add taxonomy data, minimally a list of metagenome ids

[turbomam]

• use something like curl to get the NCBITaxon semantic sql database
  • https://s3.amazonaws.com/bbop-sqlite/ncbitaxon.db.gz
• gunzip ncbitaxon.db.gz
• create a python environment with oaklib installed
  • minimally
  • mkdir NCBITaxon
  • mv ncbitaxon.db NCBITaxon
  • cd NCBITaxon
  • python -m venv venv
  • source venv/bin/activate
  • pip install oaklib

runoak -i ncbitaxon.db info "metagenomes"

NCBITaxon:408169 ! metagenomes

[turbomam]

https://incatools.github.io/ontology-access-kit/cli.html

[turbomam]

runoak -i ncbitaxon.db descendants "metagenomes"  -p i \
    | sed 's/NCBITaxon://' \
    | sed 's/ ! /\t/' > metagenomes.tsv > ncbi_metagenomes.tsv

[turbomam]

CREATE TABLE ncbi_metagenomes (
    taxon_id INTEGER PRIMARY KEY,
    description TEXT
);

[turbomam]

with credentials in a .pgpass file

psql -h localhost -p 15432 -d ncbi_biosamples_feb26  -U postgres

then: \copy ncbi_metagenomes(taxon_id, description) FROM 'ncbi_metagenomes.tsv' WITH (FORMAT csv, DELIMITER E'\t', HEADER false);

[turbomam]

minimal list added