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VEBER Philippe
codepi
Commits
639dccf8
Commit
639dccf8
authored
Jun 25, 2018
by
Philippe Veber
Browse files
fixed cyclic dependencies
parent
4ace80f0
Changes
3
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3 changed files
with
63 additions
and
60 deletions
+63
-60
lib/defs.ml
lib/defs.ml
+62
-0
lib/file_formats.ml
lib/file_formats.ml
+0
-60
lib/pipeline.ml
lib/pipeline.ml
+1
-0
No files found.
lib/defs.ml
0 → 100644
View file @
639dccf8
open
File_formats
open
Bistro
.
Std
type
parsed_input_tree
type
output_parse_input_tree
=
|
Nodes_H0
|
Nodes_Ha
|
Tree4detect
|
Tree4simu
|
Tree_diffsel
type
raw_dataset
=
{
input_tree
:
nhx
workflow
;
fna
:
nucleotide_fasta
workflow
;
}
type
ready_dataset
=
{
input_tree
:
nhx
workflow
;
tree_dataset
:
[
`tree_dataset
]
directory
workflow
;
fna
:
nucleotide_fasta
workflow
;
faa
:
aminoacid_fasta
workflow
;
}
type
(
'
a
,
'
b
)
w_dataset
=
|
Raw_dataset
of
'
a
|
Ready_dataset
of
'
b
type
dataset
=
{
model_prefix
:
string
;
tree_prefix
:
string
;
ready_dataset
:
ready_dataset
}
type
det_meth
=
|
Pcoc
|
Pcoc_gamma
|
Diffsel
let
string_of_det_meth
=
function
|
Pcoc
->
"pcoc"
|
Pcoc_gamma
->
"pcoc_gamma"
|
Diffsel
->
"diffsel"
type
'
a
w_det_meth
=
|
Pcoc_w
of
'
a
|
Pcoc_gamma_w
of
'
a
|
Diffsel
of
'
a
type
det_result
=
{
dataset
:
dataset
;
det_meth
:
det_meth
;
det_result
:
Convergence_detection
.
det_out
;
}
type
dataset_res
=
{
res_by_tools
:
det_result
list
;
merged_results
:
string
}
lib/file_formats.ml
View file @
639dccf8
...
...
@@ -26,63 +26,3 @@ class type nucleotide_phylip = object
method
format
:
[
`Nucleotide
]
end
type
parsed_input_tree
type
output_parse_input_tree
=
|
Nodes_H0
|
Nodes_Ha
|
Tree4detect
|
Tree4simu
|
Tree_diffsel
type
raw_dataset
=
{
input_tree
:
nhx
workflow
;
fna
:
nucleotide_fasta
workflow
;
}
type
ready_dataset
=
{
input_tree
:
nhx
workflow
;
tree_dataset
:
[
`tree_dataset
]
directory
workflow
;
fna
:
nucleotide_fasta
workflow
;
faa
:
aminoacid_fasta
workflow
;
}
type
(
'
a
,
'
b
)
w_dataset
=
|
Raw_dataset
of
'
a
|
Ready_dataset
of
'
b
type
dataset
=
{
model_prefix
:
string
;
tree_prefix
:
string
;
ready_dataset
:
ready_dataset
}
type
det_meth
=
|
Pcoc
|
Pcoc_gamma
|
Diffsel
let
string_of_det_meth
=
function
|
Pcoc
->
"pcoc"
|
Pcoc_gamma
->
"pcoc_gamma"
|
Diffsel
->
"diffsel"
type
'
a
w_det_meth
=
|
Pcoc_w
of
'
a
|
Pcoc_gamma_w
of
'
a
|
Diffsel
of
'
a
type
det_result
=
{
dataset
:
dataset
;
det_meth
:
det_meth
;
det_result
:
Convergence_detection
.
det_out
;
}
type
dataset_res
=
{
res_by_tools
:
det_result
list
;
merged_results
:
string
}
lib/pipeline.ml
View file @
639dccf8
...
...
@@ -3,6 +3,7 @@ open Bistro_utils
open
Bistro
.
EDSL
open
Bistro
.
Std
open
File_formats
open
Defs
let
ready_dataset_of_raw_dataset
raw_dataset
=
let
input_tree
=
raw_dataset
.
input_tree
in
...
...
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