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VEBER Philippe
codepi
Commits
3351182b
Commit
3351182b
authored
Sep 07, 2018
by
Carine Rey
Browse files
add new hypo (work in progress)
parent
4bbbe597
Changes
4
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Showing
4 changed files
with
73 additions
and
4 deletions
+73
-4
lib/convergence_hypothesis.ml
lib/convergence_hypothesis.ml
+12
-0
lib/pipeline.ml
lib/pipeline.ml
+21
-3
lib/post_analyses.ml
lib/post_analyses.ml
+36
-1
lib/tree_dataset.ml
lib/tree_dataset.ml
+4
-0
No files found.
lib/convergence_hypothesis.ml
View file @
3351182b
...
...
@@ -22,6 +22,10 @@ type t =
|
HaPC_NeG5_NeC_1
|
H0_NeG1_NeC_5
|
H0_NeG5_NeC_1
|
HaPC_NeG2_NeC_4
|
HaPC_NeG4_NeC_2
|
H0_NeG2_NeC_4
|
H0_NeG4_NeC_2
let
string_of_model
m
=
match
m
with
|
H0_NeG1
->
"H0_NeG1"
...
...
@@ -43,6 +47,10 @@ let string_of_model m = match m with
|
HaPC_NeG5_NeC_1
->
"HaPC_NeG5_NeC_1"
|
H0_NeG1_NeC_5
->
"H0_NeG1_NeC_5"
|
H0_NeG5_NeC_1
->
"H0_NeG5_NeC_1"
|
HaPC_NeG2_NeC_4
->
"HaPC_NeG2_NeC_4"
|
HaPC_NeG4_NeC_2
->
"HaPC_NeG4_NeC_2"
|
H0_NeG2_NeC_4
->
"H0_NeG2_NeC_4"
|
H0_NeG4_NeC_2
->
"H0_NeG4_NeC_2"
let
assign
k
v
=
seq
~
sep
:
"="
[
string
k
;
v
]
...
...
@@ -117,5 +125,9 @@ let bpp_config_F nodes hyp = [
|
HaPC_NeG5_NeC_1
->
bpp_config_HaPC_F_Ne
|
H0_NeG1_NeC_5
->
bpp_config_H0_F_Ne
|
H0_NeG5_NeC_1
->
bpp_config_H0_F_Ne
|
HaPC_NeG2_NeC_4
->
bpp_config_HaPC_F_Ne
|
HaPC_NeG4_NeC_2
->
bpp_config_HaPC_F_Ne
|
H0_NeG2_NeC_4
->
bpp_config_H0_F_Ne
|
H0_NeG4_NeC_2
->
bpp_config_H0_F_Ne
;
]
lib/pipeline.ml
View file @
3351182b
...
...
@@ -68,6 +68,7 @@ let derive_from_model ~model ~input_tree ~tree_dataset ~tree_prefix ~profile ~pr
|
H0_NeG3
->
3
.
|
H0_NeG4
->
4
.
|
H0_NeG5
->
5
.
|
HaPCOC
->
1
.
|
HaPC_NeG1
->
1
.
|
HaPC_NeG2
->
2
.
|
HaPC_NeG3
->
3
.
...
...
@@ -81,7 +82,10 @@ let derive_from_model ~model ~input_tree ~tree_dataset ~tree_prefix ~profile ~pr
|
HaPC_NeG5_NeC_1
->
5
.
|
H0_NeG1_NeC_5
->
1
.
|
H0_NeG5_NeC_1
->
5
.
|
_
->
1
.
|
HaPC_NeG2_NeC_4
->
2
.
|
HaPC_NeG4_NeC_2
->
4
.
|
H0_NeG2_NeC_4
->
2
.
|
H0_NeG4_NeC_2
->
4
.
in
let
ne_c
=
match
model
with
|
H0_NeG1
->
ne_g
...
...
@@ -89,6 +93,7 @@ let derive_from_model ~model ~input_tree ~tree_dataset ~tree_prefix ~profile ~pr
|
H0_NeG3
->
ne_g
|
H0_NeG4
->
ne_g
|
H0_NeG5
->
ne_g
|
HaPCOC
->
ne_g
|
HaPC_NeG1
->
ne_g
|
HaPC_NeG2
->
ne_g
|
HaPC_NeG3
->
ne_g
...
...
