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Yoann DUFRESNE
linked reads molecule ordering
Commits
37fdd729
Commit
37fdd729
authored
May 18, 2020
by
Rayan CHIKHI
Browse files
auto generation of results
parent
afe8cbe7
Changes
4
Hide whitespace changes
Inline
Side-by-side
deconvolution/main/d2_random_path_evaluation.py
View file @
37fdd729
...
...
@@ -17,6 +17,10 @@ def parse_args():
parser
=
argparse
.
ArgumentParser
(
description
=
'Process some integers.'
)
parser
.
add_argument
(
'filename'
,
type
=
str
,
help
=
'The file to evalute'
)
parser
.
add_argument
(
'experiment'
,
type
=
str
,
help
=
'name of experiment (optional, for figure print)'
)
parser
.
add_argument
(
'type'
,
type
=
str
,
help
=
'graph type (optional, for figure print)'
)
args
=
parser
.
parse_args
()
return
args
...
...
@@ -150,7 +154,9 @@ def evaluate_accuracy_paths(path_len,max_paths_per_node=5):
else
:
nb_bad_paths
+=
1
nb_paths
=
nb_bad_paths
+
nb_good_paths
print
(
"accuracy for l=%d (%d paths, %d nodes explored):"
%
(
path_len
,
nb_paths
,
nb_paths
*
path_len
),
nb_good_paths
/
(
nb_good_paths
+
nb_bad_paths
))
acc
=
nb_good_paths
/
(
nb_good_paths
+
nb_bad_paths
)
#print("accuracy for l=%d (%d paths, %d nodes explored):" % (path_len, nb_paths, nb_paths*path_len),acc)
return
acc
# ---- sensitivity evaluation
...
...
@@ -207,7 +213,9 @@ def evaluate_sensitivity_paths(path_len,overlap_length=7000):
nb_found
+=
1
else
:
nb_not_found
+=
1
print
(
"sensitivity for l=%d"
%
path_len
,
nb_found
/
(
nb_not_found
+
nb_found
))
sens
=
nb_found
/
(
nb_not_found
+
nb_found
)
#print("sensitivity for l=%d" % path_len, sens)
return
sens
from
multiprocessing
import
Pool
...
...
@@ -217,13 +225,22 @@ def main():
graph
=
load_graph
(
args
.
filename
)
p
=
Pool
(
12
)
points
=
[
2
,
4
,
10
,
25
,
50
,
75
,
100
,
150
]
#p.map(evaluate_accuracy_paths, [1,2,4,6,8,10,15,20,50,100,200,500])
p
.
map
(
evaluate_accuracy_paths
,
[
2
,
4
,
10
,
100
]
)
p
.
map
(
evaluate_sensitivity_paths
,
[
2
,
4
,
10
,
100
]
)
accs
=
p
.
map
(
evaluate_accuracy_paths
,
points
)
sens
=
p
.
map
(
evaluate_sensitivity_paths
,
points
)
#evaluate_accuracy_paths(100)
#evaluate_sensitivity_paths(1)
#evaluate_sensitivity_paths(3)
#evaluate_sensitivity_paths(10)
# latex print
#print(' & '.join("%0.2f & %0.2f" % (x,y) for (x,y) in list(zip(accs,sens))) + '\\' )
# figure print
if
len
(
sys
.
argv
)
>
2
:
experiment
=
sys
.
argv
[
2
]
type
=
sys
.
argv
[
3
]
for
i
,
l
in
enumerate
(
points
):
print
(
experiment
,
type
,
l
,
accs
[
i
],
sens
[
i
])
p
.
close
()
p
.
join
()
...
