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VEBER Philippe
codepi
Commits
0972a129
Commit
0972a129
authored
Aug 31, 2018
by
Carine Rey
Browse files
end add dataset with indels
parent
df593f00
Changes
2
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2 changed files
with
37 additions
and
9 deletions
+37
-9
lib/post_analyses.ml
lib/post_analyses.ml
+24
-6
lib/scripts/calc_t_per_meth.R
lib/scripts/calc_t_per_meth.R
+13
-3
No files found.
lib/post_analyses.ml
View file @
0972a129
...
@@ -70,7 +70,9 @@ let make_t_choices ?(tree_prefix="") ~haPCOC_mr
...
@@ -70,7 +70,9 @@ let make_t_choices ?(tree_prefix="") ~haPCOC_mr
~
haPC_NeG5_NeC_div2_mr
~
haPC_NeG5_NeC_div2_mr
~
haPC_NeG5_NeC_x2_mr
~
haPC_NeG5_NeC_x2_mr
~
h0_NeG5_NeC_div2_mr
~
h0_NeG5_NeC_div2_mr
~
h0_NeG5_NeC_x2_mr
()
:
post_analyses_dir
directory
workflow
=
~
h0_NeG5_NeC_x2_mr
~
h0_NeG5_indel_mr
~
haPC_NeG5_indel_mr
()
:
post_analyses_dir
directory
workflow
=
let
env
=
r_env
in
let
env
=
r_env
in
let
out
=
dest
//
"out"
in
let
out
=
dest
//
"out"
in
...
@@ -89,6 +91,8 @@ let make_t_choices ?(tree_prefix="") ~haPCOC_mr
...
@@ -89,6 +91,8 @@ let make_t_choices ?(tree_prefix="") ~haPCOC_mr
(
"--HaPC_NeG5_NeC_x2_res"
,
haPC_NeG5_NeC_x2_mr
);
(
"--HaPC_NeG5_NeC_x2_res"
,
haPC_NeG5_NeC_x2_mr
);
(
"--H0_NeG5_NeC_div2_res"
,
h0_NeG5_NeC_div2_mr
);
(
"--H0_NeG5_NeC_div2_res"
,
h0_NeG5_NeC_div2_mr
);
(
"--H0_NeG5_NeC_x2_res"
,
h0_NeG5_NeC_x2_mr
);
(
"--H0_NeG5_NeC_x2_res"
,
h0_NeG5_NeC_x2_mr
);
(
"--H0_NeG5_indel_res"
,
h0_NeG5_indel_mr
);
(
"--HaPC_NeG5_indel_res"
,
haPC_NeG5_indel_mr
);
(
"--HaPCOC"
,
haPCOC_mr
);
(
"--HaPCOC"
,
haPCOC_mr
);
]
~
f
:
(
fun
(
opt_name
,
mr_option
)
->
build_cmd_t_choices
opt_name
mr_option
)
]
~
f
:
(
fun
(
opt_name
,
mr_option
)
->
build_cmd_t_choices
opt_name
mr_option
)
|>
List
.
concat
in
|>
List
.
concat
in
...
@@ -190,6 +194,9 @@ type res_all_hyp = {
...
@@ -190,6 +194,9 @@ type res_all_hyp = {
haPC_NeG5_NeC_x2_res
:
dataset_res
option
;
haPC_NeG5_NeC_x2_res
:
dataset_res
option
;
h0_NeG5_NeC_div2_res
:
dataset_res
option
;
h0_NeG5_NeC_div2_res
:
dataset_res
option
;
h0_NeG5_NeC_x2_res
:
dataset_res
option
;
h0_NeG5_NeC_x2_res
:
dataset_res
option
;
h0_NeG5_indel_res
:
dataset_res
option
;
haPC_NeG5_indel_res
:
dataset_res
option
;
}
}
let
make_t_choices_per_couple
~
tree_prefix
{
ha_PCOC_res
;
let
make_t_choices_per_couple
~
tree_prefix
{
ha_PCOC_res
;
...
