# Is it required to have all 7-levels of taxonomy to add a genome to the Metaphlan database? **URL:** \ **Category:** MetaPhlAn\ **Created:** [October 9, 2023, 4:52am UTC](https://forum.biobakery.org/t/is-it-required-to-have-all-7-levels-of-taxonomy-to-add-a-genome-to-the-metaphlan-database/6019 "2023-10-09T04:52:40Z")\ **Posts on this page:** 3\ **Page:** 1
**Author:** ![jolespin](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/jolespin/32/1838_2.png) [@jolespin](https://forum.biobakery.org/u/jolespin)\ **Post date:** [October 9, 2023, 4:52am UTC](https://forum.biobakery.org/t/is-it-required-to-have-all-7-levels-of-taxonomy-to-add-a-genome-to-the-metaphlan-database/6019/1 "2023-10-09T04:52:40Z")
> **[MetaPhlAn 4](https://github.com/biobakery/MetaPhlAn/wiki/MetaPhlAn-4#customizing-the-database)** > > MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data - biobakery/MetaPhlAn Following these guidelines: ```auto 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: ```auto 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?** ---
**Author:** ![aitor.blancomiguez](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/aitor.blancomiguez/32/86_2.png) [@aitor.blancomiguez](https://forum.biobakery.org/u/aitor.blancomiguez)\ **Post date:** [March 5, 2024, 9:16am UTC](https://forum.biobakery.org/t/is-it-required-to-have-all-7-levels-of-taxonomy-to-add-a-genome-to-the-metaphlan-database/6019/2 "2024-03-05T09:16:23Z")
Hi @jolespin Yes, it is important and the database will not work well without ---
**Author:** ![HassanSaeed](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/hassansaeed/32/2885_2.png) [@HassanSaeed](https://forum.biobakery.org/u/HassanSaeed)\ **Post date:** [June 10, 2024, 1:41pm UTC](https://forum.biobakery.org/t/is-it-required-to-have-all-7-levels-of-taxonomy-to-add-a-genome-to-the-metaphlan-database/6019/3 "2024-06-10T13:41:24Z")
Hi @aitor.blancomiguez, What about the NCBI taxonomy ID of genomes? In case, genomes are not yet published. I am trying to create a new database using my genomes against which I will map corresponding metagenomics samples.