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apply_to_db.py errors out when not given to_exclude.txt #17

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robert-ervin-jones opened this issue Apr 29, 2022 · 0 comments · Fixed by #21
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apply_to_db.py errors out when not given to_exclude.txt #17

robert-ervin-jones opened this issue Apr 29, 2022 · 0 comments · Fixed by #21
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  • The --to_exclude argument should be optional
  • Output is as expected when given an empty to_exclude.txt
  • Example error when running without the optional --to_exlude argument:
File "apply_to_db.py", line 349, in <module>
        to_exclude = taxa_to_exclude()
File "apply_to_db.py", line 36, in taxa_to_exclude
        with open(args.to_exclude, 'r') as infile:
TypeError: expected str, bytes or os.PathLike object, not NoneType
@robert-ervin-jones robert-ervin-jones added the bug Something isn't working label Apr 29, 2022
@robert-ervin-jones robert-ervin-jones self-assigned this Apr 29, 2022
@robert-ervin-jones robert-ervin-jones linked a pull request Apr 30, 2022 that will close this issue
fixes issue when not using --to_exclude arg #21
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fixes issue when not using --to_exclude arg TheBrownLab/PhyloFisher
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