extract-seq-segments: Use reference sequences to extract shorter matching sequence segments from longer sequences based on a user-defined ‘perc-identity’ value.¶
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Docstring:
Usage: qiime rescript extract-seq-segments [OPTIONS]
This action provides the ability to extract a region, or segment, of
sequence without the need to specify primer pairs. This is very useful in
cases when one or more of the primer sequences are not present within the
target sequences, which prevents extraction of the (amplicon) region through
primer-pair searching. Here, VSEARCH is used to extract these segments based
on a reference pool of sequences that only span the region of interest.
Inputs:
--i-input-sequences ARTIFACT FeatureData[Sequence]
Sequences from which matching shorter sequence
segments (regions) can be extracted from. Sequences
containing segments that match those from
'reference-segment-sequences' will have those
segments extracted and written to file. [required]
--i-reference-segment-sequences ARTIFACT FeatureData[Sequence]
Reference sequence segments that will be used to
search for and extract matching segments from
'input-sequences'. [required]
Parameters:
--p-perc-identity PROPORTION Range(0, 1, inclusive_start=False,
inclusive_end=True) The percent identity at which clustering should be
performed. This parameter maps to vsearch's --id
parameter. [default: 0.7]
--p-target-coverage PROPORTION Range(0, 1, inclusive_start=False,
inclusive_end=True) The minimum fraction of coverage that
'reference-segment-sequences' must have in order to
extract matching segments from 'input-sequences'.
[default: 0.9]
--p-min-seq-len INTEGER
Range(1, None) Minimum length of sequence allowed for searching.
Any sequence less than this will be discarded. If not
set, default program settings will be used.
[optional]
--p-threads INTEGER Number of computation threads to use (1 to 256). The
Range(1, 256) number of threads should be lesser or equal to the
number of available CPU cores. [default: 1]
Outputs:
--o-extracted-sequence-segments ARTIFACT FeatureData[Sequence]
Extracted sequence segments from 'input-sequences'
that succesfully aligned to
'reference-segment-sequences'. [required]
--o-unmatched-sequences ARTIFACT FeatureData[Sequence]
Sequences in 'input-sequences' that did not have
matching sequence segments within
'reference-segment-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 extract_seq_segments
Docstring:
Use reference sequences to extract shorter matching sequence segments from
longer sequences based on a user-defined 'perc-identity' value.
This action provides the ability to extract a region, or segment, of
sequence without the need to specify primer pairs. This is very useful in
cases when one or more of the primer sequences are not present within the
target sequences, which prevents extraction of the (amplicon) region
through primer-pair searching. Here, VSEARCH is used to extract these
segments based on a reference pool of sequences that only span the region
of interest.
Parameters
----------
input_sequences : FeatureData[Sequence]
Sequences from which matching shorter sequence segments (regions) can
be extracted from. Sequences containing segments that match those from
'reference-segment-sequences' will have those segments extracted and
written to file.
reference_segment_sequences : FeatureData[Sequence]
Reference sequence segments that will be used to search for and extract
matching segments from 'input-sequences'.
perc_identity : Float % Range(0, 1, inclusive_start=False, inclusive_end=True), optional
The percent identity at which clustering should be performed. This
parameter maps to vsearch's --id parameter.
target_coverage : Float % Range(0, 1, inclusive_start=False, inclusive_end=True), optional
The minimum fraction of coverage that 'reference-segment-sequences'
must have in order to extract matching segments from 'input-sequences'.
min_seq_len : Int % Range(1, None), optional
Minimum length of sequence allowed for searching. Any sequence less
than this will be discarded. If not set, default program settings will
be used.
threads : Int % Range(1, 256), optional
Number of computation threads to use (1 to 256). The number of threads
should be lesser or equal to the number of available CPU cores.
Returns
-------
extracted_sequence_segments : FeatureData[Sequence]
Extracted sequence segments from 'input-sequences' that succesfully
aligned to 'reference-segment-sequences'.
unmatched_sequences : FeatureData[Sequence]
Sequences in 'input-sequences' that did not have matching sequence
segments within 'reference-segment-sequences'.