@@ -102,7 +107,10 @@ let derive_from_model ~model ~input_tree ~tree_dataset ~tree_prefix ~profile ~pr
|
HaPC_NeG5_NeC_1
->
1
.
|
H0_NeG1_NeC_5
->
5
.
|
H0_NeG5_NeC_1
->
1
.
|
_
->
ne_g
|
HaPC_NeG2_NeC_4
->
4
.
|
HaPC_NeG4_NeC_2
->
2
.
|
H0_NeG2_NeC_4
->
4
.
|
H0_NeG4_NeC_2
->
2
.
in
let
ne_a
=
match
model
with
|
H0_NeG1
->
ne_g
...
...
@@ -110,6 +118,7 @@ let derive_from_model ~model ~input_tree ~tree_dataset ~tree_prefix ~profile ~pr
|
H0_NeG3
->
ne_g
|
H0_NeG4
->
ne_g
|
H0_NeG5
->
ne_g
|
HaPCOC
->
ne_g
|
HaPC_NeG1
->
ne_g
|
HaPC_NeG2
->
ne_g
|
HaPC_NeG3
->
ne_g
...
...
@@ -123,7 +132,10 @@ let derive_from_model ~model ~input_tree ~tree_dataset ~tree_prefix ~profile ~pr
|
HaPC_NeG5_NeC_1
->
ne_g
|
H0_NeG1_NeC_5
->
ne_g
|
H0_NeG5_NeC_1
->
ne_g
|
_
->
ne_g
|
HaPC_NeG2_NeC_4
->
ne_g
|
HaPC_NeG4_NeC_2
->
ne_g
|
H0_NeG2_NeC_4
->
ne_g
|
H0_NeG4_NeC_2
->
ne_g
in
let
profile_f
=
profile
.
profile_f
in
let
profile_c
=
profile
.
profile_c
in
...
...
@@ -163,6 +175,8 @@ let derive_from_tree ~tree_dir ~tree ~profile ~preview ~use_concat ~ns ~no_Ne ~n
H0_NeG4
;
HaPC_NeG3
;
HaPC_NeG4
;
H0_NeG2
;
HaPC_NeG2
;
]
;
(
if
no_Ne
then
...
...
@@ -176,6 +190,10 @@ let derive_from_tree ~tree_dir ~tree ~profile ~preview ~use_concat ~ns ~no_Ne ~n
HaPC_NeG5_NeC_1
;
H0_NeG1_NeC_5
;
H0_NeG5_NeC_1
;
HaPC_NeG2_NeC_4
;
HaPC_NeG4_NeC_2
;
H0_NeG2_NeC_4
;
H0_NeG4_NeC_2
;
]
);
(
if
ne_test
then
...
...
lib/post_analyses.ml
View file @
3351182b
...
...
@@ -17,6 +17,7 @@ type t_choices = {
t_choices_plot
:
text_file
workflow
;
t_choices_condensed_plot
:
text_file
workflow
;
t_choices_condensed_plot_png
:
text_file
workflow
;
auc_tsv
:
text_file
workflow
;
rp_plot
:
text_file
workflow
;
tree_prefix
:
string
;
}
...
...
@@ -74,6 +75,10 @@ let make_t_choices ?(tree_prefix="") ~haPCOC_mr
~
haPC_NeG1_NeC_5_mr
~
h0_NeG1_NeC_5_mr
~
h0_NeG5_NeC_1_mr
~
haPC_NeG4_NeC_2_mr
~
haPC_NeG2_NeC_4_mr
~
h0_NeG2_NeC_4_mr
~
h0_NeG4_NeC_2_mr
~
haPC_NeG5_indel_mr
()
:
post_analyses_dir
directory
workflow
=
let
env
=
Env
.
env_r
in
...
...
@@ -93,6 +98,10 @@ let make_t_choices ?(tree_prefix="") ~haPCOC_mr
(
"--HaPC_NeG5_NeC_x2_res"
,
haPC_NeG5_NeC_x2_mr
);
(
"--H0_NeG5_NeC_div2_res"
,
h0_NeG5_NeC_div2_mr
);
(
"--H0_NeG5_NeC_x2_res"
,
h0_NeG5_NeC_x2_mr
);
(
"--HaPC_NeG4_NeC_2_res"
,
haPC_NeG4_NeC_2_mr
);
(
"--H0_NeG4_NeC_2_res"
,
h0_NeG4_NeC_2_mr
);
(
"--HaPC_NeG2_NeC_4_res"
,
haPC_NeG2_NeC_4_mr
);
(
"--H0_NeG2_NeC_4_res"
,
h0_NeG2_NeC_4_mr
);
(
"--HaPC_NeG5_NeC_1_res"
,
haPC_NeG5_NeC_1_mr
);
(
"--H0_NeG5_NeC_1_res"
,
h0_NeG5_NeC_1_mr
);
(
"--HaPC_NeG1_NeC_5_res"
,
haPC_NeG1_NeC_5_mr
);
...
