Is it required to have all 7-levels of taxonomy to add a genome to the Metaphlan database?

Microbial community profiling MetaPhlAn
1

Following these guidelines:

import pickle
import bz2

db = pickle.load(bz2.open('metaphlan_databases/mpa_vJan21_CHOCOPhlAnSGB_202103.pkl', 'r'))

# Add the taxonomy of the new genomes
db['taxonomy']['7-levels taxonomy with clade names of genome1'] = ('7-levels NCBI taxonomy id of genome1', length of genome1)
db['taxonomy']['7-levels taxonomy with clade names of genome2'] = ('7-levels NCBI taxonomy id of genome1', length of genome2)

# Add the information of the new marker as the other markers
db['markers'][new_marker_name] = {
                                   'clade': the clade that the marker belongs to,
                                   'ext': {the GCA of the first external genome where the marker appears,
                                           the GCA of the second external genome where the marker appears,
                                          },
                                   'len': length of the marker,
                                   'taxon': the taxon of the marker
                                }
                                   
To see an example, try to print the first marker information:
 print list(db['markers'].items())[0]

# Save the new mpa_pkl file
with bz2.BZ2File('metaphlan_databases/mpa_vJan21_CHOCOPhlAnSGB_NEW.pkl', 'w') as ofile:
    pickle.dump(db, ofile, pickle.HIGHEST_PROTOCOL)

The reason why I am asking is because there are many eukaryotes and viruses that do not have this clearly defined structure:

echo "65574" | taxonkit lineage -R
65574	cellular organisms;Eukaryota;Sar;Rhizaria;Retaria;Acantharea	no rank;superkingdom;clade;clade;clade;class

echo "335924" | taxonkit lineage -R
335924	Viruses;Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;Myoviridae;unclassified Myoviridae;Cyanobacteria phage AS-1	superkingdom;clade;kingdom;phylum;class;family;no rank;species

Is it possible to add to the database (or build custom databases) that do not have taxonomy with 7-levels defined?

2

Hi @jolespin
Yes, it is important and the database will not work well without