Docstring:
Usage: qiime rescript get-gtdb-data [OPTIONS]
Download, parse, and import SSU GTDB files, given a version number.
Downloads data directly from GTDB, parses the taxonomy files, and outputs
ready-to-use sequence and taxonomy artifacts. REQUIRES STABLE INTERNET
CONNECTION. NOTE: THIS ACTION ACQUIRES DATA FROM GTDB. SEE
https://gtdb.ecogenomic.org/about FOR MORE INFORMATION and be aware that
earlier versions may be released under a different license.
Parameters:
--p-version TEXT Choices('202.0', '207.0', '214.0', '214.1', '220.0')
GTDB database version to download. [default: '220.0']
--p-domain TEXT Choices('Both', 'Bacteria', 'Archaea')
SSU sequence and taxonomy data to download from a
given microbial domain from GTDB. 'Both' will fetch
both bacterial and archaeal data. 'Bacteria' will
only fetch bacterial data. 'Archaea' will only fetch
archaeal data. This only applies to 'db-type
SpeciesReps'. [default: 'Both']
--p-db-type TEXT Choices('All', 'SpeciesReps')
'All': All SSU data that pass the quality-control of
GTDB, but are not clustered into representative
species. 'SpeciesReps': SSU gene sequences identified
within the set of representative species. Note: if
'All' is used, the 'domain' parameter will be ignored
as GTDB does not maintain separate domain-level files
for these non-clustered data.
[default: 'SpeciesReps']
Outputs:
--o-gtdb-taxonomy ARTIFACT FeatureData[Taxonomy]
SSU GTDB reference taxonomy. [required]
--o-gtdb-sequences ARTIFACT FeatureData[Sequence]
SSU GTDB reference sequences. [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_gtdb_data
Docstring:
Download, parse, and import SSU GTDB reference data.
Download, parse, and import SSU GTDB files, given a version number.
Downloads data directly from GTDB, parses the taxonomy files, and outputs
ready-to-use sequence and taxonomy artifacts. REQUIRES STABLE INTERNET
CONNECTION. NOTE: THIS ACTION ACQUIRES DATA FROM GTDB. SEE
https://gtdb.ecogenomic.org/about FOR MORE INFORMATION and be aware that
earlier versions may be released under a different license.
Parameters
----------
version : Str % Choices('202.0', '207.0', '214.0', '214.1', '220.0'), optional
GTDB database version to download.
domain : Str % Choices('Both', 'Bacteria', 'Archaea'), optional
SSU sequence and taxonomy data to download from a given microbial
domain from GTDB. 'Both' will fetch both bacterial and archaeal data.
'Bacteria' will only fetch bacterial data. 'Archaea' will only fetch
archaeal data. This only applies to 'db-type SpeciesReps'.
db_type : Str % Choices('All', 'SpeciesReps'), optional
'All': All SSU data that pass the quality-control of GTDB, but are not
clustered into representative species. 'SpeciesReps': SSU gene
sequences identified within the set of representative species. Note: if
'All' is used, the 'domain' parameter will be ignored as GTDB does not
maintain separate domain-level files for these non-clustered data.
Returns
-------
gtdb_taxonomy : FeatureData[Taxonomy]
SSU GTDB reference taxonomy.
gtdb_sequences : FeatureData[Sequence]
SSU GTDB reference sequences.