...
@@ -201,6 +210,11 @@ type res_all_hyp = {
h0_NeG5_NeC_div2_res
:
dataset_res
option
;
h0_NeG5_NeC_x2_res
:
dataset_res
option
;
haPC_NeG4_NeC_2_res
:
dataset_res
option
;
haPC_NeG2_NeC_4_res
:
dataset_res
option
;
h0_NeG4_NeC_2_res
:
dataset_res
option
;
h0_NeG2_NeC_4_res
:
dataset_res
option
;
haPC_NeG5_NeC_1_res
:
dataset_res
option
;
haPC_NeG1_NeC_5_res
:
dataset_res
option
;
h0_NeG5_NeC_1_res
:
dataset_res
option
;
...
...
@@ -221,6 +235,10 @@ let make_t_choices_per_couple ~tree_prefix {ha_PCOC_res;
haPC_NeG5_NeC_x2_res
;
h0_NeG5_NeC_div2_res
;
h0_NeG5_NeC_x2_res
;
haPC_NeG4_NeC_2_res
;
haPC_NeG2_NeC_4_res
;
h0_NeG4_NeC_2_res
;
h0_NeG2_NeC_4_res
;
haPC_NeG5_NeC_1_res
;
haPC_NeG1_NeC_5_res
;
h0_NeG5_NeC_1_res
;
...
...
@@ -247,6 +265,11 @@ let make_t_choices_per_couple ~tree_prefix {ha_PCOC_res;
let
h0_NeG5_NeC_div2_mr
=
get_merged_results_opt
h0_NeG5_NeC_div2_res
in
let
h0_NeG5_NeC_x2_mr
=
get_merged_results_opt
h0_NeG5_NeC_x2_res
in
let
haPC_NeG4_NeC_2_mr
=
get_merged_results_opt
haPC_NeG4_NeC_2_res
in
let
haPC_NeG2_NeC_4_mr
=
get_merged_results_opt
haPC_NeG2_NeC_4_res
in
let
h0_NeG2_NeC_4_mr
=
get_merged_results_opt
h0_NeG2_NeC_4_res
in
let
h0_NeG4_NeC_2_mr
=
get_merged_results_opt
h0_NeG4_NeC_2_res
in
let
haPC_NeG5_NeC_1_mr
=
get_merged_results_opt
haPC_NeG5_NeC_1_res
in
let
haPC_NeG1_NeC_5_mr
=
get_merged_results_opt
haPC_NeG1_NeC_5_res
in
let
h0_NeG1_NeC_5_mr
=
get_merged_results_opt
h0_NeG1_NeC_5_res
in
...
...
@@ -272,6 +295,10 @@ let make_t_choices_per_couple ~tree_prefix {ha_PCOC_res;
~
h0_NeG5_NeC_x2_mr
~
h0_NeG5_indel_mr
~
haPC_NeG5_indel_mr
~
haPC_NeG4_NeC_2_mr
~
haPC_NeG2_NeC_4_mr
~
h0_NeG2_NeC_4_mr
~
h0_NeG4_NeC_2_mr
~
haPC_NeG5_NeC_1_mr
~
haPC_NeG1_NeC_5_mr
~
h0_NeG1_NeC_5_mr
...
...
@@ -299,6 +326,11 @@ let get_t_choices ~tree_prefix ~(dataset_results_l: dataset_res list) : t_choice
let
h0_NeG5_NeC_div2_res
=
List
.
find
dataset_results_l
(
is_hyp
~
hyp
:
"H0_NeG5_NeC_div2"
)
in
let
h0_NeG5_NeC_x2_res
=
List
.
find
dataset_results_l
(
is_hyp
~
hyp
:
"H0_NeG5_NeC_x2"
)
in
let
haPC_NeG4_NeC_2_res
=
List
.
find
dataset_results_l
(
is_hyp
~
hyp
:
"HaPC_NeG4_NeC_2"
)
in
let
haPC_NeG2_NeC_4_res
=
List
.
find
dataset_results_l
(
is_hyp
~
hyp
:
"HaPC_NeG2_NeC_4"
)
in
let
h0_NeG4_NeC_2_res
=
List
.
find
dataset_results_l
(
is_hyp
~
hyp
:
"H0_NeG4_NeC_2"
)
in
let
h0_NeG2_NeC_4_res
=
List
.
find
dataset_results_l
(
is_hyp
~
hyp
:
"H0_NeG2_NeC_4"
)
in
let
haPC_NeG5_NeC_1_res
=
List
.
find
dataset_results_l
(
is_hyp
~
hyp
:
"HaPC_NeG5_NeC_1"
)
in
let
haPC_NeG1_NeC_5_res
=
List
.
find
dataset_results_l
(
is_hyp
~
hyp
:
"HaPC_NeG1_NeC_5"
)
in
let
h0_NeG5_NeC_1_res
=
List
.
find
dataset_results_l
(
is_hyp
~
hyp
:
"H0_NeG5_NeC_1"
)
in
...
