let
dataset_l
=
indir_dataset_l
in
...
...
@@ -413,8 +414,10 @@ let simulation_command =
flag
"--tree-dir"
(
required
string
)
~
doc
:
"PATH Path to tree directory"
and
profile_fn
=
flag
"--profile-fn"
(
required
string
)
~
doc
:
"PATH Path to profile file"
and
seed
=
flag
"--seed"
(
optional
int
)
~
doc
:
"INT Global seed"
in
simulation_main
~
outdir
?
ns
?
np
?
mem
~
no_Ne
~
no_HaPC
~
tree_dir
~
profile_fn
~
preview
~
use_concat
simulation_main
~
outdir
?
ns
?
np
?
mem
~
no_Ne
~
no_HaPC
~
tree_dir
~
profile_fn
~
preview
~
use_concat
~
seed
]
let
detection_command
=
...
...
@@ -471,6 +474,8 @@ let validation_command =
flag
"--tree-dir"
(
required
string
)
~
doc
:
"PATH Path to tree directory"
and
profile_fn
=
flag
"--profile-fn"
(
required
string
)
~
doc
:
"PATH Path to profile file"
and
seed
=
flag
"--seed"
(
optional
int
)
~
doc
:
"INT Global seed"
in
validation_main
~
outdir
?
indir
?
ns
?
np
?
mem
~
preview
~
fast_mode
~
no_Ne
~
ne_test
~
no_HaPC
~
tree_dir
~
profile_fn
~
use_concat
~
only_simu
validation_main
~
outdir
?
indir
?
ns
?
np
?
mem
~
preview
~
fast_mode
~
no_Ne
~
ne_test
~
no_HaPC
~
tree_dir
~
profile_fn
~
use_concat
~
only_simu
?
seed
]
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