Docstring:
Usage: qiime rescript parse-silva-taxonomy [OPTIONS]
Parses several files from the SILVA reference database to produce a
GreenGenes-like fixed rank taxonomy that is 6 or 7 ranks deep, depending on
whether or not `include_species_labels` is applied. The generated ranks (and
the rank handles used to label these ranks in the resulting taxonomy) are:
domain (d__), phylum (p__), class (c__), order (o__), family (f__), genus
(g__), and species (s__). 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.
Inputs:
--i-taxonomy-tree ARTIFACT
Phylogeny[Rooted] SILVA hierarchical taxonomy tree. The SILVA release
filename typically takes the form of:
'tax_slv_ssu_X.tre', where 'X' is the SILVA version
number. [required]
--i-taxonomy-map ARTIFACT FeatureData[SILVATaxidMap]
SILVA taxonomy map. This file contains a mapping of
the sequence accessions to the numeric taxonomy
identifiers and species label information. The SILVA
release filename is typically in the form of:
'taxmap_slv_ssu_ref_X.txt', or
'taxmap_slv_ssu_ref_nr_X.txt' where 'X' is the SILVA
version number. [required]
--i-taxonomy-ranks ARTIFACT FeatureData[SILVATaxonomy]
SILVA taxonomy file. This file contains the
taxonomic rank information for each numeric taxonomy
identifier and the taxonomy. The SILVA filename
typically takes the form of: 'tax_slv_ssu_X.txt',
where 'X' is the SILVA version number. [required]
Parameters:
--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-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]
Outputs:
--o-taxonomy ARTIFACT FeatureData[Taxonomy]
The resulting fixed-rank formatted SILVA 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).
--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 parse_silva_taxonomy
Docstring:
Generates a SILVA fixed-rank taxonomy.
Parses several files from the SILVA reference database to produce a
GreenGenes-like fixed rank taxonomy that is 6 or 7 ranks deep, depending on
whether or not `include_species_labels` is applied. The generated ranks
(and the rank handles used to label these ranks in the resulting taxonomy)
are: domain (d__), phylum (p__), class (c__), order (o__), family (f__),
genus (g__), and species (s__). 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
----------
taxonomy_tree : Phylogeny[Rooted]
SILVA hierarchical taxonomy tree. The SILVA release filename typically
takes the form of: 'tax_slv_ssu_X.tre', where 'X' is the SILVA version
number.
taxonomy_map : FeatureData[SILVATaxidMap]
SILVA taxonomy map. This file contains a mapping of the sequence
accessions to the numeric taxonomy identifiers and species label
information. The SILVA release filename is typically in the form of:
'taxmap_slv_ssu_ref_X.txt', or 'taxmap_slv_ssu_ref_nr_X.txt' where 'X'
is the SILVA version number.
taxonomy_ranks : FeatureData[SILVATaxonomy]
SILVA taxonomy file. This file contains the taxonomic rank information
for each numeric taxonomy identifier and the taxonomy. The SILVA
filename typically takes the form of: 'tax_slv_ssu_X.txt', where 'X' is
the SILVA version number.
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']
include_species_labels : Bool, optional
Include species rank labels in taxonomy output. Note: species-labels
may not be reliable in all cases.
Returns
-------
taxonomy : FeatureData[Taxonomy]
The resulting fixed-rank formatted SILVA taxonomy.
