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.
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.
