converts EMBL, NCBI (GenBank), DDBJ taxon ids to full taxonomic paths modified from https://github.com/bakerccm/entrez_qiime and updated for python3 uses the cogent3 library
taxid2taxonpath.py -d* nodes.dmp -m* names.dmp -e* merged.dmp -l* delnodes.dmp -i* input_file -o* output_file -c column_of_taxid -r column_of_readname
*positional arguments
the default column of taxid is 3 and the default column of readname is 2 (for kraken2 output)
outputs the following ranks: 'superkingdom','kingdom','phylum','class','order','family','genus','species'
.dmp files can be downloaded from ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz