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MPBA
INF
Commits
3827b663
Commit
3827b663
authored
Mar 26, 2020
by
Marco Chierici
Browse files
Create list_distances.py
parent
bf9488e8
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1
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list_distances.py
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3827b663
import
argparse
import
pandas
as
pd
import
numpy
as
np
from
mlpy
import
canberra_stability
from
itertools
import
combinations
parser
=
argparse
.
ArgumentParser
()
parser
.
add_argument
(
'--resultsdir'
,
type
=
str
,
help
=
'Results folder'
)
parser
.
add_argument
(
'--dataset'
,
type
=
str
,
help
=
'Dataset name'
)
parser
.
add_argument
(
'--model'
,
type
=
str
,
default
=
'randomForest'
,
help
=
'Model (default: %default)'
)
parser
.
add_argument
(
'--target'
,
type
=
str
,
help
=
'Clinical endpoint'
)
parser
.
add_argument
(
'--layers'
,
type
=
str
,
nargs
=
'+'
,
help
=
''
)
args
=
parser
.
parse_args
()
RESULTSDIR
=
args
.
resultsdir
# top-level results directory
DATASET
=
args
.
dataset
# 'tcga_breast'
TARGET
=
args
.
target
# 'ER'
MODEL
=
args
.
model
LAYERS
=
args
.
layers
N_LAYERS
=
len
(
LAYERS
)
MODE
=
'rSNF'
for
k
in
range
(
2
,
N_LAYERS
+
1
):
for
comb
in
combinations
(
LAYERS
,
k
):
layers_concat
=
'_'
.
join
(
comb
)
bordas
=
[]
for
datatype
in
[
DATASET
,
f
'
{
DATASET
}
_SNFdap'
]:
bordaf
=
f
'
{
RESULTSDIR
}
/
{
datatype
}
/
{
TARGET
}
/
{
MODEL
}
/Borda_splits_50-60_
{
MODE
}
_
{
layers_concat
}
.txt'
bordas
.
append
(
pd
.
read_csv
(
bordaf
,
sep
=
'
\t
'
,
index_col
=
None
))
# prepare ranks for canberra_stability
ranks
=
pd
.
concat
([
np
.
argsort
(
bordas
[
0
][
'FEATURE_ID'
]),
np
.
argsort
(
bordas
[
1
][
'FEATURE_ID'
])],
axis
=
1
).
transpose
().
values
for
nf
in
np
.
arange
(
10
,
60
,
10
):
cs
=
canberra_stability
(
ranks
,
nf
)
print
(
f
'
{
MODE
}
-
{
layers_concat
}
- stability(
{
nf
}
) =
{
cs
:
.
3
f
}
'
)
print
()
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