Docstring:
Usage: qiime rescript get-bv-brc-genomes [OPTIONS]
Fetch genome sequences from BV-BRC. BV-BRC (Bacterial and Viral
Bioinformatics Resource Center) is a database for bacterial and viral
genomes, annotations, and metadata. There are three ways to query data: You
can use an RQL query to refine your search and get targeted genomes. By
providing IDs/values and a corresponding data field, you can retrieve all
genomes associated with those specific values in that data field. And as a
third option a metadata column can be provided, to use metadata obtained
with the action get-bv-brc-metadata as a new query. Check https://www.bv-
brc.org/api/doc/ for documentation.
Parameters:
--m-ids-metadata-file METADATA
--m-ids-metadata-column COLUMN MetadataColumn[Numeric | Categorical]
A metadata column obtained with the action
get-bv-brc-metadata that can be used as a query.
[optional]
--p-rql-query TEXT Query in RQL format. To download all data for
genome_ids "224308.43" and "2030927.4755", the RQL
query looks like this:
"in(genome_id,(224308.43,2030927.4755))". While "in"
is an RQL operator, "genome_id" is a data field and
"224308.43,2030927.4755" are the values. It is
important to percent encode values if they contain
illegal characters like spaces. The values "Bacillus
subtilis" and "Bacteroidales bacterium" have to be
provided with percent encoded quotes (%22) and spaces
(%20) like this:
"in(species,(%22Bacillus%20subtilis%22,%22Bacteroidal
es%20bacterium%22))". Check
https://www.bv-brc.org/api/doc/ for documentation on
data types and corresponding data fields. [optional]
--p-data-field TEXT Data field of the data type "genome_sequence". This
parameter can only be used in conjunction with the
"ids" parameter. Retrieves all genomes associated
with the IDs/values specified in parameter "ids" in
this data field. Check
https://www.bv-brc.org/api/doc/genome_sequence for
allowed data fields. [optional]
--p-ids TEXT... IDs/values of the corresponding data field. This
List[Str] parameter can only be used in conjunction with the
"data-field" parameter. Retrieves all data associated
with these IDs/values in the specified data field.
[optional]
--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.
[default: 'kingdom', 'phylum', 'class', 'order',
'family', 'genus', 'species'] [optional]
--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-genomes ARTIFACT GenomeData[DNASequence]
Genome sequences for specified query. [required]
--o-taxonomy ARTIFACT FeatureData[Taxonomy]
Taxonomy data for all 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_bv_brc_genomes
Docstring:
Get genome sequences from the BV-BRC database.
Fetch genome sequences from BV-BRC. BV-BRC (Bacterial and Viral
Bioinformatics Resource Center) is a database for bacterial and viral
genomes, annotations, and metadata. There are three ways to query data: You
can use an RQL query to refine your search and get targeted genomes. By
providing IDs/values and a corresponding data field, you can retrieve all
genomes associated with those specific values in that data field. And as a
third option a metadata column can be provided, to use metadata obtained
with the action get-bv-brc-metadata as a new query. Check https://www.bv-
brc.org/api/doc/ for documentation.
Parameters
----------
ids_metadata : MetadataColumn[Numeric | Categorical], optional
A metadata column obtained with the action get-bv-brc-metadata that can
be used as a query.
rql_query : Str, optional
Query in RQL format. To download all data for genome_ids "224308.43"
and "2030927.4755", the RQL query looks like this:
"in(genome_id,(224308.43,2030927.4755))". While "in" is an RQL
operator, "genome_id" is a data field and "224308.43,2030927.4755" are
the values. It is important to percent encode values if they contain
illegal characters like spaces. The values "Bacillus subtilis" and
"Bacteroidales bacterium" have to be provided with percent encoded
quotes (%22) and spaces (%20) like this: "in(species,(%22Bacillus%20sub
tilis%22,%22Bacteroidales%20bacterium%22))". Check https://www.bv-
brc.org/api/doc/ for documentation on data types and corresponding data
fields.
data_field : Str, optional
Data field of the data type "genome_sequence". This parameter can only
be used in conjunction with the "ids" parameter. Retrieves all genomes
associated with the IDs/values specified in parameter "ids" in this
data field. Check https://www.bv-brc.org/api/doc/genome_sequence for
allowed data fields.
ids : List[Str], optional
IDs/values of the corresponding data field. This parameter can only be
used in conjunction with the "data-field" parameter. Retrieves all data
associated with these IDs/values in the specified data field.
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. [default: 'kingdom',
'phylum', 'class', 'order', 'family', 'genus', 'species']
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
-------
genomes : GenomeData[DNASequence]
Genome sequences for specified query.
taxonomy : FeatureData[Taxonomy]
Taxonomy data for all sequences.
