[Feature Request] Fuzzy name search to taxonomy identifier
Similar to https://github.com/etetoolkit/ete/blob/1582ea2aa0d28065f4757b8b5af74367f6abe19f/ete4/ncbi_taxonomy/ncbiquery.py#L112C30-L112C30
```
def get_fuzzy_name_translation(self, name, sim=0.9):
"""Return taxid, species name and match score from the NCBI database.
The results are for the best match for name in the NCBI
database of taxa names, with a word similarity >= `sim`.
:param name: Species name (does not need to be exact).
:param 0.9 sim: Min word similarity to report a match (from 0 to 1).
"""
```
For example, EukZoo has an annotation from a source organism id `AddRef0031` labeled as species `Paramecium tetraurelia` and strain `Stock d4-2`. A manual search for this shows https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=412030 but the keyword "stock" is missing even though they are certainly the same.
Would it be possible to include this type of searching?
关闭于 2024-08-03 7 条评论