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mask: Positional conservation and gap filtering.

Citations
  • DJ Lane. 16s/23s rrna sequencing. In E Stackebrandt and M Goodfellow, editors, Nucleic Acid Techniques in Bacterial Systematics, pages 115–175. John Wiley and Sons, New York, 1991.

Docstring:

Usage: qiime alignment mask [OPTIONS]

  Mask (i.e., filter) unconserved and highly gapped columns from an
  alignment. Default min_conservation was chosen to reproduce the mask
  presented in Lane (1991).

Inputs:
  --i-alignment ARTIFACT FeatureData[AlignedSequence]
                          The alignment to be masked.               [required]
Parameters:
  --p-max-gap-frequency PROPORTION Range(0, 1, inclusive_end=True)
                          The maximum relative frequency of gap characters in
                          a column for the column to be retained. This
                          relative frequency must be a number between 0.0 and
                          1.0 (inclusive), where 0.0 retains only those
                          columns without gap characters, and 1.0 retains all
                          columns regardless of gap character frequency.
                                                                [default: 1.0]
  --p-min-conservation PROPORTION Range(0, 1, inclusive_end=True)
                          The minimum relative frequency of at least one
                          non-gap character in a column for that column to be
                          retained. This relative frequency must be a number
                          between 0.0 and 1.0 (inclusive). For example, if a
                          value of 0.4 is provided, a column will only be
                          retained if it contains at least one character that
                          is present in at least 40% of the sequences.
                                                                [default: 0.4]
Outputs:
  --o-masked-alignment ARTIFACT FeatureData[AlignedSequence]
                          The masked alignment.                     [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.alignment.methods import mask

Docstring:

Positional conservation and gap filtering.

Mask (i.e., filter) unconserved and highly gapped columns from an
alignment. Default min_conservation was chosen to reproduce the mask
presented in Lane (1991).

Parameters
----------
alignment : FeatureData[AlignedSequence]
    The alignment to be masked.
max_gap_frequency : Float % Range(0, 1, inclusive_end=True), optional
    The maximum relative frequency of gap characters in a column for the
    column to be retained. This relative frequency must be a number between
    0.0 and 1.0 (inclusive), where 0.0 retains only those columns without
    gap characters, and 1.0 retains all columns regardless of gap character
    frequency.
min_conservation : Float % Range(0, 1, inclusive_end=True), optional
    The minimum relative frequency of at least one non-gap character in a
    column for that column to be retained. This relative frequency must be
    a number between 0.0 and 1.0 (inclusive). For example, if a value of
    0.4 is provided, a column will only be retained if it contains at least
    one character that is present in at least 40% of the sequences.

Returns
-------
masked_alignment : FeatureData[AlignedSequence]
    The masked alignment.