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VEBER Philippe
codepi
Commits
2edb60ab
Commit
2edb60ab
authored
Jul 08, 2020
by
Philippe Veber
Browse files
Detection_pipeline: fixed mock tdg09
parent
63e14e8c
Changes
2
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2 changed files
with
14 additions
and
12 deletions
+14
-12
app/orthomam_app.ml
app/orthomam_app.ml
+13
-11
lib/detection_pipeline.ml
lib/detection_pipeline.ml
+1
-1
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app/orthomam_app.ml
View file @
2edb60ab
open
Reviewphiltrans
module
Top
=
Bistro_utils
.
Toplevel_eval
.
Make
(
struct
let
np
=
8
let
mem
=
10
end
)()
module
Top
=
Bistro_utils
.
Toplevel_eval
.
Make
(
struct
let
np
=
3
let
mem
=
10
end
)()
let
()
=
Reviewphiltrans_toolbox
.
Orthomam_db
.
make
"/disk/data/omm"
|>
Orthomam
.(
site_ranking
~
subset
:
5
~
convergent_species
:
species_with_echolocation
~
meth
:
`tdg09
)
|>
Top
.
eval
|>
List
.
length
|>
print_int
try
Reviewphiltrans_toolbox
.
Orthomam_db
.
make
"/disk/data/omm"
|>
Orthomam
.(
site_ranking
~
convergent_species
:
species_with_echolocation
~
meth
:
`tdg09
)
|>
Top
.
eval
|>
Core
.(
Fn
.
flip
List
.
take
10
)
|>
List
.
iter
Reviewphiltrans
.
Orthomam
.
Candidate_site
.(
fun
x
->
print_endline
x
.
alignment_id
)
with
|
Failure
_
->
()
lib/detection_pipeline.ml
View file @
2edb60ab
...
...
@@ -111,7 +111,7 @@ module Make(Q : Query) = struct
|
Ok
(
_
,
item
::
_
)
->
let
open
Core_kernel
in
let
n
=
String
.
length
item
.
sequence
in
"Sites
Tdg09_1MinusFDR
Tdg09_1MinusLRT
Tdg09_prob_post"
"Sites
\t
Tdg09_1MinusFDR
\t
Tdg09_1MinusLRT
\t
Tdg09_prob_post"
::
List
.
init
n
~
f
:
(
fun
i
->
sprintf
"%d
\t
0.0
\t
0.0
\t
NA"
(
i
+
1
))
|>
Out_channel
.
write_lines
[
%
dest
]
|
_
->
failwith
"couldn't read an item in fasta"
...
...
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