From 2f703afe5e5f0542d89089be8e7047b8bd2d560c Mon Sep 17 00:00:00 2001
From: David Cain <davidjosephcain@gmail.com>
Date: Mon, 1 Aug 2022 14:45:37 -0700
Subject: [PATCH] Fix invalid escape sequences in regex strings
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Summary
=======
This commit fixes deprecation warnings that arise from using backslashes
in strings, but *not* as part of an escape sequence. It will help this
library be used with newer versions of Python.

String literals do not change (for current versions of Python)
==============================================================
```python
>>> r'[\[\]]' == '[\[\]]'
True
```

Examples
========
```bash
$ python -Wd -c 'print("\d")'
DeprecationWarning: invalid escape sequence \d
$ python -W error -c 'print("\d")'
SyntaxError: invalid escape sequence \d
```

Explanation
===========
For an explanation of the problem (and the recommended solution),
see: https://docs.python.org/3/library/re.html

>  Also, please note that any invalid escape sequences in Python’s usage
> of the backslash in string literals now generate a DeprecationWarning
> and in the future this will become a SyntaxError. This behaviour will
> happen even if it is a valid escape sequence for a regular expression.
>
> The solution is to use Python’s raw string notation for regular
> expression patterns; backslashes are not handled in any special way in
> a string literal prefixed with 'r'.

How to keep these errors from source code
=========================================
I didn't make any proposed changes in this commit, but there are a few
ways to make sure that *new* invalid escape sequences are not used:

- Use a linter!
    - `pylint` has `anomalous-backslash-in-string`
    - `flake8` has `W605`
    - other linters work too!
- Escalate deprecation warnings to full errors at test time
  (e.g. `error:invalid escape sequence:DeprecationWarning` with
  `filterwarnings`  will change these warnings to errors)
---
 vcf/parser.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/vcf/parser.py b/vcf/parser.py
index c3c3d082..e454ea41 100644
--- a/vcf/parser.py
+++ b/vcf/parser.py
@@ -275,7 +275,7 @@ def __init__(self, fsock=None, filename=None, compressed=None, prepend_chr=False
             self._separator = '\t| +'
 
         self._row_pattern = re.compile(self._separator)
-        self._alt_pattern = re.compile('[\[\]]')
+        self._alt_pattern = re.compile(r'[\[\]]')
 
         self.reader = (line.strip() for line in self._reader if line.strip())
 
@@ -533,7 +533,7 @@ def _parse_alt(self, str):
                 withinMainAssembly = True
             pos = remoteCoords[1]
             orientation = (str[0] == '[' or str[0] == ']')
-            remoteOrientation = (re.search('\[', str) is not None)
+            remoteOrientation = (re.search(r'\[', str) is not None)
             if orientation:
                 connectingSequence = items[2]
             else: