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MPBA
INF
Commits
44b870ae
Commit
44b870ae
authored
Mar 26, 2020
by
Alessia Marcolini
Browse files
Update argument parser help
parent
60b08093
Changes
5
Hide whitespace changes
Inline
Side-by-side
postprocessing/borda_global_juxt_rSNF.py
View file @
44b870ae
...
...
@@ -17,22 +17,10 @@ def load_data(filename):
#%%
class
myArgumentParser
(
argparse
.
ArgumentParser
):
def
__init__
(
self
,
*
args
,
**
kwargs
):
super
(
myArgumentParser
,
self
).
__init__
(
*
args
,
**
kwargs
)
def
convert_arg_line_to_args
(
self
,
line
):
for
arg
in
line
.
split
():
if
not
arg
.
strip
():
continue
if
arg
[
0
]
==
'#'
:
break
yield
arg
parser
=
myArgumentParser
(
description
=
'Concatenate omic layers files'
,
fromfile_prefix_chars
=
'@'
parser
=
argparse
.
ArgumentParser
(
description
=
'Compute Borda of Bordas for juXT and rSNF'
)
parser
.
add_argument
(
'--datafolder'
,
type
=
str
,
help
=
'Main data folder'
)
parser
.
add_argument
(
'--outfolder'
,
type
=
str
,
help
=
'Results folder'
)
parser
.
add_argument
(
'--dataset'
,
type
=
str
,
help
=
'Dataset name'
)
...
...
@@ -40,10 +28,12 @@ parser.add_argument('--target', type=str, help='Clinical endpoint')
parser
.
add_argument
(
'--model'
,
type
=
str
,
help
=
'Classifiers implemented, randomForest or LSVM'
)
parser
.
add_argument
(
'--layers'
,
type
=
str
,
nargs
=
'+'
,
help
=
''
)
parser
.
add_argument
(
'--n_splits_end'
,
type
=
int
,
help
=
''
)
parser
.
add_argument
(
'--n_splits_start'
,
type
=
int
,
help
=
''
)
parser
.
add_argument
(
'--mode'
,
type
=
str
,
help
=
'rSNF, rSNFi, single'
)
parser
.
add_argument
(
'--layers'
,
type
=
str
,
nargs
=
'+'
,
help
=
'List of omic layers'
)
parser
.
add_argument
(
'--n_splits_end'
,
type
=
int
,
help
=
'Upper end of splits range - not inclusive'
)
parser
.
add_argument
(
'--n_splits_start'
,
type
=
int
,
help
=
'Lower end of splits range'
)
parser
.
add_argument
(
'--mode'
,
type
=
str
,
help
=
'juXT or rSNF'
)
args
=
parser
.
parse_args
()
...
...
@@ -57,7 +47,7 @@ LAYERS = args.layers
N_SPLITS_START
=
args
.
n_splits_start
N_SPLITS_END
=
args
.
n_splits_end
MODE
=
args
.
mode
assert
MODE
in
[
'juxt'
,
'rSNF'
,
'single'
]
assert
MODE
in
[
'juxt'
,
'rSNF'
]
N_LAYERS
=
len
(
LAYERS
)
...
...
postprocessing/borda_global_rSNFi.py
View file @
44b870ae
...
...
@@ -7,24 +7,11 @@ from itertools import combinations
import
numpy
as
np
import
pandas
as
pd
#%%
class
myArgumentParser
(
argparse
.
ArgumentParser
):
def
__init__
(
self
,
*
args
,
**
kwargs
):
super
(
myArgumentParser
,
self
).
__init__
(
*
args
,
**
kwargs
)
def
convert_arg_line_to_args
(
self
,
line
):
for
arg
in
line
.
split
():
if
not
arg
.
strip
():
continue
if
arg
[
0
]
==
'#'
:
break
yield
arg
parser
=
myArgumentParser
(
description
=
'Concatenate omic layers files'
,
fromfile_prefix_chars
=
'@'
parser
=
argparse
.
