library("tima")
copy_backbone()
go_to_cache()
prepare_annotations_sirius()
unlink("data", recursive = TRUE)Prepare annotations SIRIUS
Description
Prepares SIRIUS annotation results (structure predictions, CANOPUS chemical classifications, and formula predictions) by harmonizing formats across SIRIUS versions (v5/v6), standardizing column names, and integrating with structure metadata.
Usage
prepare_annotations_sirius(
input_directory = get_params(step =
"prepare_annotations_sirius")\$files\$annotations\$raw\$sirius,
output_ann = get_params(step =
"prepare_annotations_sirius")\$files\$annotations\$prepared\$structural\$sirius,
output_can = get_params(step =
"prepare_annotations_sirius")\$files\$annotations\$prepared\$canopus,
output_for = get_params(step =
"prepare_annotations_sirius")\$files\$annotations\$prepared\$formula,
sirius_version = get_params(step = "prepare_annotations_sirius")\$tools\$sirius\$version,
str_stereo = get_params(step =
"prepare_annotations_sirius")\$files\$libraries\$sop\$merged\$structures\$stereo,
str_met = get_params(step =
"prepare_annotations_sirius")\$files\$libraries\$sop\$merged\$structures\$metadata,
str_nam = get_params(step =
"prepare_annotations_sirius")\$files\$libraries\$sop\$merged\$structures\$names,
str_tax_cla = get_params(step =
"prepare_annotations_sirius")\$files\$libraries\$sop\$merged\$structures\$taxonomies\$cla,
str_tax_npc = get_params(step =
"prepare_annotations_sirius")\$files\$libraries\$sop\$merged\$structures\$taxonomies\$npc
)
Arguments
input_directory
|
Character path to directory or zip file containing SIRIUS results. |
output_ann
|
Character path for prepared structure annotation output. |
output_can
|
Character path for prepared CANOPUS output. |
output_for
|
Character path for prepared formula output. |
sirius_version
|
Character SIRIUS version ("5" or "6"). |
str_stereo
|
Character path to structure stereochemistry file. |
str_met
|
Character path to structure metadata file. |
str_nam
|
Character path to structure names file. |
str_tax_cla
|
Character path to ClassyFire taxonomy file. |
str_tax_npc
|
Character path to NPClassifier taxonomy file. |
Details
This function:
-
Validates inputs (version, paths, file existence).
-
Loads SIRIUS output files (CANOPUS, formulas, structures, denovo).
-
Harmonizes column names across SIRIUS v5 and v6.
-
Joins with structure metadata (stereochemistry, names, taxonomy).
-
Splits results into three output files: annotations, CANOPUS, formulas.
-
Exports parameters and results.
If the input directory does not exist, returns an empty template with expected columns to ensure downstream compatibility.
Value
Character path to the prepared SIRIUS annotations file (invisible).