syntax cleaning

tools/segalign/diagonal_partition.py

@@ -14,7 +14,7 @@
 def chunks(lst, n):
     """Yield successive n-sized chunks from list."""
     for i in range(0, len(lst), n):
-        yield lst[i : i + n]
+        yield lst[i: i + n]
 
 
 if __name__ == "__main__":
@@ -34,9 +34,9 @@ def chunks(lst, n):
     for index, value in enumerate(params):
         if value[: len(segment_key)] == segment_key:
             segment_index = index
-            input_file = value[len(segment_key) :]
+            input_file = value[len(segment_key):]
             break
-    if segment_index == None:
+    if segment_index is None:
         print(f"Error: could not segment key {segment_key} in parameters {params}")
         exit(0)
 
@@ -62,16 +62,16 @@ def chunks(lst, n):
     for index, value in enumerate(params):
         if value[: len(output_key)] == output_key:
             output_index = index
-            output_alignment_file = value[len(output_key) :]
+            output_alignment_file = value[len(output_key):]
             output_alignment_file_base, output_format = output_alignment_file.rsplit(
                 ".", 1
             )
         if value[: len(strand_key)] == strand_key:
             strand_index = index
-    if segment_index == None:
+    if segment_index is None:
         print(f"Error: could not output key {output_key} in parameters {params}")
         exit(0)
-    if strand_index == None:
+    if strand_index is None:
         print(f"Error: could not output key {strand_key} in parameters {params}")
         exit(0)
 

tools/segalign/package_output.py

@@ -1,15 +1,14 @@
 #!/usr/bin/env python
 
-import typing
-
 import argparse
-import bashlex
 import configparser
 import json
 import os
-import re
 import sys
 import tarfile
+import typing
+
+import bashlex
 
 
 class PackageFile:
@@ -152,7 +151,7 @@ def _parse_lines(self) -> None:
         self.package_file.add_config("commands.json")
 
     def _parse_line(self, line: str) -> typing.Dict[str, typing.Any]:
-        ## resolve shell redirects
+        # resolve shell redirects
         trees: typing.List[typing.Any] = bashlex.parse(line, strictmode=False)  # type: ignore[attr-defined]
         positions: typing.List[typing.Tuple[int, int]] = []
 
@@ -178,7 +177,6 @@ def _parse_line(self, line: str) -> typing.Dict[str, typing.Any]:
 
     def _parse_processed_line(self, line: str) -> typing.Dict[str, typing.Any]:
         argv: typing.List[str] = list(bashlex.split(line))  # type: ignore[attr-defined]
-        options: typing.Dict[str, typing.Any] = {}
         self.executable = argv.pop(0)
 
         parser: argparse.ArgumentParser = argparse.ArgumentParser(add_help=False)
@@ -280,7 +278,7 @@ def main() -> None:
 
     package_file = PackageFile()
     lastz_command_file = "lastz_commands.txt"
-    foo = bashCommandLineFile(lastz_command_file, config, package_file)
+    bashCommandLineFile(lastz_command_file, config, package_file)
     package_file.close()