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VEBER Philippe
codepi
Commits
e51ad99e
Commit
e51ad99e
authored
Jul 20, 2018
by
Carine Rey
Browse files
add 2 hypothesis based on different Ne, H0_BigNeInSmallNe and H0_SmallNeInBigNe
parent
0c1575dd
Changes
5
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5 changed files
with
23 additions
and
5 deletions
+23
-5
lib/bppsuite.ml
lib/bppsuite.ml
+4
-4
lib/bppsuite.mli
lib/bppsuite.mli
+1
-0
lib/convergence_hypothesis.ml
lib/convergence_hypothesis.ml
+6
-0
lib/pipeline.ml
lib/pipeline.ml
+10
-1
lib/tree_dataset.ml
lib/tree_dataset.ml
+2
-0
No files found.
lib/bppsuite.ml
View file @
e51ad99e
...
...
@@ -46,13 +46,13 @@ let bppseqgen ?(descr="") ~nb_sites ~tree ~config : nucleotide_fasta workflow =
)
]
/
selector
[
"seq.fa"
]
let
conf_file_bppseqgen_multi_profiles
~
tree
~
profile_f
~
ne_c
~
config
~
nb_sites_per_profile
=
let
conf_file_bppseqgen_multi_profiles
~
tree
~
profile_f
~
ne_c
~
ne_a
~
config
~
nb_sites_per_profile
=
seq
~
sep
:
"
\n
"
(
[
assign
"input.tree.file"
(
dep
tree
)
;
assign
"PROFILE_F"
(
dep
profile_f
)
;
assign
"number_of_sites"
(
int
nb_sites_per_profile
)
;
assign
"NE_1"
(
int
1
)
;
assign
"NE_1"
(
float
ne_a
)
;
assign
"NE_C"
(
float
ne_c
)
;
assign
"NE_T"
(
float
ne_c
)
;
]
...
...
@@ -91,7 +91,7 @@ let bppseqgen_multi_profiles_script ~config ~nb_combis ~out ~profile_f =
|
}
let
bppseqgen_multi_profiles
?
(
descr
=
""
)
~
profile_f
~
nb_sites
~
tree
~
config
~
ne_c
:
bppseqgen_multi_profiles
directory
workflow
=
let
bppseqgen_multi_profiles
?
(
descr
=
""
)
~
profile_f
~
nb_sites
~
tree
~
config
~
ne_c
~
ne_a
:
bppseqgen_multi_profiles
directory
workflow
=
let
nb_sites_per_profile
=
1
in
let
nb_combis
=
Pervasives
.(
nb_sites
/
nb_sites_per_profile
)
in
let
config_f
=
dest
//
"config.bpp"
in
...
...
@@ -102,7 +102,7 @@ let bppseqgen_multi_profiles ?(descr="") ~profile_f ~nb_sites ~tree ~config ~ne_
mkdir_p
dest
;
mkdir_p
tmp
;
cd
tmp
;
cmd
"cat"
~
stdout
:
config_f
[(
file_dump
(
conf_file_bppseqgen_multi_profiles
~
tree
~
profile_f
~
config
~
ne_c
~
nb_sites_per_profile
))];
cmd
"cat"
~
stdout
:
config_f
[(
file_dump
(
conf_file_bppseqgen_multi_profiles
~
tree
~
profile_f
~
config
~
ne_c
~
ne_a
~
nb_sites_per_profile
))];
cmd
"bash"
[(
file_dump
(
bppseqgen_multi_profiles_script
~
config
:
config_f
~
nb_combis
~
out
~
profile_f
))];
]
)
...
...
lib/bppsuite.mli
View file @
e51ad99e
...
...
@@ -18,6 +18,7 @@ val bppseqgen_multi_profiles :
tree
:
nhx
workflow
->
config
:
Bistro
.
Template
.
t
list
->
ne_c
:
float
->
ne_a
:
float
->
bppseqgen_multi_profiles
directory
workflow
val
bppseqgen_multi_profiles_get_fa
:
...
...
lib/convergence_hypothesis.ml
View file @
e51ad99e
...
