metabarcode: matabar; tools for metabarcoding

# library(xml2)
# library(tidyverse)
#
# # xml <- read_xml("6.xml")
# #
# # xml_list <- as_list(xml)
# #
# # test1 <- xml_list[[1]]
# #
# # return_NA_pluck = function(.x, ..., .default = NA) {
# #   rlt <- purrr::pluck(.x = .x, ..., .default = .default)
# #   return(rlt)
# # }
# #
# # prepare = function(.xml) {
# #   # convert to list.
# #   .xml_list <- xml2::as_list(.xml)
# #   # split by sample.
# #   ## make vector.
# #   by_sample <- vector("list", length(.xml_list[["GBSet"]]))
# #   ## split.
# #   for(i in 1:length(.xml_list[["GBSet"]])) {
# #     by_sample[[i]] <- list("GBSeq" = .xml_list[["GBSet"]][[i]])
# #   }
# #   return(by_sample)
# # }
# #
# # parse_xml = function(.xml_list) {
# #     # extract base information.
# #     spec1 <- list(
# #       "GBSeq_definition", "GBSeq_length", "GBSeq_moltype",
# #       "GBSeq_primary-accession", "GBSeq_taxonomy", "GBSeq_organism", "GBSeq_sequence"
# #     )
# #     # make vector.
# #     value <- vector(mode = "character", length = length(spec1))
# #     # make tibble.
# #     base_info <- tibble::tibble(
# #       name = rep(NA_character_, length(spec1)),
# #       value = rep(NA_character_, length(spec1))
# #     )
# #     for(i in 1:length(spec1)) {
# #       value[i] <- return_NA_pluck(
# #         .x = .xml_list,
# #         "GBSeq", spec1[[i]]
# #       )
# #       base_info[i, "name"] <- spec1[[i]]
# #       base_info[i, "value"] <- value[i]
# #     }
# #     # extract title.
# #     spec2 <- list(
# #       "GBSeq",
# #       "GBSeq_references",
# #       "GBReference",
# #       "GBReference_title"
# #     )
# #     title_df <- tibble::tibble(
# #       name = "title",
# #       value = NA_character_
# #     )
# #     title <- return_NA_pluck(
# #       .x = .xml_list,
# #       spec2[[1]], spec2[[2]], spec2[[3]], spec2[[4]]
# #     )
# #     title_df[1, 2] <- title
# #     # extratct GBFeature.
# #     spec3 <- list(
# #       "GBSeq_feature-table", "GBFeature", "GBFeature_quals"
# #     )
# #     qual <- return_NA_pluck(
# #       .x = .xml_list,
# #       "GBSeq", spec3[[1]], spec3[[2]], spec3[[3]]
# #     )
# #     feature <- purrr::map(qual, parse_GBQualifier) %>%
# #       dplyr::bind_rows()
# #   rlt <- dplyr::bind_rows(
# #     base_info, title_df, feature)
# #   return(rlt)
#
# # }
# #
# # parse_xml(test1)
# # parse_xml(by_sample[[2]])
# #
# # by_sample <- prepare(
# #   .xml = xml
# # )
# #
# # result <- map_dfr(.x = by_sample, .f = parse_xml, .id = "id") %>%
# #   pivot_wider(names_from = "name", values_from = "value")
# #
#
# xml <- read_xml("demo1.xml")
# list <- as_list(xml)
#
# by_sample <- prepare(
#   .xml = xml
# )
#
# result <- map_dfr(.x = by_sample, .f = parse_xml, .id = "id")
#