@@ -203,6 +210,8 @@ let make_t_choices_per_couple ~tree_prefix {ha_PCOC_res;
...
@@ -203,6 +210,8 @@ let make_t_choices_per_couple ~tree_prefix {ha_PCOC_res;
haPC_NeG5_NeC_x2_res
;
haPC_NeG5_NeC_x2_res
;
h0_NeG5_NeC_div2_res
;
h0_NeG5_NeC_div2_res
;
h0_NeG5_NeC_x2_res
;
h0_NeG5_NeC_x2_res
;
h0_NeG5_indel_res
;
haPC_NeG5_indel_res
;
}
=
}
=
let
haPCOC_mr
=
get_merged_results_opt
ha_PCOC_res
in
let
haPCOC_mr
=
get_merged_results_opt
ha_PCOC_res
in
...
@@ -222,6 +231,9 @@ let make_t_choices_per_couple ~tree_prefix {ha_PCOC_res;
...
@@ -222,6 +231,9 @@ let make_t_choices_per_couple ~tree_prefix {ha_PCOC_res;
let
haPC_NeG5_NeC_x2_mr
=
get_merged_results_opt
haPC_NeG5_NeC_x2_res
in
let
haPC_NeG5_NeC_x2_mr
=
get_merged_results_opt
haPC_NeG5_NeC_x2_res
in
let
h0_NeG5_NeC_div2_mr
=
get_merged_results_opt
h0_NeG5_NeC_div2_res
in
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
h0_NeG5_NeC_x2_mr
=
get_merged_results_opt
h0_NeG5_NeC_x2_res
in
let
h0_NeG5_indel_mr
=
get_merged_results_opt
h0_NeG5_indel_res
in
let
haPC_NeG5_indel_mr
=
get_merged_results_opt
haPC_NeG5_indel_res
in
make_t_choices
~
tree_prefix
~
haPCOC_mr
make_t_choices
~
tree_prefix
~
haPCOC_mr
~
h0_NeG1_mr
~
h0_NeG1_mr
...
@@ -238,6 +250,8 @@ let make_t_choices_per_couple ~tree_prefix {ha_PCOC_res;
...
@@ -238,6 +250,8 @@ let make_t_choices_per_couple ~tree_prefix {ha_PCOC_res;
~
haPC_NeG5_NeC_x2_mr
~
haPC_NeG5_NeC_x2_mr
~
h0_NeG5_NeC_div2_mr
~
h0_NeG5_NeC_div2_mr
~
h0_NeG5_NeC_x2_mr
~
h0_NeG5_NeC_x2_mr
~
h0_NeG5_indel_mr
~
haPC_NeG5_indel_mr
()
()
...
@@ -256,10 +270,13 @@ let get_t_choices ~tree_prefix ~(dataset_results_l: dataset_res list) : t_choice
...
@@ -256,10 +270,13 @@ let get_t_choices ~tree_prefix ~(dataset_results_l: dataset_res list) : t_choice
let
haPC_NeG4_res
=
List
.
find
dataset_results_l
(
is_hyp
~
hyp
:
"HaPC_NeG4"
)
in
let
haPC_NeG4_res
=
List
.
find
dataset_results_l
(
is_hyp
~
hyp
:
"HaPC_NeG4"
)
in
let
haPC_NeG5_res
=
List
.
find
dataset_results_l
(
is_hyp
~
hyp
:
"HaPC_NeG5"
)
in
let
haPC_NeG5_res
=
List
.
find
dataset_results_l
(
is_hyp
~
hyp
:
"HaPC_NeG5"
)
in
let
haPC_NeG5_NeC_div2_res
=
List
.
find
dataset_results_l
(
is_hyp
~
hyp
:
"HaPC_NeG5_NeC_div2"
)
in
let
haPC_NeG5_NeC_div2_res
=
List
.
find
dataset_results_l
(
is_hyp
~
hyp
:
"HaPC_NeG5_NeC_div2"
)
in
let
haPC_NeG5_NeC_x2_res
=
List
.
