Modify code/get_genome_id_taxonomy.R to use the NCBI tax id column from data/raw/rrnDB-5.6.tsv to generate an NCBI-based taxonomy for each genome such that we get new columns indicating their kingdom, phylum, class, order, family, and genus
We'll need taxdmp.zip (see README). This contains a file with the parent nodes for each NCBI tax id (nodes.dmp) and the names for each NCBI tax id (names.dmp). The README has the names for each column since these files don't have columns
Rename output file to reflect that it contains the NCBI taxonomy - data/references/genome_id_ncbi_taxonomy.tsv
code/get_genome_id_taxonomy.R
to use theNCBI tax id
column fromdata/raw/rrnDB-5.6.tsv
to generate an NCBI-based taxonomy for each genome such that we get new columns indicating their kingdom, phylum, class, order, family, and genustaxdmp.zip
(see README). This contains a file with the parent nodes for each NCBI tax id (nodes.dmp
) and the names for each NCBI tax id (names.dmp
). The README has the names for each column since these files don't have columnsdata/references/genome_id_ncbi_taxonomy.tsv
Makefile