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classify-consensus-blast: BLAST+ consensus taxonomy classifier

Citations
  • Christiam Camacho, George Coulouris, Vahram Avagyan, Ning Ma, Jason Papadopoulos, Kevin Bealer, and Thomas L Madden. Blast+: architecture and applications. BMC bioinformatics, 10(1):421, 2009. doi:10.1186/1471-2105-10-421.

Docstring:

Usage: qiime feature-classifier classify-consensus-blast [OPTION
                                                         S]

  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]
                          Sequences to classify taxonomically.      [required]
  --i-reference-reads ARTIFACT FeatureData[Sequence]
                          reference sequences.                      [required]
  --i-reference-taxonomy ARTIFACT FeatureData[Taxonomy]
                          reference taxonomy labels.                [required]
Parameters:
  --p-maxaccepts INTEGER  Maximum number of hits to keep for each query. Must
    Range(1, None)        be in range [1, infinity]. BLAST will choose the
                          first N hits in the reference database that exceed
                          perc-identity similarity to query.     [default: 10]
  --p-perc-identity PROPORTION Range(0.0, 1.0, inclusive_end=True)
                          Reject match if percent identity to query is lower.
                          Must be in range [0.0, 1.0].          [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. Must be in range [0.0,
                          1.0].                                 [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-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. Must be in
                          range (0.5, 1.0].                    [default: 0.51]
  --p-unassignable-label TEXT
                                                       [default: 'Unassigned']
Outputs:
  --o-classification ARTIFACT FeatureData[Taxonomy]
                          Taxonomy classifications of query 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).
  --citations             Show citations and exit.
  --help                  Show this message and exit.

Import:

from qiime2.plugins.feature_classifier.methods 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]
    Sequences to classify taxonomically.
reference_reads : FeatureData[Sequence]
    reference sequences.
reference_taxonomy : FeatureData[Taxonomy]
    reference taxonomy labels.
maxaccepts : Int % Range(1, None), optional
    Maximum number of hits to keep for each query. Must be in range [1,
    infinity]. BLAST will choose the first N hits in the reference database
    that exceed perc_identity similarity to query.
perc_identity : Float % Range(0.0, 1.0, inclusive_end=True), optional
    Reject match if percent identity to query is lower. Must be in range
    [0.0, 1.0].
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. Must be in range [0.0, 1.0].
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.
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. Must be in range (0.5, 1.0].
unassignable_label : Str, optional

Returns
-------
classification : FeatureData[Taxonomy]
    Taxonomy classifications of query sequences.