Warning is triggered even with use_index=False

[hguturu]

pyteomics/pyteomics/auxiliary/file_helpers.py

Line 918 in 1ef7a09

warnings.warn('Could not check mode on {}. Specify `use_index` explicitly to avoid errors.'.format(source))

Is there a way to avoid this warning? I am passing a seekable, non-binary file handle and use_index=False. Specifically a smart_open.open object. It doesn't have a mode attribute when opening s3 objects. It works, just was wondering if I can suppress the warning since the warning doesn't seem to match the issue.

[mobiusklein]

You shouldn't need to worry in your case. This is situation probably needs to be fixed with an unset value to handle default behavior more precisely.

[levitsky]

Thanks for reporting. This checking logic is taking me a lot of attempts to get right.
Does the current master behave as expected?

[hguturu]

I was triggering this error on 4.4.2.

Using a master, it looks like the warning is suppressed for use_index=False, shows warning for use_index=None, and it errors out with use_index=True, where it tried to load an IndexedFASTA and I have a regular FASTA. I believe this how it should work?

[levitsky]

I think so! Thank you.