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classify-consensus-blast: BLAST+ consensus taxonomy classifierΒΆ

Citations

[feature-classifier:classify-consensus-blast:CCA+09]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 [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.

Options:
  --i-query ARTIFACT PATH FeatureData[Sequence]
                                  Sequences to classify taxonomically.
                                  [required]
  --i-reference-reads ARTIFACT PATH FeatureData[Sequence]
                                  reference sequences.  [required]
  --i-reference-taxonomy ARTIFACT PATH FeatureData[Taxonomy]
                                  reference taxonomy labels.  [required]
  --p-maxaccepts INTEGER RANGE    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.  [default: 10]
  --p-perc-identity FLOAT         Reject match if percent identity to query is
                                  lower. Must be in range [0.0, 1.0].
                                  [default: 0.8]
  --p-strand [minus|both|plus]    Align against reference sequences in forward
                                  ("plus"), reverse ("minus"), or both
                                  directions ("both").  [default: both]
  --p-evalue FLOAT                BLAST expectation value (E) threshold for
                                  saving hits.  [default: 0.001]
  --p-min-consensus FLOAT         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]
  --o-classification ARTIFACT PATH FeatureData[Taxonomy]
                                  Taxonomy classifications of query sequences.
                                  [required if not passing --output-dir]
  --output-dir DIRECTORY          Output unspecified results to a directory
  --cmd-config FILE               Use config file for command options
  --verbose                       Display verbose output to stdout and/or
                                  stderr during execution of this action.
                                  [default: False]
  --quiet                         Silence output if execution is successful
                                  (silence is golden).  [default: False]
  --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].
strand : Str % Choices({'both', 'minus', 'plus'}), 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.