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VEBER Philippe
codepi
Commits
0d244e52
Commit
0d244e52
authored
Feb 01, 2019
by
Philippe Veber
Browse files
added diffseldsparse to new benchmark
parent
86183156
Changes
6
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6 changed files
with
31 additions
and
3 deletions
+31
-3
lib/convergence_detection.ml
lib/convergence_detection.ml
+2
-1
lib/convergence_detection.mli
lib/convergence_detection.mli
+1
-0
lib/diffseldsparse.ml
lib/diffseldsparse.ml
+14
-0
lib/diffseldsparse.mli
lib/diffseldsparse.mli
+5
-1
lib/pipeline2.ml
lib/pipeline2.ml
+2
-0
lib/scripts/merge_det_results.py
lib/scripts/merge_det_results.py
+7
-1
No files found.
lib/convergence_detection.ml
View file @
0d244e52
...
...
@@ -78,13 +78,14 @@ let merge_results ?fna_infos ~(res_by_tools : result list) () : text_file pworkf
]
;
]
let
merge_result_tables
?
fna_infos
?
oracle
?
multinomial
?
diffsel
()
:
text_file
pworkflow
=
let
merge_result_tables
?
fna_infos
?
oracle
?
multinomial
?
diffsel
?
diffseldsparse
()
:
text_file
pworkflow
=
Workflow
.
shell
~
descr
:
"convergence_detection.merge_results"
[
cmd
"python"
~
img
:
Env
.
env_py
[
file_dump
(
string
Scripts
.
merge_det_results
)
;
opt
"-o"
ident
dest
;
option
(
opt
"--multinomial"
dep
)
multinomial
;
option
(
opt
"--diffsel"
dep
)
diffsel
;
option
(
opt
"--diffseldsparse"
dep
)
diffseldsparse
;
option
(
opt
"--oracle"
dep
)
oracle
;
option
(
opt
"--fna_infos"
dep
)
fna_infos
;
]
;
...
...
lib/convergence_detection.mli
View file @
0d244e52
...
...
@@ -37,6 +37,7 @@ val merge_result_tables :
?
oracle
:
text_file
pworkflow
->
?
multinomial
:
text_file
pworkflow
->
?
diffsel
:
text_file
pworkflow
->
?
diffseldsparse
:
text_file
pworkflow
->
unit
->
text_file
pworkflow
...
...
lib/diffseldsparse.ml
View file @
0d244e52
...
...
@@ -148,3 +148,17 @@ let posterior_probabilities run_diffseldsparse : text_file pworkflow =
]
)
]
let
%
pworkflow
results
dir
=
Filename
.
concat
[
%
path
dir
]
"myrun_1.sitepp"
|>
In_channel
.
read_lines
|>
Fn
.
flip
List
.
drop
1
|>
List
.
map
~
f
:
(
String
.
split
~
on
:
'\t'
)
|>
List
.
map
~
f
:
(
function
|
site
::
pp
::
_
->
Int
.
of_string
site
+
1
,
Float
.
of_string
pp
/.
100
.
|
_
->
failwith
"parsing readdiffseldsparse results"
)
|>
List
.
map
~
f
:
(
fun
(
site
,
pp
)
->
sprintf
"%d
\t
%f"
site
pp
)
|>
(
fun
xs
->
"Sites
\t
Diffseldsparse"
::
xs
)
|>
Out_channel
.
write_lines
[
%
dest
]
lib/diffseldsparse.mli
View file @
0d244e52
...
...
@@ -18,8 +18,12 @@ val posterior_probabilities :
val
readdiffseldsparse
:
[
`diffseldsparse
]
dworkflow
->
text_file
p
workflow
[
`readdiffseldsparse
]
d
workflow
val
check_conv
:
[
`diffseldsparse
]
dworkflow
->
directory
pworkflow
val
results
:
[
`readdiffseldsparse
]
dworkflow
->
text_file
pworkflow
lib/pipeline2.ml
View file @
0d244e52
...
...
@@ -109,6 +109,7 @@ let diffseldsparse ?pi ?shiftprob ?eps d =
~
n_cycles
:
50
()
|>
Diffseldsparse
.
readdiffseldsparse
|>
Diffseldsparse
.
results
let
alignment_plot
d
=
Convergence_detection
.
plot_convergent_sites
...
...
@@ -133,6 +134,7 @@ let benchmark d =
Convergence_detection
.
merge_result_tables
~
multinomial
:
(
multinomial
d
)
~
diffsel
:
(
diffsel
d
)
~
diffseldsparse
:
(
diffseldsparse
~
eps
:
1e-3
d
)
~
oracle
:
(
oracle
d
)
()
|>
Convergence_detection
.
recall_precision_curve
lib/scripts/merge_det_results.py
View file @
0d244e52
...
...
@@ -60,6 +60,8 @@ availableOptions.add_argument('--diffsel', type=str,
help
=
"Diffsel output name"
,
default
=
None
)
availableOptions
.
add_argument
(
'--diffsel_bis'
,
type
=
str
,
help
=
"Diffsel_bis output name"
,
default
=
None
)
availableOptions
.
add_argument
(
'--diffseldsparse'
,
type
=
str
,
help
=
"Diffseldsparse output name"
,
default
=
None
)
availableOptions
.
add_argument
(
'--identical_LG'
,
type
=
str
,
help
=
"Identical_LG output name"
,
default
=
None
)
availableOptions
.
add_argument
(
'--identical_WAG'
,
type
=
str
,
...
...
@@ -89,6 +91,7 @@ df_pcoc = pd.DataFrame()
df_pcoc_gamma
=
pd
.
DataFrame
()
df_pcoc_C60
=
pd
.
DataFrame
()
df_diffsel
=
pd
.
DataFrame
()
df_diffseldsparse
=
pd
.
DataFrame
()
df_diffsel_bis
=
pd
.
DataFrame
()
df_identical_LG
=
pd
.
DataFrame
()
df_identical_WAG
=
pd
.
DataFrame
()
...
...
@@ -127,6 +130,9 @@ if args.diffsel_bis :
if
args
.
diffsel
:
df_diffsel
=
pd
.
read_csv
(
args
.
diffsel
,
sep
=
"
\t
"
)
if
args
.
diffseldsparse
:
df_diffseldsparse
=
pd
.
read_csv
(
args
.
diffseldsparse
,
sep
=
"
\t
"
)
if
args
.
oracle
:
df_oracle
=
pd
.
read_csv
(
args
.
oracle
,
sep
=
"
\t
"
)
df_oracle
.
rename
(
columns
=
{
'Oracle'
:
'Oracle'
},
inplace
=
True
)
...
...
@@ -172,7 +178,7 @@ if args.fna_infos :
#df_fna_infos = df_fna_infos[['Sites','P_distance']]
df_list
=
[
df
for
df
in
[
df_pcoc
,
df_pcoc_gamma
,
df_pcoc_C60
,
df_diffsel
,
df_diffsel_bis
,
df_diffsel
,
df_diffsel_bis
,
df_diffseldsparse
,
df_identical_LG
,
df_identical_WAG
,
df_topological_LG
,
df_topological_WAG
,
df_tdg09
,
...
...
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