search

fhcrc / taxtastic

Create and maintain phylogenetic "reference packages" of biological sequences.
GNU General Public License v3.0
21 stars 10 forks source link

Handling circular taxonomic lineages #120

Closed crosenth closed 4 years ago

crosenth commented 6 years ago

Occastionally ncbi taxonomic lineages will have a (grand) parent and child with the same rank other than no_rank. For example I have seen it in Fungi and Gastropoda ncbi lineages. When building a taxit taxtable the current approach is to randomly pick a tax_id to assign to a rank column to handle this situation. A better approach would be to set the lower rank to no_rank before building the lineage.

crosenth commented 4 years ago

See UNORDERED_RANKS - https://github.com/fhcrc/taxtastic/pull/137/files