Prepare merged structure organism pairs libraries

Description

This function prepares the libraries made of all sub-libraries containing structure-organism pairs

Usage

prepare_libraries_sop_merged(
  files = get_params(step = "prepare_libraries_sop_merged")\$files\$libraries\$sop\$prepared,
  filter = get_params(step = "prepare_libraries_sop_merged")\$organisms\$filter\$mode,
  level = get_params(step = "prepare_libraries_sop_merged")\$organisms\$filter\$level,
  value = get_params(step = "prepare_libraries_sop_merged")\$organisms\$filter\$value,
  cache = get_params(step =
    "prepare_libraries_sop_merged")\$files\$libraries\$sop\$merged\$structures\$processed,
  output_key = get_params(step =
    "prepare_libraries_sop_merged")\$files\$libraries\$sop\$merged\$keys,
  output_org_tax_ott = get_params(step =
    "prepare_libraries_sop_merged")\$files\$libraries\$sop\$merged\$organisms\$taxonomies\$ott,
  output_str_stereo = get_params(step =
    "prepare_libraries_sop_merged")\$files\$libraries\$sop\$merged\$structures\$stereo,
  output_str_met = get_params(step =
    "prepare_libraries_sop_merged")\$files\$libraries\$sop\$merged\$structures\$metadata,
  output_str_nam = get_params(step =
    "prepare_libraries_sop_merged")\$files\$libraries\$sop\$merged\$structures\$names,
  output_str_tax_cla = get_params(step =
    "prepare_libraries_sop_merged")\$files\$libraries\$sop\$merged\$structures\$taxonomies\$cla,
  output_str_tax_npc = get_params(step =
    "prepare_libraries_sop_merged")\$files\$libraries\$sop\$merged\$structures\$taxonomies\$npc
)

Arguments

files	List of libraries to be merged
filter	Boolean. TRUE or FALSE if you want to filter the library
level	Biological rank to be filtered. Kingdom, phylum, family, genus, …
value	Name of the taxon or taxa to be kept, e.g. ‘Gentianaceae|Apocynaceae’
cache	Cache where already processed SMILES are located
output_key	Output file for keys
output_org_tax_ott	Output file for organisms taxonomy (OTT)
output_str_stereo	Output file for structures stereo
output_str_met	Output file for structures metadata
output_str_nam	Output file for structures names
output_str_tax_cla	Output file for structures taxonomy (Classyfire)
output_str_tax_npc	Output file for structures taxonomy (NPC)

Details

It can be restricted to specific taxa to have more biologically meaningful annotation.

Value

The path to the prepared structure-organism pairs library MERGED

Examples

library("tima")

copy_backbone()
go_to_cache()
github <- "https://raw.githubusercontent.com/"
repo <- "taxonomicallyinformedannotation/tima-example-files/main/"
dir <- paste0(github, repo)
files <- get_params(step = "prepare_libraries_sop_merged")$files$libraries$sop$prepared$lotus |>
  gsub(
    pattern = ".gz",
    replacement = "",
    fixed = TRUE
  )
get_file(url = paste0(dir, files), export = files)
prepare_libraries_sop_merged(files = files)
unlink("data", recursive = TRUE)