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extract-reads: Extract reads from referenceΒΆ

Docstring:

Usage: qiime feature-classifier extract-reads [OPTIONS]

  Extract sequencing-like reads from a reference database.

Options:
  --i-sequences ARTIFACT PATH FeatureData[Sequence]
                                  [required]
  --p-f-primer TEXT               forward primer sequence  [required]
  --p-r-primer TEXT               reverse primer sequence  [required]
  --p-trunc-len INTEGER           read is cut to trunc_len if trunc_len is
                                  positive. Applied before trim_left.
                                  [default: 0]
  --p-trim-left INTEGER           trim_left nucleotides are removed from the
                                  5' end if trim_left is positive. Applied
                                  after trunc_len.  [default: 0]
  --p-identity FLOAT              minimum combined primer match identity
                                  threshold.  [default: 0.8]
  --p-min-length INTEGER RANGE    Minimum amplicon length. Shorter amplicons
                                  are discarded. Applied after trimming and
                                  truncation, so be aware that trimming may
                                  impact sequence retention. Set to zero to
                                  disable min length filtering.  [default: 50]
  --p-max-length INTEGER RANGE    Maximum amplicon length. Longer amplicons
                                  are discarded. Applied before trimming and
                                  truncation, so plan accordingly. Set to zero
                                  (default) to disable max length filtering.
                                  [default: 0]
  --o-reads ARTIFACT PATH FeatureData[Sequence]
                                  [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 extract_reads

Docstring:

Extract reads from reference

Extract sequencing-like reads from a reference database.

Parameters
----------
sequences : FeatureData[Sequence]
f_primer : Str
    forward primer sequence
r_primer : Str
    reverse primer sequence
trunc_len : Int, optional
    read is cut to trunc_len if trunc_len is positive. Applied before
    trim_left.
trim_left : Int, optional
    trim_left nucleotides are removed from the 5' end if trim_left is
    positive. Applied after trunc_len.
identity : Float, optional
    minimum combined primer match identity threshold.
min_length : Int % Range(0, None), optional
    Minimum amplicon length. Shorter amplicons are discarded. Applied after
    trimming and truncation, so be aware that trimming may impact sequence
    retention. Set to zero to disable min length filtering.
max_length : Int % Range(0, None), optional
    Maximum amplicon length. Longer amplicons are discarded. Applied before
    trimming and truncation, so plan accordingly. Set to zero (default) to
    disable max length filtering.

Returns
-------
reads : FeatureData[Sequence]