Include empty fields in taxonomy for easier parsing
PR for issue #39.
Changes to `taxonomy.py` include:
- line 8-15: add function to loop over all possible ranks (see line 72-82) and add an empty value if the key is missing in the dictionary. The "Viruses" rank is still included to make sure there are no downstream issues.
- line 71: use `taxopy`'s `rank_name_dictionary` instead of `name_lineage` on the majority taxon.
- line 72-82: List of all possible ranks in genomad's DB (`nodes.dmp`) ordered from lowest to highest taxon level.
- line 85-86: commented out original code, because it is not necessary anymore
合并状态:已合并 合并于 2024-04-10 关闭于 2024-04-10 6 条评论