get-ncbi-genomes: Fetch entire genomes and associated taxonomies and metadata using NCBI Datasets.¶

Docstring:

Usage: qiime rescript get-ncbi-genomes [OPTIONS]

  Uses NCBI Datasets to fetch genomes for indicated taxa. Nucleotide sequences
  and protein/gene annotations will be fetched and supplemented with full
  taxonomy of every sequence.

Parameters:
  --p-taxon TEXT         NCBI Taxonomy ID or name (common or scientific) at
                         any taxonomic rank.                        [required]
  --p-assembly-source TEXT Choices('refseq', 'genbank', 'all')
                         Fetch only RefSeq or GenBank genome assemblies.
                                                           [default: 'refseq']
  --p-assembly-levels TEXT... Choices('complete_genome', 'chromosome',
    'scaffold', 'contig')
                         Fetch only genome assemblies that are one of the
                         specified assembly levels.
                                                [default: ['complete_genome']]
  --p-only-reference / --p-no-only-reference
                         Fetch only reference and representative genome
                         assemblies.                           [default: True]
  --p-only-genomic / --p-no-only-genomic
                         Exclude plasmid, mitochondrial and chloroplast
                         molecules from the final results (i.e., keep only
                         genomic DNA).                        [default: False]
  --p-tax-exact-match / --p-no-tax-exact-match
                         If true, only return assemblies with the given NCBI
                         Taxonomy ID, or name. Otherwise, assemblies from
                         taxonomy subtree are included, too.  [default: False]
  --p-page-size INTEGER Range(20, 1000, inclusive_end=True)
                         The maximum number of genome assemblies to return
                         per request. If number of genomes to fetch is higher
                         than this number, requests will be repeated until all
                         assemblies are fetched.                 [default: 20]
  --p-ranks TEXT... Choices('domain', 'superkingdom', 'kingdom',
    'subkingdom', 'superphylum', 'phylum', 'subphylum', 'infraphylum',
    'superclass', 'class', 'subclass', 'infraclass', 'cohort', 'superorder',
    'order', 'suborder', 'infraorder', 'parvorder', 'superfamily', 'family',
    'subfamily', 'tribe', 'subtribe', 'genus', 'subgenus', 'species group',
    'species subgroup', 'species', 'subspecies', 'forma')
                         List of taxonomic ranks for building a taxonomy from
                         the NCBI Taxonomy database.
[default: ['kingdom', 'phylum', 'class', 'order', 'family', 'genus', 'species']]
  --p-rank-propagation / --p-no-rank-propagation
                         If a rank has no taxonomy associated with it, the
                         taxonomy from the upper-level rank of that lineage,
                         will be propagated downward. For example, if we are
                         missing the genus label for 'f__Pasteurellaceae;
                         g__'then the 'f__' rank will be propagated to become:
                         'f__Pasteurellaceae; g__Pasteurellaceae'.
                                                               [default: True]
Outputs:
  --o-genome-assemblies ARTIFACT FeatureData[Sequence]
                         Nucleotide sequences of requested genomes. [required]
  --o-loci ARTIFACT      Loci features of requested genomes.
    GenomeData[Loci]                                                [required]
  --o-proteins ARTIFACT GenomeData[Proteins]
                         Protein sequences originating from requested
                         genomes.                                   [required]
  --o-taxonomies ARTIFACT FeatureData[Taxonomy]
                         Taxonomies of requested genomes.           [required]
Miscellaneous:
  --output-dir PATH      Output unspecified results to a directory
  --verbose / --quiet    Display verbose output to stdout and/or stderr
                         during execution of this action. Or silence output if
                         execution is successful (silence is golden).
  --example-data PATH    Write example data and exit.
  --citations            Show citations and exit.
  --use-cache DIRECTORY  Specify the cache to be used for the intermediate
                         work of this action. If not provided, the default
                         cache under $TMP/qiime2/ will be used.
                         IMPORTANT FOR HPC USERS: If you are on an HPC system
                         and are using parallel execution it is important to
                         set this to a location that is globally accessible to
                         all nodes in the cluster.
  --help                 Show this message and exit.