I believe you are misinterpreting what you are seeing. Empty lines read from a file do not produce an empty string, you get "\n" instead which is true in a boolean context.

Try

[line.split()[0] for line in lines if line.strip() and not line.startswith("#")]

or add an extra check for all-whitespace line

[... if line and not line.isspace() and not line.startswith("#")]