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shenwei356 / taxonkit

A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV
https://bioinf.shenwei.me/taxonkit
MIT License
361 stars 29 forks source link

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

Closed standage closed 3 years ago

standage commented 3 years ago

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 commented 3 years ago 
      --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 commented 3 years ago

Yes, that helps, thanks!

shenwei356 commented 3 years ago

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 .