Update argument parser help

postprocessing/borda_global_juxt_rSNF.py

@@ -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

@@ -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

@@ -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

 # %%
-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

@@ -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()