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mafft-add: Add sequences to multiple sequence alignment with MAFFT.

Citations
  • Kazutaka Katoh and Daron M Standley. Mafft multiple sequence alignment software version 7: improvements in performance and usability. Molecular biology and evolution, 30(4):772–780, 2013. doi:10.1093/molbev/mst010.

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]
  --p-keeplength / --p-no-keeplength
                          If selected, the alignment length will be
                          unchanged. Any added sequence that would otherwise
                          introduce new insertions into the alignment, will
                          have those insertions deleted, to preserve original
                          alignment length.                   [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.
  --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 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.
keeplength : Bool, optional
    If selected, the alignment length will be unchanged. Any added sequence
    that would otherwise introduce new insertions into the alignment, will
    have those insertions deleted, to preserve original alignment length.

Returns
-------
expanded_alignment : FeatureData[AlignedSequence]
    Alignment containing the provided aligned and unaligned sequences.