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filter-seqs-length: Filter sequences by length.¶
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Docstring:
Usage: qiime rescript filter-seqs-length [OPTIONS]
Filter sequences by length with VSEARCH. For a combination of global and
conditional taxonomic filtering, see filter_seqs_length_by_taxon.
Inputs:
--i-sequences ARTIFACT FeatureData[Sequence]
Sequences to be filtered by length. [required]
Parameters:
--p-global-min INTEGER The minimum length threshold for filtering all
Range(1, None) sequences. Any sequence shorter than this length
will be removed. [optional]
--p-global-max INTEGER The maximum length threshold for filtering all
Range(1, None) sequences. Any sequence longer than this length will
be removed. [optional]
--p-threads INTEGER Number of computation threads to use (1 to 256).
Range(1, 256) The number of threads should be lesser or equal to
the number of available CPU cores. [default: 1]
Outputs:
--o-filtered-seqs ARTIFACT FeatureData[Sequence]
Sequences that pass the filtering thresholds.
[required]
--o-discarded-seqs ARTIFACT FeatureData[Sequence]
Sequences that fall outside the filtering
thresholds. [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.rescript.methods import filter_seqs_length
Docstring:
Filter sequences by length.
Filter sequences by length with VSEARCH. For a combination of global and
conditional taxonomic filtering, see filter_seqs_length_by_taxon.
Parameters
----------
sequences : FeatureData[Sequence]
Sequences to be filtered by length.
global_min : Int % Range(1, None), optional
The minimum length threshold for filtering all sequences. Any sequence
shorter than this length will be removed.
global_max : Int % Range(1, None), optional
The maximum length threshold for filtering all sequences. Any sequence
longer than this length will be removed.
threads : Int % Range(1, 256), optional
Number of computation threads to use (1 to 256). The number of threads
should be lesser or equal to the number of available CPU cores.
Returns
-------
filtered_seqs : FeatureData[Sequence]
Sequences that pass the filtering thresholds.
discarded_seqs : FeatureData[Sequence]
Sequences that fall outside the filtering thresholds.