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mask: Positional conservation and gap filtering.

Citations

[alignment:mask:Lan91]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).

Options:
  --i-alignment ARTIFACT PATH FeatureData[AlignedSequence]
                                  The alignment to be masked.  [required]
  --p-max-gap-frequency FLOAT     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 FLOAT      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]
  --o-masked-alignment ARTIFACT PATH FeatureData[AlignedSequence]
                                  The masked alignment.  [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.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.