find
dataset_results_l
(
is_hyp
~
hyp
:
"HaPC_NeG5_NeC_x2"
)
in
let
haPC_NeG5_NeC_x2_res
=
List
.
find
dataset_results_l
(
is_hyp
~
hyp
:
"HaPC_NeG5_NeC_x2"
)
in
let
h0_NeG5_NeC_div2_res
=
List
.
find
dataset_results_l
(
is_hyp
~
hyp
:
"H0_NeG5_NeC_div2"
)
in
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
h0_NeG5_NeC_x2_res
=
List
.
find
dataset_results_l
(
is_hyp
~
hyp
:
"H0_NeG5_NeC_x2"
)
in
let
h0_NeG5_indel_res
=
List
.
find
dataset_results_l
(
is_hyp
~
hyp
:
"H0_NeG5_0.33_i"
)
in
let
haPC_NeG5_indel_res
=
List
.
find
dataset_results_l
(
is_hyp
~
hyp
:
"HaPC_NeG5_0.33_i"
)
in
match
(
ha_PCOC_res
)
with
match
(
ha_PCOC_res
)
with
...
@@ -267,7 +284,8 @@ let get_t_choices ~tree_prefix ~(dataset_results_l: dataset_res list) : t_choice
...
@@ -267,7 +284,8 @@ let get_t_choices ~tree_prefix ~(dataset_results_l: dataset_res list) : t_choice
let
t_choices_dir
=
make_t_choices_per_couple
~
tree_prefix
{
ha_PCOC_res
;
let
t_choices_dir
=
make_t_choices_per_couple
~
tree_prefix
{
ha_PCOC_res
;
h0_NeG1_res
;
h0_NeG2_res
;
h0_NeG3_res
;
h0_NeG4_res
;
h0_NeG5_res
;
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_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
}
in
haPC_NeG5_NeC_div2_res
;
haPC_NeG5_NeC_x2_res
;
h0_NeG5_NeC_div2_res
;
h0_NeG5_NeC_x2_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
let
t_choices_max
=
t_choices_dir
/
selector
[
"out.max_MCC_per_meth.tsv"
]
in
let
t_choices_recall09
=
t_choices_dir
/
selector
[
"out.recall09_per_meth.tsv"
]
in
let
t_choices_recall09
=
t_choices_dir
/
selector
[
"out.recall09_per_meth.tsv"
]
in
let
t_choices_complete
=
t_choices_dir
/
selector
[
"out.complete.tsv"
]
in
let
t_choices_complete
=
t_choices_dir
/
selector
[
"out.complete.tsv"
]
in
...
...
lib/scripts/calc_t_per_meth.R
View file @
0972a129
...
@@ -25,6 +25,8 @@ option_list = list(
...
@@ -25,6 +25,8 @@ option_list = list(
make_option
(
c
(
"--HaPC_NeG5_NeC_x2_res"
)
,
type
=
"character"
,
default
=
NA
,
help
=
"merged_results HaPC_NeG5_NeC_x2_res"
,
metavar
=
"character"
),
make_option
(
c
(
"--HaPC_NeG5_NeC_x2_res"
)
,
type
=
"character"
,
default
=
NA
,
help
=
"merged_results HaPC_NeG5_NeC_x2_res"
,
metavar
=
"character"
),
make_option
(
c
(
"--H0_NeG5_NeC_div2_res"
)
,
type
=
"character"
,
default
=
NA
,
help
=
"merged_results H0_NeG5_NeC_div2_res"
,
metavar
=
"character"
),
make_option
(
c
(
"--H0_NeG5_NeC_div2_res"
)
,
type
=
"character"
,
default
=
NA
,
help
=
"merged_results H0_NeG5_NeC_div2_res"
,
metavar
=
"character"
),
make_option
(
c
(
"--H0_NeG5_NeC_x2_res"
)
,
type
