Fix all flake8 linter problems (#6189)

* fix flake8 linter problems

* one more

tools/add_input_name_as_column/add_input_name_as_column.py

@@ -4,11 +4,28 @@
 
 def Parser():
     the_parser = argparse.ArgumentParser(description="add label to last column of file")
-    the_parser.add_argument('--input', required=True, action="store", type=str, help="input tabular file")
-    the_parser.add_argument('--output', required=True, action="store", type=str, help="output file path")
-    the_parser.add_argument('--label', required=True, action="store", type=str, help="label to add in last column")
-    the_parser.add_argument('--header', action="store", type=str, help="column label for last column")
-    the_parser.add_argument('--prepend', action='store_true', default=False, help='Prepend column instead of appending' )
+    the_parser.add_argument(
+        "--input", required=True, action="store", type=str, help="input tabular file"
+    )
+    the_parser.add_argument(
+        "--output", required=True, action="store", type=str, help="output file path"
+    )
+    the_parser.add_argument(
+        "--label",
+        required=True,
+        action="store",
+        type=str,
+        help="label to add in last column",
+    )
+    the_parser.add_argument(
+        "--header", action="store", type=str, help="column label for last column"
+    )
+    the_parser.add_argument(
+        "--prepend",
+        action="store_true",
+        default=False,
+        help="Prepend column instead of appending",
+    )
 
     args = the_parser.parse_args()
     return args
@@ -17,9 +34,11 @@ def Parser():
 args = Parser()
 
 
-with io.open(args.input, encoding="utf-8") as input, io.open(args.output, 'w', encoding="utf-8") as output:
+with io.open(args.input, encoding="utf-8") as input, io.open(
+    args.output, "w", encoding="utf-8"
+) as output:
     for i, line in enumerate(input):
-        line = line.strip('\n')
+        line = line.strip("\n")
         if (i == 0) and args.header:
             new_entry = args.header
         else:

tools/column_order_header_sort/column_order_header_sort.py

@@ -11,25 +11,35 @@
 key_column = sys.argv[4]
 
 try:
-    key_column = int( key_column ) - 1
+    key_column = int(key_column) - 1
 except Exception:
     key_column = None
 
 header = None
-with open( input_filename, 'r' ) as fh:
-    header = fh.readline().strip( '\r\n' )
-header = header.split( delimiter )
-assert len( header ) == len( set( header ) ), "Header values must be unique"
-sorted_header = list( header )
+with open(input_filename, "r") as fh:
+    header = fh.readline().strip("\r\n")
+header = header.split(delimiter)
+assert len(header) == len(set(header)), "Header values must be unique"
+sorted_header = list(header)
 if key_column is None:
     columns = []
 else:
-    columns = [ key_column ]
-    sorted_header.pop( key_column )
+    columns = [key_column]
+    sorted_header.pop(key_column)
 sorted_header.sort()
 
 for key in sorted_header:
-    columns.append( header.index( key ) )
+    columns.append(header.index(key))
 
-awk_cmd = AWK_CMD % ( delimiter, delimiter, ",".join( map( lambda x: "$%i" % ( x + 1 ), columns ) ) )
-sys.exit( subprocess.call( [ 'gawk', awk_cmd, input_filename ], stdout=open( output_filename, 'wb+' ), shell=False ) )
+awk_cmd = AWK_CMD % (
+    delimiter,
+    delimiter,
+    ",".join(map(lambda x: "$%i" % (x + 1), columns)),
+)
+sys.exit(
+    subprocess.call(
+        ["gawk", awk_cmd, input_filename],
+        stdout=open(output_filename, "wb+"),
+        shell=False,
+    )
+)

