Exclude nodes from the taxonomy

[fgvieira]

Is it possible to remove a node (or a list of nodes) and (optionally) all those downstream? I am trying to remove all branches of the taxonomy that are unclassified (e.g. 12908).

Something like (when #93 is done):

echo unclassified | taxonkit name2taxid | taxonkit list | taxonkit filter --exclude | taxonkit create-taxdump

[shenwei356]

How about directly editing the nodes.dmp file.

1. get a list of ids with taxonkit list or other ways.
2. csvtk grep -Ht -f 1 -v -P list.txt nodes.dmp > nodes.new

[shenwei356]

How's it going?

[fgvieira]

Would removing from just the nodes.dmp file work? Don't you need to also edit the names.dmp file?

If not, the I guess I could just do:

echo unclassified | taxonkit name2taxid --fuzzy --fuzzy-top-n 9999999 | cut -f 2 | taxonkit list --indent '' > list.txt
csvtk grep -Ht -f 1 -v -P list.txt nodes.dmp > nodes.new

[shenwei356]

Try it.