ArgumentParser
(
description
=
'Compute Borda of Bordas for juXT and rSNF'
)
parser
.
add_argument
(
'--datafolder'
,
type
=
str
,
help
=
'Main data folder'
)
parser
.
add_argument
(
'--outfolder'
,
type
=
str
,
help
=
'Results folder'
)
parser
.
add_argument
(
'--dataset'
,
type
=
str
,
help
=
'Dataset name'
)
...
...
@@ -32,10 +19,12 @@ parser.add_argument('--target', type=str, help='Clinical endpoint')
parser
.
add_argument
(
'--model'
,
type
=
str
,
help
=
'Classifiers implemented, randomForest or LSVM'
)
parser
.
add_argument
(
'--layers'
,
type
=
str
,
nargs
=
'+'
,
help
=
''
)
parser
.
add_argument
(
'--n_splits_end'
,
type
=
int
,
help
=
''
)
parser
.
add_argument
(
'--n_splits_start'
,
type
=
int
,
help
=
''
)
parser
.
add_argument
(
'--mode'
,
type
=
str
,
help
=
'rSNFi custom Borda'
)
parser
.
add_argument
(
'--layers'
,
type
=
str
,
nargs
=
'+'
,
help
=
'List of omic layers'
)
parser
.
add_argument
(
'--n_splits_end'
,
type
=
int
,
help
=
'Upper end of splits range - not inclusive'
)
parser
.
add_argument
(
'--n_splits_start'
,
type
=
int
,
help
=
'Lower end of splits range'
)
parser
.
add_argument
(
'--mode'
,
type
=
str
,
help
=
'rSNF'
)
args
=
parser
.
parse_args
()
...
...
@@ -49,6 +38,7 @@ LAYERS = args.layers
N_SPLITS_START
=
args
.
n_splits_start
N_SPLITS_END
=
args
.
n_splits_end
MODE
=
args
.
mode
assert
MODE
==
'rSNFi'
N_LAYERS
=
len
(
LAYERS
)
...
...
postprocessing/compute_all_metrics.py
View file @
44b870ae
...
...
@@ -10,23 +10,9 @@ import bootstrapped.stats_functions as bs_stats
import
numpy
as
np
import
pandas
as
pd
#%%
class
myArgumentParser
(
argparse
.
ArgumentParser
):
def
__init__
(
self
,
*
args
,
**
kwargs
):
super
(
myArgumentParser
,
self
).
__init__
(
*
args
,
**
kwargs
)
def
convert_arg_line_to_args
(
self
,
line
):
for
arg
in
line
.
split
():
if
not
arg
.
strip
():
continue
if
arg
[
0
]
==
'#'
:
break
yield
arg
parser
=
myArgumentParser
(
description
=
'Compute metrics on all splits'
,
fromfile_prefix_chars
=
'@'
parser
=
argparse
.
ArgumentParser
(
description
=
'Compute Borda of Bordas for juXT and rSNF'
)
parser
.
add_argument
(
'--outfolder'
,
type
=
str
,
help
=
'Results folder'
)
parser
.
add_argument
(
'--dataset'
,
type
=
str
,
help
=
'Dataset name'
)
...
...
@@ -34,10 +20,12 @@ parser.add_argument('--target', type=str, help='Clinical endpoint')
parser
.
add_argument
(
'--model'
,
type
=
str
,
help
=
'classifiers implemented, randomForest or LSVM'
)
parser
.
add_argument
(
'--layers'
,
type
=
str
,
nargs
=
'+'
,
help
=
''
)
parser
.
add_argument
(
'--n_splits_end'
,
type
=
int
,
help
=
''
)
parser
.
add_argument
(
'--n_splits_start'
,
type
=
int
,
help
=
''
)
parser
.
add_argument
(
'--mode'
,
type
=
str
,
help
=
'juxt, rSNF, rSNFi, single'
)
parser
.
add_argument
(
'--layers'
,
type
=
str
,
nargs
=
'+'
,
help
=
'List of omic layers'
)
parser
.
add_argument
(
'--n_splits_end'
,
type
=
int
,
help
=
'Upper end of splits range - not inclusive'
)
parser
.
add_argument
(
'--n_splits_start'
,
type
=
int
,
help
=
'Lower end of splits range'
)
parser
.
add_argument
(
'--mode'
,
type
=
str
,
help
=
'juXT, rSNF, rSNFi or single'
)
args
=
parser
.
parse_args
()
...
