Version 0.2 Tête de veau

  • New colon ncbi_rank in curate.csv which gives the known rank level in NCBI taxonomy
  • ncbi_rank is generated by curegen command
  • validate --curate handle ncbi_rank command following:
    • species_rank value is species then no need to create new node in NCBI, just apply the taxonomy name correction
    • species_rank value is genus then a new node is created in NCBI with current_name as species name and genus as parent node.
    • species_rank value is family then
      • new node with taxonomy name genus is created at genus rank with family as parent
      • new node with taxonomy name current_name is created at species rank with genus as parent
  • module arguments check ncbi_taxdump files argument
  • module arguments check curate file argument
  • Curation of taxonomy is factorised