tools/cwpair2/cwpair2.py

@@ -17,18 +17,63 @@
 
 import cwpair2_util
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     parser = argparse.ArgumentParser()
-    parser.add_argument('--input', dest='inputs', action='append', nargs=2, help="Input datasets")
-    parser.add_argument('--method', dest='method', default='mode', help='Method of finding match.')
-    parser.add_argument('--up_distance', dest='up_distance', type=int, default=50, help='Distance upstream from a pair.')
-    parser.add_argument('--down_distance', dest='down_distance', type=int, default=100, help='Distance downstream of a pair.')
-    parser.add_argument('--binsize', dest='binsize', type=int, default=1, help='Width of bins for plots and mode.')
-    parser.add_argument('--threshold_format', dest='threshold_format', help='Percentage to filter the 95th percentile.')
-    parser.add_argument('--relative_threshold', dest='relative_threshold', type=float, default=0.0, help='Percentage to filter the 95th percentile.')
-    parser.add_argument('--absolute_threshold', dest='absolute_threshold', type=float, default=0.0, help='Absolute value to filter.')
-    parser.add_argument('--output_files', dest='output_files', default='matched_pair', help='Restrict output dataset collections.')
-    parser.add_argument('--statistics_output', dest='statistics_output', help='Statistics output file.')
+    parser.add_argument(
+        "--input", dest="inputs", action="append", nargs=2, help="Input datasets"
+    )
+    parser.add_argument(
+        "--method", dest="method", default="mode", help="Method of finding match."
+    )
+    parser.add_argument(
+        "--up_distance",
+        dest="up_distance",
+        type=int,
+        default=50,
+        help="Distance upstream from a pair.",
+    )
+    parser.add_argument(
+        "--down_distance",
+        dest="down_distance",
+        type=int,
+        default=100,
+        help="Distance downstream of a pair.",
+    )
+    parser.add_argument(
+        "--binsize",
+        dest="binsize",
+        type=int,
+        default=1,
+        help="Width of bins for plots and mode.",
+    )
+    parser.add_argument(
+        "--threshold_format",
+        dest="threshold_format",
+        help="Percentage to filter the 95th percentile.",
+    )
+    parser.add_argument(
+        "--relative_threshold",
+        dest="relative_threshold",
+        type=float,
+        default=0.0,
+        help="Percentage to filter the 95th percentile.",
+    )
+    parser.add_argument(
+        "--absolute_threshold",
+        dest="absolute_threshold",
+        type=float,
+        default=0.0,
+        help="Absolute value to filter.",
+    )
+    parser.add_argument(
+        "--output_files",
+        dest="output_files",
+        default="matched_pair",
+        help="Restrict output dataset collections.",
+    )
+    parser.add_argument(
+        "--statistics_output", dest="statistics_output", help="Statistics output file."
+    )
     args = parser.parse_args()
 
     cwpair2_util.create_directories()
@@ -41,28 +86,32 @@
     else:
         threshold = 0
     for (dataset_path, hid) in args.inputs:
-        stats = cwpair2_util.process_file(dataset_path,
-                                          hid,
-                                          args.method,
-                                          threshold,
-                                          args.up_distance,
-                                          args.down_distance,
-                                          args.binsize,
-                                          args.output_files)
+        stats = cwpair2_util.process_file(
+            dataset_path,
+            hid,
+            args.method,
+            threshold,
+            args.up_distance,
+            args.down_distance,
+            args.binsize,
+            args.output_files,
+        )
         statistics.extend(stats)
     # Accumulate statistics.
     by_file = {}
     for stats in statistics:
         # Skip "None" statistics from failed files
         if not stats:
             continue
-        path = stats['stats_path']
+        path = stats["stats_path"]
         if path not in by_file:
             by_file[path] = []
         by_file[path].append(stats)
     # Write tabular statistics file.
-    keys = ['fname', 'final_mode', 'preview_mode', 'perc95', 'paired', 'orphans']
-    statistics_out = csv.writer(open(args.statistics_output, 'wt'), delimiter='\t', lineterminator="\n")
+    keys = ["fname", "final_mode", "preview_mode", "perc95", "paired", "orphans"]
+    statistics_out = csv.writer(
+        open(args.statistics_output, "wt"), delimiter="\t", lineterminator="\n"
+    )
     statistics_out.writerow(keys)
     for file_path, statistics in by_file.items():
         for stats in statistics: