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