...
@@ -8,6 +8,8 @@ type t =
|
HaPCOC
|
H0_NeSmall
|
H0_NeVerySmall
|
H0_BigNeInSmallNe
|
H0_SmallNeInBigNe
|
HaPCOC_NeSmall
|
HaPC_NeSmall
|
H0_NeBig
...
...
@@ -20,6 +22,8 @@ let string_of_model m = match m with
|
HaPCOC
->
"HaPCOC"
|
H0_NeSmall
->
"H0_NeSmall"
|
H0_NeVerySmall
->
"H0_NeVerySmall"
|
H0_BigNeInSmallNe
->
"H0_BigNeInSmallNe"
|
H0_SmallNeInBigNe
->
"H0_SmallNeInBigNe"
|
HaPCOC_NeSmall
->
"HaPCOC_NeSmall"
|
HaPC_NeSmall
->
"HaPC_NeSmall"
|
H0_NeBig
->
"H0_NeBig"
...
...
@@ -86,6 +90,8 @@ let bpp_config_F nodes hyp = [
|
HaPCOC
->
bpp_config_HaPCOC_F
|
H0_NeSmall
->
bpp_config_H0_F_Ne
|
H0_NeVerySmall
->
bpp_config_H0_F_Ne
|
H0_BigNeInSmallNe
->
bpp_config_H0_F_Ne
|
H0_SmallNeInBigNe
->
bpp_config_H0_F_Ne
|
HaPC_NeSmall
->
bpp_config_HaPC_F_Ne
|
HaPCOC_NeSmall
->
bpp_config_HaPCOC_F_Ne
|
H0_NeBig
->
bpp_config_H0_F_Ne
...
...
lib/pipeline.ml
View file @
e51ad99e
...
...
@@ -64,9 +64,16 @@ let derive_from_model ~model ~input_tree ~tree_dataset ~tree_prefix ~profile_f ~
|
H0_NeBig
->
10
.
|
HaPC_NeBig
->
10
.
|
HaPCOC_NeBig
->
10
.
|
H0_BigNeInSmallNe
->
10
.
|
H0_SmallNeInBigNe
->
0
.
1
|
_
->
1
.
in
let
run_fna
=
Bppsuite
.
bppseqgen_multi_profiles
~
descr
~
nb_sites
~
tree
~
config
:
config_p
~
profile_f
~
ne_c
in
let
ne_a
=
match
model
with
|
H0_BigNeInSmallNe
->
0
.
1
|
H0_SmallNeInBigNe
->
10
.
|
_
->
1
.
in
let
run_fna
=
Bppsuite
.
bppseqgen_multi_profiles
~
descr
~
nb_sites
~
tree
~
config
:
config_p
~
profile_f
~
ne_c
~
ne_a
in
let
fna
=
Bppsuite
.
bppseqgen_multi_profiles_get_fa
run_fna
in
let
fna_infos
=
Some
(
Bppsuite
.
bppseqgen_multi_profiles_get_info
run_fna
)
in
...
...
@@ -101,6 +108,8 @@ let derive_from_tree ~tree_dir ~tree ~profile_f ~preview ~use_concat ~ns ~no_Ne
HaPC_NeSmall
;
H0_NeBig
;
HaPC_NeBig
;
H0_BigNeInSmallNe
;
H0_SmallNeInBigNe
;
]
)
]
|>
List
.
concat
...
...
lib/tree_dataset.ml
View file @
e51ad99e
...
...
@@ -27,6 +27,8 @@ let nodes dataset (model : Convergence_hypothesis.t) =
|
H0_NeSmall
->
[
"tree.H0_a.node_ids"
]
|
H0_NeVerySmall
->
[
"tree.H0_a.node_ids"
]
|
H0_NeBig
->
[
"tree.H0_a.node_ids"
]
|
H0_BigNeInSmallNe
->
[
"tree.H0_a.node_ids"
]
|
H0_SmallNeInBigNe
->
[
"tree.H0_a.node_ids"
]
)
let
tree
dataset
mode
=
...
...
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