how to use taxid-changelog

[Phylloxera]

Describe your issue

Hello,

I'm confused regarding the exact purpose/use case of taxid-changelog.

Would I want to run the following:

wget ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump_archive/taxdmp*.zip
ls taxdmp*.zip | rush -j 1 'unzip {} names.dmp nodes.dmp merged.dmp delnodes.dmp -d {@_(.+)\.}'
cd ..
taxonkit taxid-changelog -i archive -o taxid-changelog.csv.gz --verbose

to ensure I have the most up-to-date lineage for use with taxonkit list?

Thanks!

[shenwei356]

https://github.com/shenwei356/taxid-changelog

[Phylloxera]

Sorry, but I read this and still don't understand. Maybe a better way to phrase my question is this: Is there anything that needs to be done periodically to ensure that one has the most up-to-date lineage for use with taxonkit list ? If so, can you be more explicit about what those things are and the rationale behind them (maybe as an addition to your very nice tutorial)? Or, alternatively, are the results of the taxon list command deterministic and independent of any changes that occur with the taxdmp* files? Thanks!

[shenwei356]

ncbi taxonomy database (dump file) update nearly every day, the only way to keep up to date is to update ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz daily.

taxonkit taxid-changelog is a command for tracking changes between different taxdumps (monthly dumpped).

[Phylloxera]

The taxdump archive is not listed as a dependency for taxonkit so I'm guessing some fixed time point version of it is incorporated into the binary. Regardless, I'll go ahead and close this ticket and perhaps open a new one since my question has changed. Thanks.