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VEBER Philippe
codepi
Commits
63e14e8c
Commit
63e14e8c
authored
Jun 19, 2020
by
Philippe Veber
Browse files
Detection_pipeline: added failsafe version of tdg09
parent
ddd66484
Changes
3
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3 changed files
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15 additions
and
1 deletion
+15
-1
lib/detection_pipeline.ml
lib/detection_pipeline.ml
+13
-0
lib/detection_pipeline.mli
lib/detection_pipeline.mli
+1
-0
lib/orthomam.ml
lib/orthomam.ml
+1
-1
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lib/detection_pipeline.ml
View file @
63e14e8c
...
...
@@ -26,6 +26,7 @@ module type S = sig
val
multinomial_asymptotic_lrt
:
query
->
text
file
val
multinomial_asymptotic_sparse
:
query
->
text
file
val
tdg09
:
query
->
text
file
val
failsafe_tdg09
:
query
->
text
file
val
pcoc
:
?
gamma
:
bool
->
?
ncat
:
int
->
query
->
text
file
val
pcoc_v2
:
?
gamma
:
bool
->
...
...
@@ -105,6 +106,18 @@ module Make(Q : Query) = struct
()
|>
Tamuri
.
results
let
%
pworkflow
mock_tdg09
d
=
match
Biotk
.
Fasta
.
from_file
[
%
path
amino_acid_alignment
d
]
with
|
Ok
(
_
,
item
::
_
)
->
let
open
Core_kernel
in
let
n
=
String
.
length
item
.
sequence
in
"Sites Tdg09_1MinusFDR Tdg09_1MinusLRT 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"
let
failsafe_tdg09
d
=
Workflow
.
trywith
(
tdg09
d
)
(
mock_tdg09
d
)
let
diffseltree
d
=
Tree_dataset
.
prepare_diffsel_tree
(
tree
~
branch_length_unit
:
`Amino_acid
d
)
...
...
lib/detection_pipeline.mli
View file @
63e14e8c
...
...
@@ -26,6 +26,7 @@ module type S = sig
val
multinomial_asymptotic_lrt
:
query
->
text
file
val
multinomial_asymptotic_sparse
:
query
->
text
file
val
tdg09
:
query
->
text
file
val
failsafe_tdg09
:
query
->
text
file
val
pcoc
:
?
gamma
:
bool
->
?
ncat
:
int
->
query
->
text
file
val
pcoc_v2
:
?
gamma
:
bool
->
...
...
lib/orthomam.ml
View file @
63e14e8c
...
...
@@ -535,7 +535,7 @@ let site_ranking ?subset ~meth ~convergent_species db =
|
`multinomial_asymptotic_lrt
->
multinomial_asymptotic_lrt
,
"1MinusLRT"
|
`tdg09
->
tdg09
,
"Tdg09_1MinusFDR"
failsafe_
tdg09
,
"Tdg09_1MinusFDR"
in
let
queries
=
alignments_of_db
db
...
...
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