...
interval_graphs_acc_sens.sh
0 → 100644
View file @
37fdd729
for
n
in
5000 10000
do
for
d
in
5
do
for
m
in
2 3
do
for
dev
in
0 1
do
echo
"n=
$n
d=
$d
m=
$m
m_dev=
$dev
"
rm
-f
snake_exec/simu_0_bar_n
"
$n
"
_d
"
$d
"
_m
"
$m
"
-dev0
.gexf
&&
snakemake
-s
Snakefile_data_simu
--config
n
=
$n
d
=
$d
m
=
$m
m_dev
=
$dev
>
/dev/null 2>&1
cd
snake_exec
&&
source
CMD_acc_sens
&&
cd
..
done
done
done
done
snake_exec/CMD_acc_sens
0 → 100644
View file @
37fdd729
#!/bin/bash
python3 ../deconvolution/main/to_d2_graph.py simu_0_bar_n
"
$n
"
_d
"
$d
"
_m
"
$m
"
-dev
"
$dev
"
.gexf
>
/dev/null 2>&1
mv
d2_graph.gexf simu_0_bar_n
"
$n
"
_d
"
$d
"
_m
"
$m
"
-dev
"
$dev
"
.gexf.d2_graph.gexf
python ../deconvolution/main/d2_reduction.py
--output_d2_name
simu_0_bar_n
"
$n
"
_d
"
$d
"
_m
"
$m
"
-dev
"
$dev
"
.gexf.d2_graph_reduced.gexf simu_0_bar_n
"
$n
"
_d
"
$d
"
_m
"
$m
"
-dev
"
$dev
"
.gexf simu_0_bar_n
"
$n
"
_d
"
$d
"
_m
"
$m
"
-dev
"
$dev
"
.gexf.d2_graph.gexf 2>&1
>
/dev/null
echo
"Gb
$n
$d
$m
$dev
"
python ../deconvolution/main/d2_random_path_evaluation.py simu_0_bar_n
"
$n
"
_d
"
$d
"
_m
"
$m
"
-dev
"
$dev
"
.gexf
$n
-
$d
-
$dev
Gb
echo
"Lcp
$n
$d
$m
$dev
"
python ../deconvolution/main/d2_random_path_evaluation.py simu_0_bar_n
"
$n
"
_d
"
$d
"
_m
"
$m
"
-dev
"
$dev
"
.gexf.d2_graph_reduced.gexf
$n
-
$d
-
$dev
Lcp
snake_exec/CMD_table_evaluate
0 → 100644
View file @
37fdd729
#!/bin/bash
python3 ../deconvolution/main/to_d2_graph.py simu_0_bar_n
"
$n
"
_d
"
$d
"
_m
"
$m
"
-dev
"
$dev
"
.gexf
mv
d2_graph.gexf simu_0_bar_n
"
$n
"
_d
"
$d
"
_m
"
$m
"
-dev
"
$dev
"
.gexf.d2_graph.gexf
python ../deconvolution/main/d2_reduction.py
--output_d2_name
simu_0_bar_n
"
$n
"
_d
"
$d
"
_m
"
$m
"
-dev
"
$dev
"
.gexf.d2_graph_reduced.gexf simu_0_bar_n
"
$n
"
_d
"
$d
"
_m
"
$m
"
-dev
"
$dev
"
.gexf simu_0_bar_n
"
$n
"
_d
"
$d
"
_m
"
$m
"
-dev
"
$dev
"
.gexf.d2_graph.gexf
python ../deconvolution/main/d2_to_path_simple.py simu_0_bar_n
"
$n
"
_d
"
$d
"
_m
"
$m
"
-dev
"
$dev
"
.gexf simu_0_bar_n
"
$n
"
_d
"
$d
"
_m
"
$m
"
-dev
"
$dev
"
.gexf.d2_graph_reduced.gexf
python ../deconvolution/main/evaluate.py
--type
path
--barcode_graph
simu_0_bar_n
"
$n
"
_d
"
$d
"
_m
"
$m
"
-dev
"
$dev
"
.gexf simu_0_bar_n
"
$n
"
_d
"
$d
"
_m
"
$m
"
-dev
"
$dev
"
.gexf.d2_graph_reduced_path.gexf
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