Database_config:
  email:  "rgilmore@umc.edu"
  driver: "sqlite3"
  Full:
    configure_flag: True
    archive_flag: True
    delete_flag: False
    project_flag: False
    path: "!!python/object/apply:pathlib.Path ['']"
    Projects:
      Project_Name_1:
        configure_flag: True
        archive_flag: True
        delete_flag: False
        path: "!!python/object/apply:pathlib.Path ['Project_Name_1']"
      Project_Name_2: False
        configure_flag: True
        archive_flag: True
        delete_flag: False
        path: "!!python/object/apply:pathlib.Path ['Project_Name_2']"
      Project_Name_3: False
        configure_flag: True
        archive_flag: True
        delete_flag: False
        path: "!!python/object/apply:pathlib.Path ['Project_Name_3']"
    NCBI:
      configure_flag: True
      archive_flag: True
      delete_flag: False
      path: "!!python/object/apply:pathlib.Path ['NCBI']"
      NCBI_blast:
        configure_flag: True
        archive_flag: True
        delete_flag: False
        path: "!!python/object/apply:pathlib.Path ['NCBI', 'blast']"
        NCBI_blast_db:
          configure_flag: True
          archive_flag:  True
          delete_flag: False
          path: "!!python/object/apply:pathlib.Path ['NCBI', 'blast', 'db']"
        NCBI_blast_windowmasker_files:
          configure_flag: True
          archive_flag: True
          delete_flag: False
          path: "!!python/object/apply:pathlib.Path ['NCBI', 'blast', 'windowmasker_files']"
      NCBI_pub_taxonomy:
        configure_flag: True
        archive_flag: True
        delete_flag: False
        path: "!!python/object/apply:pathlib.Path ['NCBI', 'pub', taxonomy']"
      NCBI_refseq_release:
        Collection_Subset_1: # For us this value would be "vertebrate_mammalian:"
          seqtype_1: # For us this value would be "rna:"
            configure_flag: True
            archive_flag: True
            delete_flag: False
            upload_flag: True
            path: "!!python/object/apply:pathlib.Path ['NCBI', 'refseq', 'release']"
            db_type: "biosql"
            sub_path: "/refseq/release"
            filetype: "gbff"
            upload_list: []
            extension: ".gbk.db"
          rna: # Other seqtypes are protein and genomic
            configure_flag: True
            archive_flag: True
            delete_flag: False
            upload_flag: True
            path: "!!python/object/apply:pathlib.Path ['NCBI', 'refseq', 'release']"
            db_type: "biosql"
            sub_path: "/refseq/release"
            filetype: "gbff"
            upload_list: []
            extension: ".gbk.db"
    ITIS:
      configure_flag: True
      archive_flag: True
      delete_flag: False
      path: "!!python/object/apply:pathlib.Path ['ITIS']"
      ITIS_taxonomy:
        configure_flag: True
        archive_flag: True
        delete_flag: False
        path: "!!python/object/apply:pathlib.Path ['ITIS', 'taxonomy']"