Fork me on GitHub

filter-seqs-length: Filter sequences by length.

Citations
  • Torbjørn Rognes, Tomáš Flouri, Ben Nichols, Christopher Quince, and Frédéric Mahé. Vsearch: a versatile open source tool for metagenomics. PeerJ, 4:e2584, 2016. doi:10.7717/peerj.2584.

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.