Docstring:
Usage: qiime rescript edit-taxonomy [OPTIONS]
A method that allows the user to edit taxonomy strings. This is often used
to fix inconsistent and/or inccorect taxonomic annotations. The user can
either provide two separate lists of strings, i.e. 'search-strings', and
'replacement-strings', on the command line, and/or a single tab-delimited
replacement map file containing a list of these strings. In both cases the
number of search strings must match the number of replacement strings. That
is the first string in 'search-strings' is replaced with the first string in
'replacement-strings', and so on. In the case that both search / replacement
strings, and a replacement map file are provided, they will be merged.
Inputs:
--i-taxonomy ARTIFACT FeatureData[Taxonomy]
Taxonomy strings data to be edited. [required]
Parameters:
--m-replacement-map-file METADATA
--m-replacement-map-column COLUMN MetadataColumn[Categorical]
A tab-delimitad metadata file in which the strings
in the 'id' column are replaced by the
'replacement-strings' in the second column. All
strings in the 'id' column must be unique! [optional]
--p-search-strings TEXT...
List[Str] Only used in conjuntion with 'replacement-strings'.
Each string in this list is searched for and replaced
with a string in the list of 'replace-ment-strings'.
That is the first string in 'search-strings' is
replaced with the first string in
'replacement-strings', and so on. The number of
'search-strings' must be equal to the number of
replacement strings. [optional]
--p-replacement-strings TEXT...
List[Str] Only used in conjuntion with 'search-strings'. This
must contain the same number of replacement strings
as search strings. See 'search-strings' parameter
text for more details. [optional]
--p-use-regex / --p-no-use-regex
Toggle regular expressions. By default, only
litereal substring matching is performed.
[default: False]
Outputs:
--o-edited-taxonomy ARTIFACT FeatureData[Taxonomy]
Taxonomy in which the original strings are replaced
by user-supplied strings. [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.rescript.methods import edit_taxonomy
Docstring:
Edit taxonomy strings with find and replace terms.
A method that allows the user to edit taxonomy strings. This is often used
to fix inconsistent and/or inccorect taxonomic annotations. The user can
either provide two separate lists of strings, i.e. 'search-strings', and
'replacement-strings', on the command line, and/or a single tab-delimited
replacement map file containing a list of these strings. In both cases the
number of search strings must match the number of replacement strings. That
is the first string in 'search-strings' is replaced with the first string
in 'replacement-strings', and so on. In the case that both search /
replacement strings, and a replacement map file are provided, they will be
merged.
Parameters
----------
taxonomy : FeatureData[Taxonomy]
Taxonomy strings data to be edited.
replacement_map : MetadataColumn[Categorical], optional
A tab-delimitad metadata file in which the strings in the 'id' column
are replaced by the 'replacement-strings' in the second column. All
strings in the 'id' column must be unique!
search_strings : List[Str], optional
Only used in conjuntion with 'replacement-strings'. Each string in this
list is searched for and replaced with a string in the list of
'replace-ment-strings'. That is the first string in 'search-strings' is
replaced with the first string in 'replacement-strings', and so on. The
number of 'search-strings' must be equal to the number of replacement
strings.
replacement_strings : List[Str], optional
Only used in conjuntion with 'search-strings'. This must contain the
same number of replacement strings as search strings. See 'search-
strings' parameter text for more details.
use_regex : Bool, optional
Toggle regular expressions. By default, only litereal substring
matching is performed.
Returns
-------
edited_taxonomy : FeatureData[Taxonomy]
Taxonomy in which the original strings are replaced by user-supplied
strings.
