Docstring:
Usage: qiime alignment mafft-add [OPTIONS]
Add new sequences to an existing alignment with MAFFT.
Inputs:
--i-alignment ARTIFACT FeatureData[AlignedSequence]
The alignment to which sequences should be added.
[required]
--i-sequences ARTIFACT FeatureData[Sequence]
The sequences to be added. [required]
Parameters:
--p-n-threads NTHREADS The number of threads. (Use `auto` to automatically
use all available cores) [default: 1]
--p-parttree / --p-no-parttree
This flag is required if the number of sequences
being aligned are larger than 1000000. Disabled by
default [default: False]
--p-addfragments / --p-no-addfragments
Optimize for the addition of short sequence
fragments (for example, primer or amplicon
sequences). If not set, default sequence addition is
used. [default: False]
Outputs:
--o-expanded-alignment ARTIFACT FeatureData[AlignedSequence]
Alignment containing the provided aligned and
unaligned 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.
--help Show this message and exit.
Import:
from qiime2.plugins.alignment.methods import mafft_add
Docstring:
Add sequences to multiple sequence alignment with MAFFT.
Add new sequences to an existing alignment with MAFFT.
Parameters
----------
alignment : FeatureData[AlignedSequence]
The alignment to which sequences should be added.
sequences : FeatureData[Sequence]
The sequences to be added.
n_threads : Threads, optional
The number of threads. (Use `auto` to automatically use all available
cores)
parttree : Bool, optional
This flag is required if the number of sequences being aligned are
larger than 1000000. Disabled by default
addfragments : Bool, optional
Optimize for the addition of short sequence fragments (for example,
primer or amplicon sequences). If not set, default sequence addition is
used.
Returns
-------
expanded_alignment : FeatureData[AlignedSequence]
Alignment containing the provided aligned and unaligned sequences.
