Cleanup: explicitly disable autopep8 for rna_manual_reference
Currently the "exclude" option for autopep8 isn't as reliable as it should be since passing in absolute paths to autopep8 causes the paths not to match. See: D14686 for details. So explicitly disable autopep8 in this generated file (the generator has already been updated). Also use spaces for indentation otherwise autopep8 re-indents them. This seems like a bug in autopep8 since it's changing lines with autopep8 disabled. Use a workaround instead of looking into a fix since it's simpler for all our Python files to use spaces instead of tabs and there isn't much benefit mixing indentation for scripts.
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