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filter-distance-matrix: Filter samples from a distance matrix.ΒΆ

Docstring:

Usage: qiime diversity filter-distance-matrix [OPTIONS]

  Filter samples from a distance matrix, retaining only the samples matching
  search criteria specified by `metadata` and `where` parameters (or
  retaining only the samples not matching that criteria, if `exclude_ids` is
  True). See the filtering tutorial on https://docs.qiime2.org for
  additional details.

Options:
  --i-distance-matrix ARTIFACT PATH DistanceMatrix
                                  Distance matrix to filter by sample.
                                  [required]
  --m-metadata-file MULTIPLE FILE
                                  Metadata file or artifact viewable as
                                  metadata. This option may be supplied
                                  multiple times to merge metadata. Sample
                                  metadata used with `where` parameter when
                                  selecting samples to retain, or with
                                  `exclude_ids` when selecting samples to
                                  discard.  [required]
  --p-where TEXT                  SQLite WHERE clause specifying sample
                                  metadata criteria that must be met to be
                                  included in the filtered distance matrix. If
                                  not provided, all samples in `metadata` that
                                  are also in the input distance matrix will
                                  be retained.  [optional]
  --p-exclude-ids / --p-no-exclude-ids
                                  If `True`, the samples selected by
                                  `metadata` or `where` parameters will be
                                  excluded from the filtered distance matrix
                                  instead of being retained.  [default: False]
  --o-filtered-distance-matrix ARTIFACT PATH DistanceMatrix
                                  Distance matrix filtered to include samples
                                  matching search criteria  [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.diversity.methods import filter_distance_matrix

Docstring:

Filter samples from a distance matrix.

Filter samples from a distance matrix, retaining only the samples matching
search criteria specified by `metadata` and `where` parameters (or
retaining only the samples not matching that criteria, if `exclude_ids` is
True). See the filtering tutorial on https://docs.qiime2.org for additional
details.

Parameters
----------
distance_matrix : DistanceMatrix
    Distance matrix to filter by sample.
metadata : Metadata
    Sample metadata used with `where` parameter when selecting samples to
    retain, or with `exclude_ids` when selecting samples to discard.
where : Str, optional
    SQLite WHERE clause specifying sample metadata criteria that must be
    met to be included in the filtered distance matrix. If not provided,
    all samples in `metadata` that are also in the input distance matrix
    will be retained.
exclude_ids : Bool, optional
    If `True`, the samples selected by `metadata` or `where` parameters
    will be excluded from the filtered distance matrix instead of being
    retained.

Returns
-------
filtered_distance_matrix : DistanceMatrix
    Distance matrix filtered to include samples matching search criteria