...
prepare_data_snf.py
View file @
44b870ae
# %%
import
numpy
as
np
from
sklearn.model_selection
import
StratifiedKFold
import
argparse
import
os
import
numpy
as
np
import
pandas
as
pd
from
sklearn.model_selection
import
StratifiedKFold
from
tqdm
import
tqdm
import
argparse
#%%
class
myArgumentParser
(
argparse
.
ArgumentParser
):
def
__init__
(
self
,
*
args
,
**
kwargs
):
super
(
myArgumentParser
,
self
).
__init__
(
*
args
,
**
kwargs
)
def
convert_arg_line_to_args
(
self
,
line
):
for
arg
in
line
.
split
():
if
not
arg
.
strip
():
continue
if
arg
[
0
]
==
'#'
:
break
yield
arg
parser
=
myArgumentParser
(
description
=
'Run a training experiment (10x5-CV fold) using Random Forest as classifier.'
,
fromfile_prefix_chars
=
'@'
,
)
parser
=
argparse
.
ArgumentParser
()
parser
.
add_argument
(
'--datafiles'
,
type
=
str
,
nargs
=
'+'
,
help
=
'Training datafile'
)
parser
.
add_argument
(
'--labelsfile'
,
type
=
str
,
help
=
'Sample labels'
)
...
...
@@ -61,7 +46,6 @@ for datafile in DATAFILES:
cv_data
=
original_data
.
iloc
[
idx_tr
]
cv_labels
=
original_labels
.
iloc
[
idx_tr
]
# print(cv_data.shape)
layer_filename
=
os
.
path
.
splitext
(
datafile
)[
0
]
layer_ext
=
os
.
path
.
splitext
(
datafile
)[
1
]
layer_filename_new
=
f
'
{
layer_filename
}
_
{
n
}
_
{
i
}{
layer_ext
}
'
...
...
preprocessing/concat_layers.py
View file @
44b870ae
...
...
@@ -5,28 +5,14 @@ from itertools import combinations
import
pandas
as
pd
#%%
parser
=
argparse
.
ArgumentParser
(
description
=
'Concatenate omic layers files'
)
class
myArgumentParser
(
argparse
.
ArgumentParser
):
def
__init__
(
self
,
*
args
,
**
kwargs
):
super
(
myArgumentParser
,
self
).
__init__
(
*
args
,
**
kwargs
)
def
convert_arg_line_to_args
(
self
,
line
):
for
arg
in
line
.
split
():
if
not
arg
.
strip
():
continue
if
arg
[
0
]
==
'#'
:
break
yield
arg
parser
=
myArgumentParser
(
description
=
'Concatenate omic layers files'
,
fromfile_prefix_chars
=
'@'
)
parser
.
add_argument
(
'--datafolder'
,
type
=
str
,
help
=
'Main data folder'
)
parser
.
add_argument
(
'--dataset'
,
type
=
str
,
help
=
'Dataset name'
)
parser
.
add_argument
(
'--target'
,
type
=
str
,
help
=
'Clinical endpoint'
)
parser
.
add_argument
(
'--split_id'
,
type
=
int
,
help
=
''
)
parser
.
add_argument
(
'--layers'
,
type
=
str
,
nargs
=
'+'
,
help
=
''
)
parser
.
add_argument
(
'--split_id'
,
type
=
int
,
help
=
'
Split ID
'
)
parser
.
add_argument
(
'--layers'
,
type
=
str
,
nargs
=
'+'
,
help
=
'
List of omic layers
'
)
args
=
parser
.
parse_args
()
...
...
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