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Difference between --list-order and --list-ranks unclear #38

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standage opened this issue Jan 22, 2021 · 3 comments
Closed

Difference between --list-order and --list-ranks unclear #38

standage opened this issue Jan 22, 2021 · 3 comments

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@standage
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For the new taxonkit filter command, I'm not sure what the difference is between the --list-ranks and --list-order flags. I can see that --list-order is more comprehensive. Can you explain the difference? Thank you for your patience! 😄

@shenwei356
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      --list-order           list defined ranks in order
      --list-ranks           list ordered ranks in taxonomy database

--list-order is for listing user defined ranks in $HOME/.taxonkit/ranks.txt.

--list-ranks is for listing ranks in taxonomy database, which are sorted in user defined order. And all ranks in DB should be defined $HOME/.taxonkit/ranks.txt.

Is it clear? :)

@standage
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Yes, that helps, thanks!

@shenwei356
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Some ranks in $HOME/.taxonkit/ranks.txt may be not appeared in current version of NCBI taxonomy database. I tried to cover al possible values. Most are from https://en.wikipedia.org/wiki/Taxonomic_rank .

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