mask: Positional conservation and gap filtering.¶

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).
  --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.