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filter-samples: Filter samples from table

Docstring:

Usage: qiime feature-table filter-samples [OPTIONS]

  Filter samples from table based on frequency and/or metadata. Any features
  with a frequency of zero after sample filtering will also be removed. See
  the filtering tutorial on https://docs.qiime2.org for additional details.

Inputs:
  --i-table ARTIFACT FeatureTable[Frequency¹ | RelativeFrequency² |
    PresenceAbsence³ | Composition⁴]
                         The feature table from which samples should be
                         filtered.                                  [required]
Parameters:
  --p-min-frequency INTEGER
                         The minimum total frequency that a sample must have
                         to be retained.                          [default: 0]
  --p-max-frequency INTEGER
                         The maximum total frequency that a sample can have
                         to be retained. If no value is provided this will
                         default to infinity (i.e., no maximum frequency
                         filter will be applied).                   [optional]
  --p-min-features INTEGER
                         The minimum number of features that a sample must
                         have to be retained.                     [default: 0]
  --p-max-features INTEGER
                         The maximum number of features that a sample can
                         have to be retained. If no value is provided this
                         will default to infinity (i.e., no maximum feature
                         filter will be applied).                   [optional]
  --m-metadata-file METADATA...
    (multiple            Sample metadata used with `where` parameter when
     arguments will be   selecting samples to retain, or with `exclude-ids`
     merged)             when selecting samples to discard.         [optional]
  --p-where TEXT         SQLite WHERE clause specifying sample metadata
                         criteria that must be met to be included in the
                         filtered feature table. If not provided, all samples
                         in `metadata` that are also in the feature table 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
                         table instead of being retained.     [default: False]
  --p-filter-empty-features / --p-no-filter-empty-features
                         If true, features which are not present in any
                         retained samples are dropped.         [default: True]
  --p-allow-empty-table / --p-no-allow-empty-table
                         If true, the filtered table may be empty. Default
                         behavior is to raise an error if the filtered table
                         is empty.                            [default: False]
Outputs:
  --o-filtered-table ARTIFACT FeatureTable[Frequency¹ | RelativeFrequency²
    | PresenceAbsence³ | Composition⁴]
                         The resulting feature table filtered by sample.
                                                                    [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.

Examples:
  # ### example: filter to subject1
  qiime feature-table filter-samples \
    --i-table feature-table.qza \
    --m-metadata-file sample-metadata.tsv \
    --p-where '[subject]="subject-1"' \
    --o-filtered-table filtered-table.qza

  # ### example: filter to skin
  qiime feature-table filter-samples \
    --i-table feature-table.qza \
    --m-metadata-file sample-metadata.tsv \
    --p-where '[body-site] IN ("left palm", "right palm")' \
    --o-filtered-table filtered-table.qza

  # ### example: filter to subject1 gut
  qiime feature-table filter-samples \
    --i-table feature-table.qza \
    --m-metadata-file sample-metadata.tsv \
    --p-where '[subject]="subject-1" AND [body-site]="gut"' \
    --o-filtered-table filtered-table.qza

  # ### example: filter to gut or abx
  qiime feature-table filter-samples \
    --i-table feature-table.qza \
    --m-metadata-file sample-metadata.tsv \
    --p-where '[body-site]="gut" OR [reported-antibiotic-usage]="Yes"' \
    --o-filtered-table filtered-table.qza

  # ### example: filter to subject1 not gut
  qiime feature-table filter-samples \
    --i-table feature-table.qza \
    --m-metadata-file sample-metadata.tsv \
    --p-where '[subject]="subject-1" AND NOT [body-site]="gut"' \
    --o-filtered-table filtered-table.qza

  # ### example: filter min features
  qiime feature-table filter-samples \
    --i-table feature-table.qza \
    --p-min-features 10 \
    --o-filtered-table filtered-table.qza

  # ### example: filter min frequency
  qiime feature-table filter-samples \
    --i-table feature-table.qza \
    --p-min-frequency 1500 \
    --o-filtered-table filtered-table.qza

Import:

from qiime2.plugins.feature_table.methods import filter_samples

Docstring:

Filter samples from table

Filter samples from table based on frequency and/or metadata. Any features
with a frequency of zero after sample filtering will also be removed. See
the filtering tutorial on https://docs.qiime2.org for additional details.

Parameters
----------
table : FeatureTable[Frequency¹ | RelativeFrequency² | PresenceAbsence³ | Composition⁴]
    The feature table from which samples should be filtered.
min_frequency : Int, optional
    The minimum total frequency that a sample must have to be retained.
max_frequency : Int, optional
    The maximum total frequency that a sample can have to be retained. If
    no value is provided this will default to infinity (i.e., no maximum
    frequency filter will be applied).
min_features : Int, optional
    The minimum number of features that a sample must have to be retained.
max_features : Int, optional
    The maximum number of features that a sample can have to be retained.
    If no value is provided this will default to infinity (i.e., no maximum
    feature filter will be applied).
metadata : Metadata, optional
    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 feature table. If not provided, all
    samples in `metadata` that are also in the feature table will be
    retained.
exclude_ids : Bool, optional
    If true, the samples selected by `metadata` or `where` parameters will
    be excluded from the filtered table instead of being retained.
filter_empty_features : Bool, optional
    If true, features which are not present in any retained samples are
    dropped.
allow_empty_table : Bool, optional
    If true, the filtered table may be empty. Default behavior is to raise
    an error if the filtered table is empty.

Returns
-------
filtered_table : FeatureTable[Frequency¹ | RelativeFrequency² | PresenceAbsence³ | Composition⁴]
    The resulting feature table filtered by sample.