Skip to contents

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$value,
  output_key = get_params(step =
    "prepare_libraries_sop_merged")$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'

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)

Value

The path to the prepared structure-organism pairs library MERGED

Details

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

Examples

if (FALSE) { # \dontrun{
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)
} # }