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classify-consensus-blast: BLAST+ consensus taxonomy classifier¶
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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. --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.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.