format python code

bin/suppa_groups.py

@@ -6,41 +6,43 @@
 import argparse
 import itertools
 
-def main(args):
 
-    handle = open(args.file, 'r')
+def main(args):
+    # Open file
+    handle = open(args.file, "r")
 
+    # Read header only
     header = handle.readline()
 
-    samples = header.split('\t')
+    # Split header by delimiter (e.g., transcript_GBR_1)
+    samples = header.split("\t")
 
-    conditions = [sample.rsplit('_', 1)[0] for sample in samples]
+    # Trim replicate number (e.g., transcript_GBR_1 -> transcript_GBR)
+    conditions = [sample.rsplit("_", 1)[0] for sample in samples]
 
+    # Close file
     handle.close()
 
-    # # #
-
+    # Create list of consecutive condition indices (e.g., [[1,2], [3,4]])
     last_index = 0
     out = []
     for v, g in itertools.groupby(enumerate(conditions), lambda k: k[1]):
         l = [*g]
         out.append([last_index + 1, l[-1][0] + 1])
         last_index += len(l)
 
+    # Assert that condition indices are consecutive
     assert len(out) == 2, "Column numbers have to be continuous, with no overlapping or missing columns between them."
 
-    # # #
-
-    groups = [f'{start}-{end}' for start, end in out]
-
-    groups = ','.join(groups)
-
-    print(groups, end = "")
+    # Format ranges for printing
+    groups = ",".join([f"{start}-{end}" for start, end in out])
 
+    # Print to stdout without newline
+    print(groups, end="")
 
-if __name__ == '__main__':
 
+if __name__ == "__main__":
     parser = argparse.ArgumentParser()
-    parser.add_argument('file')
+    parser.add_argument("file")
     args = parser.parse_args()
     main(args)