Docstring:
Usage: qiime feature-classifier classify-consensus-blast [OPTIONS]
Assign taxonomy to query sequences using BLAST+. Performs BLAST+ local
alignment between query and reference_reads, then assigns consensus taxonomy
to each query sequence from among maxaccepts hits, min_consensus of which
share that taxonomic assignment. Note that maxaccepts selects the first N
hits with > perc_identity similarity to query, not the top N matches. For
top N hits, use classify-consensus-vsearch.
Inputs:
--i-query ARTIFACT FeatureData[Sequence]
Query sequences. [required]
--i-reference-taxonomy ARTIFACT FeatureData[Taxonomy]
reference taxonomy labels. [required]
--i-blastdb ARTIFACT BLAST indexed database. Incompatible with
BLASTDB reference-reads. [optional]
--i-reference-reads ARTIFACT FeatureData[Sequence]
Reference sequences. Incompatible with blastdb.
[optional]
Parameters:
--p-maxaccepts INTEGER Maximum number of hits to keep for each query.
Range(1, None) BLAST will choose the first N hits in the reference
database that exceed perc-identity similarity to
query. NOTE: the database is not sorted by
similarity to query, so these are the first N hits
that pass the threshold, not necessarily the top N
hits. [default: 10]
--p-perc-identity PROPORTION Range(0.0, 1.0, inclusive_end=True)
Reject match if percent identity to query is lower.
[default: 0.8]
--p-query-cov PROPORTION Range(0.0, 1.0, inclusive_end=True)
Reject match if query alignment coverage per
high-scoring pair is lower. Note: this uses blastn's
qcov_hsp_perc parameter, and may not behave
identically to the query-cov parameter used by
classify-consensus-vsearch. [default: 0.8]
--p-strand TEXT Choices('both', 'plus', 'minus')
Align against reference sequences in forward
("plus"), reverse ("minus"), or both directions
("both"). [default: 'both']
--p-evalue NUMBER BLAST expectation value (E) threshold for saving
hits. [default: 0.001]
--p-output-no-hits / --p-no-output-no-hits
Report both matching and non-matching queries.
WARNING: always use the default setting for this
option unless if you know what you are doing! If you
set this option to False, your sequences and feature
table will need to be filtered to exclude
unclassified sequences, otherwise you may run into
errors downstream from missing feature IDs. Set to
FALSE to mirror default BLAST search.
[default: True]
--p-min-consensus NUMBER Range(0.5, 1.0, inclusive_start=False,
inclusive_end=True) Minimum fraction of assignments must match top hit
to be accepted as consensus assignment.
[default: 0.51]
--p-unassignable-label TEXT
Annotation given to sequences without any hits.
[default: 'Unassigned']
--p-num-threads NTHREADS
Number of threads (CPUs) to use in the BLAST
search. Pass 0 to use all available CPUs.
[default: 1]
Outputs:
--o-classification ARTIFACT FeatureData[Taxonomy]
Taxonomy classifications of query sequences.
[required]
--o-search-results ARTIFACT
FeatureData[BLAST6] Top hits for each query. [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.feature_classifier.pipelines import classify_consensus_blast
Docstring:
BLAST+ consensus taxonomy classifier
Assign taxonomy to query sequences using BLAST+. Performs BLAST+ local
alignment between query and reference_reads, then assigns consensus
taxonomy to each query sequence from among maxaccepts hits, min_consensus
of which share that taxonomic assignment. Note that maxaccepts selects the
first N hits with > perc_identity similarity to query, not the top N
matches. For top N hits, use classify-consensus-vsearch.
Parameters
----------
query : FeatureData[Sequence]
Query sequences.
reference_taxonomy : FeatureData[Taxonomy]
reference taxonomy labels.
blastdb : BLASTDB, optional
BLAST indexed database. Incompatible with reference_reads.
reference_reads : FeatureData[Sequence], optional
Reference sequences. Incompatible with blastdb.
maxaccepts : Int % Range(1, None), optional
Maximum number of hits to keep for each query. BLAST will choose the
first N hits in the reference database that exceed perc_identity
similarity to query. NOTE: the database is not sorted by similarity to
query, so these are the first N hits that pass the threshold, not
necessarily the top N hits.
perc_identity : Float % Range(0.0, 1.0, inclusive_end=True), optional
Reject match if percent identity to query is lower.
query_cov : Float % Range(0.0, 1.0, inclusive_end=True), optional
Reject match if query alignment coverage per high-scoring pair is
lower. Note: this uses blastn's qcov_hsp_perc parameter, and may not
behave identically to the query_cov parameter used by classify-
consensus-vsearch.
strand : Str % Choices('both', 'plus', 'minus'), optional
Align against reference sequences in forward ("plus"), reverse
("minus"), or both directions ("both").
evalue : Float, optional
BLAST expectation value (E) threshold for saving hits.
output_no_hits : Bool, optional
Report both matching and non-matching queries. WARNING: always use the
default setting for this option unless if you know what you are doing!
If you set this option to False, your sequences and feature table will
need to be filtered to exclude unclassified sequences, otherwise you
may run into errors downstream from missing feature IDs. Set to FALSE
to mirror default BLAST search.
min_consensus : Float % Range(0.5, 1.0, inclusive_start=False, inclusive_end=True), optional
Minimum fraction of assignments must match top hit to be accepted as
consensus assignment.
unassignable_label : Str, optional
Annotation given to sequences without any hits.
num_threads : Threads, optional
Number of threads (CPUs) to use in the BLAST search. Pass 0 to use all
available CPUs.
Returns
-------
classification : FeatureData[Taxonomy]
Taxonomy classifications of query sequences.
search_results : FeatureData[BLAST6]
Top hits for each query.
