taxtable: ValueError: 'section' is not in list

openpaul commented 5 years ago

I ran:

taxit new_database taxonomy.db

Followed by

taxit taxtable taxonomy.db -t 5599

And get the error:

Traceback (most recent call last):
  File "taxtastic-env/bin/taxit", line 11, in <module>
    load_entry_point('taxtastic==0.8.9', 'console_scripts', 'taxit')()
  File "taxtastic-env/lib/python3.6/site-packages/taxtastic/scripts/taxit.py", line 51, in main
    return action(arguments)
  File "taxtastic-env/lib/python3.6/site-packages/taxtastic/subcommands/taxtable.py", line 150, in action
    sorted_ranks = sorted(all_ranks, key=order_ranks(tax.ranks[::-1]))
  File "taxtastic-env/lib/python3.6/site-packages/taxtastic/subcommands/taxtable.py", line 77, in _inner
    return (ref_ranks.index(rank), 0)
ValueError: 'section' is not in list

Other taxids work fine. I am unsure what seems to be the issue here.

I am using

taxit --version
taxit v0.8.9

crosenth commented 5 years ago

Thank you Paul for raising this Issue. I am able to reproduce and am working on a fix. I will get back to you shortly.

crosenth commented 5 years ago

Go ahead and update taxtastic to version v0.8.11 either with pip (from PyPi) or from Github (https://github.com/fhcrc/taxtastic/releases/tag/v0.8.11).

Thanks again for raising this Issue. Let me know if anything else comes up.

openpaul commented 5 years ago

This seems to have fixed it. Thank you.

fhcrc / taxtastic

taxtable: ValueError: 'section' is not in list #128