Prepare annotations SIRIUS

Description

This function 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 string path to directory or zip file containing SIRIUS results
output_ann	Character string path for prepared annotation results output
output_can	Character string path for prepared CANOPUS results output
output_for	Character string path for prepared formula results output
sirius_version	Character string SIRIUS version ("v5" or "v6")
str_stereo	Character string path to file with structure stereochemistry
str_met	Character string path to file with structure metadata
str_nam	Character string path to file with structure names
str_tax_cla	Character string path to file with ClassyFire taxonomy
str_tax_npc	Character string path to file with NPClassifier taxonomy

Value

Character string path to the prepared SIRIUS annotations file

Examples

library("tima")

copy_backbone()
go_to_cache()
prepare_annotations_sirius()
unlink("data", recursive = TRUE)