tanghaibao / goatools

Python library to handle Gene Ontology (GO) terms
BSD 2-Clause "Simplified" License
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`log = None` cannot complete suppress stdout in GOEnrichmentStudyNS #238

Closed illumination-k closed 1 year ago

illumination-k commented 2 years ago

Thanks for the great project!

I want to stop logging completely, but __init__ function in GOEnrichmentStudy has print regardless of log kwd, so I cannot.

https://github.com/tanghaibao/goatools/blob/d3a63f9738efcdb9f2f49e40cf1fadeb58de9bac/goatools/go_enrichment.py#L256

I think if log is None, nothing should be output to stdout. This is not a so big problem, but not useful when redirecting or something.

tanghaibao commented 2 years ago

@illumination-k

Thank you for the issue report. I added the fix that considered the log keyword.

tanghaibao commented 2 years ago

@dvklopfenstein

Longer-term, we could move to using logging instead of using prt and log parameter throughout the code, as suggested in #159.