# 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]
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]
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
-------
The masked alignment.