...
@@ -314,6 +346,7 @@ let get_t_choices ~tree_prefix ~(dataset_results_l: dataset_res list) : t_choice
h0_NeG1_res
;
h0_NeG2_res
;
h0_NeG3_res
;
h0_NeG4_res
;
h0_NeG5_res
;
haPC_NeG1_res
;
haPC_NeG2_res
;
haPC_NeG3_res
;
haPC_NeG4_res
;
haPC_NeG5_res
;
haPC_NeG5_NeC_div2_res
;
haPC_NeG5_NeC_x2_res
;
h0_NeG5_NeC_div2_res
;
h0_NeG5_NeC_x2_res
;
haPC_NeG4_NeC_2_res
;
haPC_NeG2_NeC_4_res
;
h0_NeG2_NeC_4_res
;
h0_NeG4_NeC_2_res
;
haPC_NeG5_NeC_1_res
;
haPC_NeG1_NeC_5_res
;
h0_NeG1_NeC_5_res
;
h0_NeG5_NeC_1_res
;
h0_NeG5_indel_res
;
haPC_NeG5_indel_res
}
in
let
t_choices_max
=
t_choices_dir
/
selector
[
"out.max_MCC_per_meth.tsv"
]
in
...
...
@@ -323,8 +356,9 @@ let get_t_choices ~tree_prefix ~(dataset_results_l: dataset_res list) : t_choice
let
t_choices_condensed_plot
=
t_choices_dir
/
selector
[
"out_condensed.pdf"
]
in
let
t_choices_condensed_plot_png
=
t_choices_dir
/
selector
[
"out_condensed.png"
]
in
let
rp_plot
=
t_choices_dir
/
selector
[
"out_condensed.recall_precision_ok.pdf"
]
in
let
auc_tsv
=
t_choices_dir
/
selector
[
"out.auc_condensed.tsv"
]
in
let
tree_prefix
=
ha_PCOC
.
tree_prefix
in
Some
{
t_choices_max
;
t_choices_recall09
;
t_choices_complete
;
t_choices_plot
;
t_choices_condensed_plot
;
t_choices_condensed_plot_png
;
rp_plot
;
tree_prefix
}
Some
{
t_choices_max
;
t_choices_recall09
;
t_choices_complete
;
t_choices_plot
;
t_choices_condensed_plot
;
t_choices_condensed_plot_png
;
rp_plot
;
auc_tsv
;
tree_prefix
}
|
_
->
None
...
...
@@ -477,6 +511,7 @@ let repo_of_post_analyses_res ~prefix ~post_analyses_res =
item
[
prefix
^
".t_choices.condensed.pdf"
]
w
.
t_choices_condensed_plot
;
item
[
prefix
^
".t_choices.condensed.png"
]
w
.
t_choices_condensed_plot_png
;
item
[
prefix
^
".recall_precision_ok.pdf"
]
w
.
rp_plot
;
item
[
prefix
^
".auc_condensed.tsv"
]
w
.
auc_tsv
;
]
]
|>
List
.
concat
);
...
...
lib/tree_dataset.ml
View file @
3351182b
...
...
@@ -36,6 +36,10 @@ let nodes dataset (model : Convergence_hypothesis.t) =
|
HaPC_NeG5_NeC_1
->
[
"tree.Ha.node_ids"
]
|
H0_NeG1_NeC_5
->
[
"tree.H0_a.node_ids"
]
|
H0_NeG5_NeC_1
->
[
"tree.H0_a.node_ids"
]
|
HaPC_NeG2_NeC_4
->
[
"tree.Ha.node_ids"
]
|
HaPC_NeG4_NeC_2
->
[
"tree.Ha.node_ids"
]
|
H0_NeG2_NeC_4
->
[
"tree.H0_a.node_ids"
]
|
H0_NeG4_NeC_2
->
[
"tree.H0_a.node_ids"
]
)
let
tree
dataset
mode
=
...
...
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