Joseph7e
commented
4 years ago Hello, I added a script with directions to construct an updated taxonomy lookup file. Basically download the script "genbank_nodes_and_names_to_taxonomy.py" and run these commands from a terminal.
mkdir ncbi_taxonomy/ && cd ncbi_taxonomy/ wget ftp://ftp.ncbi.nih.gov/pub/taxonomy/new_taxdump/new_taxdump.tar.gz tar xvzf *.tar.gz python3 genbank_nodes_and_names_to_taxonomy.py names.dmp nodes.dmp
This file should be good for any sequence data on NCBI.
If you construct a database from this NCBI this file will work but any custom database that satisfies the data structure should work with the script.
The custom database format is a seq_id followed by a tab followed by a semicolon separated taxonomy string. like this
2315627 Viruses;unknown_kingdom;unknown_phylum;unknown_subphylum;unknown_superclass;unknown_class;unknown_subclass;unknown_superorder;Caudovirales;unknown_superfamily;Siphoviridae;unknown_subfamily;unknown_genus;Bacillus phage Ray17
The sequence identifier (2315627 in the above example) should match the headers in the input reference fasta.
Hi,
The link to the customized database ncbi taxonomy database for this script: --> http://cobb.unh.edu/ncbi_taxonomy_expanded.tsv.gz is broken/the file can not be downloaded. Could you please give an example of a customized database? What should be the format of a customized database to be able to use the assign_taxonomy_with_blast.py script please?
Many thanks