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.
Import:
from qiime2.plugins.rescript.methods import get_ncbi_genomes
Docstring:
Fetch entire genomes and associated taxonomies and metadata using NCBI
Datasets.
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
----------
taxon : Str
NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank.
assembly_source : Str % Choices('refseq', 'genbank', 'all'), optional
Fetch only RefSeq or GenBank genome assemblies.
assembly_levels : List[Str % Choices('complete_genome', 'chromosome', 'scaffold', 'contig')], optional
Fetch only genome assemblies that are one of the specified assembly
levels.
only_reference : Bool, optional
Fetch only reference and representative genome assemblies.
only_genomic : Bool, optional
Exclude plasmid, mitochondrial and chloroplast molecules from the final
results (i.e., keep only genomic DNA).
tax_exact_match : Bool, optional
If true, only return assemblies with the given NCBI Taxonomy ID, or
name. Otherwise, assemblies from taxonomy subtree are included, too.
page_size : Int % Range(20, 1000, inclusive_end=True), optional
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.
ranks : List[Str % 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')], optional
List of taxonomic ranks for building a taxonomy from the NCBI Taxonomy
database.
rank_propagation : Bool, optional
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'.
Returns
-------
genome_assemblies : FeatureData[Sequence]
Nucleotide sequences of requested genomes.
loci : GenomeData[Loci]
Loci features of requested genomes.
proteins : GenomeData[Proteins]
Protein sequences originating from requested genomes.
taxonomies : FeatureData[Taxonomy]
Taxonomies of requested genomes.
