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trim-alignment: Trim alignment based on provided primers or specific positions.ΒΆ

Docstring:

Usage: qiime rescript trim-alignment [OPTIONS]

  Trim an existing alignment based on provided primers or specific, pre-
  defined positions. Primers take precedence over the positions,i.e. if both
  are provided, positions will be ignored.When using primers in combination
  with a DNA alignment, a new alignment will be generated to locate primer
  positions. Subsequently, start (5'-most) and end (3'-most) position from fwd
  and rev primer located within the new alignment is identified and used for
  slicing the original alignment.

Inputs:
  --i-aligned-sequences ARTIFACT FeatureData[AlignedSequence]
                          Aligned DNA sequences.                    [required]
Parameters:
  --p-primer-fwd TEXT     Forward primer used to find the start position for
                          alignment trimming. Provide as 5'-3'.     [optional]
  --p-primer-rev TEXT     Reverse primer used to find the end position for
                          alignment trimming. Provide as 5'-3'.     [optional]
  --p-position-start INTEGER
    Range(1, None)        Position within the alignment where the trimming
                          will begin. If not provided, alignment will notbe
                          trimmed at the beginning. If forward primer
                          isspecified this parameter will be ignored.
                                                                    [optional]
  --p-position-end INTEGER
    Range(1, None)        Position within the alignment where the trimming
                          will end. If not provided, alignment will not be
                          trimmed at the end. If reverse primer is specified
                          this parameter will be ignored.           [optional]
  --p-n-threads INTEGER   Number of threads to use for primer-based trimming,
    Range(1, None)        otherwise ignored. (Use `auto` to automatically use
                          all available cores)                    [default: 1]
Outputs:
  --o-trimmed-sequences ARTIFACT FeatureData[AlignedSequence]
                          Trimmed sequence alignment.               [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).
  --recycle-pool TEXT     Use a cache pool for pipeline resumption. QIIME 2
                          will cache your results in this pool for reuse by
                          future invocations. These pool are retained until
                          deleted by the user. If not provided, QIIME 2 will
                          create a pool which is automatically reused by
                          invocations of the same action and removed if the
                          action is successful. Note: these pools are local to
                          the cache you are using.
  --no-recycle            Do not recycle results from a previous failed
                          pipeline run or save the results from this run for
                          future recycling.
  --parallel              Execute your action in parallel. This flag will use
                          your default parallel config.
  --parallel-config FILE  Execute your action in parallel using a config at
                          the indicated path.
  --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.pipelines import trim_alignment

Docstring:

Trim alignment based on provided primers or specific positions.

Trim an existing alignment based on provided primers or specific, pre-
defined positions. Primers take precedence over the positions,i.e. if both
are provided, positions will be ignored.When using primers in combination
with a DNA alignment, a new alignment will be generated to locate primer
positions. Subsequently, start (5'-most) and end (3'-most) position from
fwd and rev primer located within the new alignment is identified and used
for slicing the original alignment.

Parameters
----------
aligned_sequences : FeatureData[AlignedSequence]
    Aligned DNA sequences.
primer_fwd : Str, optional
    Forward primer used to find the start position for alignment trimming.
    Provide as 5'-3'.
primer_rev : Str, optional
    Reverse primer used to find the end position for alignment trimming.
    Provide as 5'-3'.
position_start : Int % Range(1, None), optional
    Position within the alignment where the trimming will begin. If not
    provided, alignment will notbe trimmed at the beginning. If forward
    primer isspecified this parameter will be ignored.
position_end : Int % Range(1, None), optional
    Position within the alignment where the trimming will end. If not
    provided, alignment will not be trimmed at the end. If reverse primer
    is specified this parameter will be ignored.
n_threads : Int % Range(1, None), optional
    Number of threads to use for primer-based trimming, otherwise ignored.
    (Use `auto` to automatically use all available cores)

Returns
-------
trimmed_sequences : FeatureData[AlignedSequence]
    Trimmed sequence alignment.