Docstring:
Usage: qiime rescript get-silva-data [OPTIONS]
Download, parse, and import SILVA database files, given a version number and
reference target. Downloads data directly from SILVA, parses the taxonomy
files, and outputs ready-to-use sequence and taxonomy artifacts. REQUIRES
STABLE INTERNET CONNECTION. NOTE: THIS ACTION ACQUIRES DATA FROM THE SILVA
DATABASE. SEE https://www.arb-silva.de/silva-license-information/ FOR MORE
INFORMATION and be aware that earlier versions may be released under a
different license.
Parameters:
--p-version VALUE Str % Choices('128', '132')¹ | Str % Choices('138')² |
Str % Choices('138.1')³
SILVA database version to download.
[default: '138.1']
--p-target VALUE Str % Choices('SSURef_NR99', 'SSURef', 'LSURef')¹ | Str
% Choices('SSURef_NR99', 'SSURef')² | Str % Choices('SSURef_NR99',
'SSURef', 'LSURef_NR99', 'LSURef')³
Reference sequence target to download. SSURef =
redundant small subunit reference. LSURef =
redundant large subunit reference. SSURef_NR99 =
non-redundant (clustered at 99% similarity) small
subunit reference. [default: 'SSURef_NR99']
--p-include-species-labels / --p-no-include-species-labels
Include species rank labels in taxonomy output.
Note: species-labels may not be reliable in all
cases. [default: False]
--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]
--p-ranks TEXT... Choices('domain', 'superkingdom', 'kingdom',
'subkingdom', 'superphylum', 'phylum', 'subphylum', 'infraphylum',
'superclass', 'class', 'subclass', 'infraclass', 'superorder', 'order',
'suborder', 'superfamily', 'family', 'subfamily', 'genus')
List of taxonomic ranks for building a taxonomy
from the SILVA Taxonomy database. Use
'include-species-labels' to append the organism name
as the species label. [default: 'domain', 'phylum',
'class', 'order', 'family', 'genus'] [optional]
--p-download-sequences / --p-no-download-sequences
Toggle whether or not to download and import the
SILVA reference sequences associated with the
release. Skipping the sequences is useful if you
only want to download and parse the taxonomy, e.g.,
a local copy of the sequences already exists or for
testing purposes. NOTE: if this option is used, a
`silva-sequences` output is still created, but
contains no data. [default: True]
Outputs:
--o-silva-sequences ARTIFACT FeatureData[RNASequence]
SILVA reference sequences. [required]
--o-silva-taxonomy ARTIFACT FeatureData[Taxonomy]
SILVA reference taxonomy. [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).
--recycle-pool TEXT Use a cache pool for pipeline resumption. QIIME 2
will cache your results in this pool for reuse by
future invocations. These pool are retained until
deleted by the user. If not provided, QIIME 2 will
create a pool which is automatically reused by
invocations of the same action and removed if the
action is successful. Note: these pools are local to
the cache you are using.
--no-recycle Do not recycle results from a previous failed
pipeline run or save the results from this run for
future recycling.
--parallel Execute your action in parallel. This flag will use
your default parallel config.
--parallel-config FILE Execute your action in parallel using a config at
the indicated path.
--use-cache DIRECTORY Specify the cache to be used for the intermediate
work of this pipeline. 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.
--example-data PATH Write example data and exit.
--citations Show citations and exit.
--help Show this message and exit.
Import:
from qiime2.plugins.rescript.pipelines import get_silva_data
Docstring:
Download, parse, and import SILVA database.
Download, parse, and import SILVA database files, given a version number
and reference target. Downloads data directly from SILVA, parses the
taxonomy files, and outputs ready-to-use sequence and taxonomy artifacts.
REQUIRES STABLE INTERNET CONNECTION. NOTE: THIS ACTION ACQUIRES DATA FROM
THE SILVA DATABASE. SEE https://www.arb-silva.de/silva-license-information/
FOR MORE INFORMATION and be aware that earlier versions may be released
under a different license.
Parameters
----------
version : Str % Choices('128', '132')¹ | Str % Choices('138')² | Str % Choices('138.1')³, optional
SILVA database version to download.
target : Str % Choices('SSURef_NR99', 'SSURef', 'LSURef')¹ | Str % Choices('SSURef_NR99', 'SSURef')² | Str % Choices('SSURef_NR99', 'SSURef', 'LSURef_NR99', 'LSURef')³, optional
Reference sequence target to download. SSURef = redundant small subunit
reference. LSURef = redundant large subunit reference. SSURef_NR99 =
non-redundant (clustered at 99% similarity) small subunit reference.
include_species_labels : Bool, optional
Include species rank labels in taxonomy output. Note: species-labels
may not be reliable in all cases.
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'.
ranks : List[Str % Choices('domain', 'superkingdom', 'kingdom', 'subkingdom', 'superphylum', 'phylum', 'subphylum', 'infraphylum', 'superclass', 'class', 'subclass', 'infraclass', 'superorder', 'order', 'suborder', 'superfamily', 'family', 'subfamily', 'genus')], optional
List of taxonomic ranks for building a taxonomy from the SILVA Taxonomy
database. Use 'include_species_labels' to append the organism name as
the species label. [default: 'domain', 'phylum', 'class', 'order',
'family', 'genus']
download_sequences : Bool, optional
Toggle whether or not to download and import the SILVA reference
sequences associated with the release. Skipping the sequences is useful
if you only want to download and parse the taxonomy, e.g., a local copy
of the sequences already exists or for testing purposes. NOTE: if this
option is used, a `silva_sequences` output is still created, but
contains no data.
Returns
-------
silva_sequences : FeatureData[RNASequence]
SILVA reference sequences.
silva_taxonomy : FeatureData[Taxonomy]
SILVA reference taxonomy.
