[BUG] <title>SyntaxWarning in pgap.py

[junkim83]

Describe the bug

A syntax warning message keeps showing when I run the './pgap.py --update'.

"/home/junkim/./pgap.py:133: SyntaxWarning: invalid escape sequence '['
r = "^[(?P[^\]]+)] (?P[^ ]+) [(?P[^ ]) (?P[^\]])] (?P.*)"
/home/junkim/./pgap.py:978: SyntaxWarning: invalid escape sequence '-'
if not re.match("^[a-zA-Z0-9_-]+$", prefix):
/home/junkim/./pgap.py:1109: SyntaxWarning: invalid escape sequence '-'
parser.error("Invalid Command Line Argument Error: Both arguments -s--organism and -g--genome must be provided if no YAML file is provided.")"

Expected behavior

I think it's a code issue in pgap.py, how do I fix it?

Software versions (please complete the following information):

• OS: ubuntu 24.04.01 LTS
• Docker version 26.1.3, build 26.1.3-0ubuntu1~24.04.1

[azat-badretdin]

Thank you for your report, user @junkim83

You can prepend offending characters with backslash

[junkim83]

So, I can modify the code by myself, correct? @azat-badretdin

[azat-badretdin]

Yes. But please make sure to run it with -no-self-update flag after modification, otherwise it will try to replace your local modified copy with the intact server copy.