=
"character"
,
default
=
NA
,
help
=
"merged_results H0_NeG5_NeC_x2_res"
,
metavar
=
"character"
),
make_option
(
c
(
"--H0_NeG5_NeC_x2_res"
)
,
type
=
"character"
,
default
=
NA
,
help
=
"merged_results H0_NeG5_NeC_x2_res"
,
metavar
=
"character"
),
make_option
(
c
(
"--H0_NeG5_indel_res"
)
,
type
=
"character"
,
default
=
NA
,
help
=
"merged_results H0_NeG5_indel_res"
,
metavar
=
"character"
),
make_option
(
c
(
"--HaPC_NeG5_indel_res"
)
,
type
=
"character"
,
default
=
NA
,
help
=
"merged_results HaPC_NeG5_indel_res"
,
metavar
=
"character"
),
make_option
(
c
(
"--HaPCOC"
)
,
type
=
"character"
,
default
=
NA
,
help
=
"merged_results HaPCOC"
,
metavar
=
"character"
),
make_option
(
c
(
"--HaPCOC"
)
,
type
=
"character"
,
default
=
NA
,
help
=
"merged_results HaPCOC"
,
metavar
=
"character"
),
make_option
(
c
(
"--tree_prefix"
)
,
type
=
"character"
,
default
=
""
,
help
=
"tree_prefix"
,
metavar
=
"character"
),
make_option
(
c
(
"--tree_prefix"
)
,
type
=
"character"
,
default
=
""
,
help
=
"tree_prefix"
,
metavar
=
"character"
),
...
@@ -83,7 +85,8 @@ df_HaPC_NeG5_NeC_x2 = read_hyp(opt$HaPC_NeG5_NeC_x2 )
...
@@ -83,7 +85,8 @@ df_HaPC_NeG5_NeC_x2 = read_hyp(opt$HaPC_NeG5_NeC_x2 )
df_H0_NeG5_NeC_div2
=
read_hyp
(
opt
$
H0_NeG5_NeC_div2
)
df_H0_NeG5_NeC_div2
=
read_hyp
(
opt
$
H0_NeG5_NeC_div2
)
df_H0_NeG5_NeC_x2
=
read_hyp
(
opt
$
H0_NeG5_NeC_x2
)
df_H0_NeG5_NeC_x2
=
read_hyp
(
opt
$
H0_NeG5_NeC_x2
)
df_HaPC_NeG5_indel
=
read_hyp
(
opt
$
HaPC_NeG5_indel_res
)
df_H0_NeG5_indel
=
read_hyp
(
opt
$
H0_NeG5_indel_res
)
df_HaPCOC
=
read_hyp
(
opt
$
HaPCOC
)
df_HaPCOC
=
read_hyp
(
opt
$
HaPCOC
)
...
@@ -120,6 +123,8 @@ df_d_H0HaPC_NeG5 = build_df_dist_couple(df_H0_NeG5, df_HaPC_NeG5, "H0/HaPC NeG
...
@@ -120,6 +123,8 @@ df_d_H0HaPC_NeG5 = build_df_dist_couple(df_H0_NeG5, df_HaPC_NeG5, "H0/HaPC NeG
df_d_H0HaPC_NeG5_NeC_div2
=
build_df_dist_couple
(
df_H0_NeG5_NeC_div2
,
df_HaPC_NeG5_NeC_div2
,
"H0/HaPC NeG5_NeC_div2"
)
df_d_H0HaPC_NeG5_NeC_div2
=
build_df_dist_couple
(
df_H0_NeG5_NeC_div2
,
df_HaPC_NeG5_NeC_div2
,
"H0/HaPC NeG5_NeC_div2"
)
df_d_H0HaPC_NeG5_NeC_x2
=
build_df_dist_couple
(
df_H0_NeG5_NeC_x2
,
df_HaPC_NeG5_NeC_x2
,
"H0/HaPC NeG5_NeC_x2"
)
df_d_H0HaPC_NeG5_NeC_x2
=
build_df_dist_couple
(
df_H0_NeG5_NeC_x2
,
df_HaPC_NeG5_NeC_x2
,
"H0/HaPC NeG5_NeC_x2"
)
df_d_H0HaPC_NeG5_indel
=
build_df_dist_couple
(
df_H0_NeG5_indel
,
df_HaPC_NeG5_indel
,
"H0/HaPC NeG5_indel"
)
df_d
=
rbind.data.frame
(
df_d
=
rbind.data.frame
(
df_d_H0HaPCOC_NeG1
,
df_d_H0HaPCOC_NeG1
,
df_d_H0HaPC_NeG1
,
df_d_H0HaPC_NeG1
,
...
@@ -128,7 +133,9 @@ df_d = rbind.data.frame(
...
@@ -128,7 +133,9 @@ df_d = rbind.data.frame(
df_d_H0HaPC_NeG4
,
df_d_H0HaPC_NeG4
,
df_d_H0HaPC_NeG5
,
df_d_H0HaPC_NeG5
,
df_d_H0HaPC_NeG5_NeC_div2
,
df_d_H0HaPC_NeG5_NeC_div2
,
df_d_H0HaPC_NeG5_NeC_x2
)
df_d_H0HaPC_NeG5_NeC_x2
,
df_d_H0HaPC_NeG5_indel
)
df_d
=
df_d
[
order
(
df_d
$
methode
),]
df_d
=
df_d
[
order
(
df_d
$
methode
),]
...
@@ -205,9 +212,12 @@ df_H0HaPC_NeG5 = build_df_couple(df_H0_NeG5, df_HaPC_NeG5, "H0/HaPC NeG5")
...
@@ -205,9 +212,12 @@ df_H0HaPC_NeG5 = build_df_couple(df_H0_NeG5, df_HaPC_NeG5, "H0/HaPC NeG5")
df_H0HaPC_NeG5_NeC_div2
=
build_df_couple
(
df_H0_NeG5_NeC_div2
,
df_HaPC_NeG5_NeC_div2
,
"H0/HaPC NeG5_NeC_div2"
)
df_H0HaPC_NeG5_NeC_div2
=
build_df_couple
(
df_H0_NeG5_NeC_div2
,
df_HaPC_NeG5_NeC_div2
,
"H0/HaPC NeG5_NeC_div2"
)
df_H0HaPC_NeG5_NeC_x2
=
build_df_couple
(
df_H0_NeG5_NeC_x2
,
df_HaPC_NeG5_NeC_x2
,
"H0/HaPC NeG5_NeC_x2"
)
df_H0HaPC_NeG5_NeC_x2
=
build_df_couple
(
df_H0_NeG5_NeC_x2
,
df_HaPC_NeG5_NeC_x2
,
"H0/HaPC NeG5_NeC_x2"
)
df_H0HaPC_NeG5_indel
=
build_df_couple
(
df_H0_NeG5_indel
,
df_HaPC_NeG5_indel
,
"H0/HaPC NeG5_indel"
)
df_l
=
list
(
df_H0HaPCOC_NeG1
,
df_H0HaPC_NeG1
,
df_H0HaPC_NeG2
,
df_H0HaPC_NeG3
,
df_l
=
list
(
df_H0HaPCOC_NeG1
,
df_H0HaPC_NeG1
,
df_H0HaPC_NeG2
,
df_H0HaPC_NeG3
,
df_H0HaPC_NeG4
,
df_H0HaPC_NeG5
,
df_H0HaPC_NeG5_NeC_div2
,
df_H0HaPC_NeG4
,
df_H0HaPC_NeG5
,
df_H0HaPC_NeG5_NeC_div2
,
df_H0HaPC_NeG5_NeC_x2
)
df_H0HaPC_NeG5_NeC_x2
,
df_H0HaPC_NeG5_indel
)
df_l
=
df_l
[
-
which
(
sapply
(
df_l
,
is.null
))]
df_l
=
df_l
[
-
which
(
sapply
(
df_l
,
is.null
))]
df
=
do.call
(
"rbind"
,
df_l
)
df
=
do.call
(
"rbind"
,
df_l
)
...
...
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