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degap-seqs: Remove gaps from DNA sequence alignments.¶
Docstring:
Usage: qiime rescript degap-seqs [OPTIONS]
This method converts aligned DNA sequences to unaligned DNA sequences by
removing gaps ("-") and missing data (".") characters from the sequences.
Essentially, 'unaligning' the sequences.
Inputs:
--i-aligned-sequences ARTIFACT FeatureData[AlignedSequence]
Aligned DNA Sequences to be degapped. [required]
Parameters:
--p-min-length INTEGER Minimum length of sequence to be returned after
Range(1, None) degapping. [default: 1]
Outputs:
--o-degapped-sequences ARTIFACT FeatureData[Sequence]
The resulting unaligned (degapped) DNA sequences.
[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 degap_seqs
Docstring:
Remove gaps from DNA sequence alignments.
This method converts aligned DNA sequences to unaligned DNA sequences by
removing gaps ("-") and missing data (".") characters from the sequences.
Essentially, 'unaligning' the sequences.
Parameters
----------
aligned_sequences : FeatureData[AlignedSequence]
Aligned DNA Sequences to be degapped.
min_length : Int % Range(1, None), optional
Minimum length of sequence to be returned after degapping.
Returns
-------
degapped_sequences : FeatureData[Sequence]
The resulting unaligned (degapped) DNA sequences.