inst/scripts/make-metadata.R

In waldronlab/HMP16SData: 16S rRNA Sequencing Data from the Human Microbiome Project

# I. Notes
# ==============================================================================
# For now, HMP16Sdata is a two trick pony — further tricks are possible in the
# future. What this means for documentation is that the script written below is
# expecting exactly two datasets (one for variable region 1–3 and another for
# variable region 3–5) and can produce metadata for them without issue. There
# would only be an issue if further data were added (e.g. a dataset for variable
# region 6–9, although it doesn't exists). If such a change were needed, it
# would require a few additional strings below. Why isn't the process of
# generating metadata fully automated then? This is because automated metadata
# generation would require a good deal of work for very little payoff and
# HMP16Sdata is, after all, only a two trick pony. That said, automated metadata
# generation should be considered if the package grows larger (unlikely, given
# that funding for the HMP ended in 2010). So, enjoy the script for what it is
# and consider automated metadata generation if you have a boatload more data.

if (!require("magrittr", character.only = TRUE)) {
    BiocManager::install("magrittr")
    require("magrittr", character.only = TRUE)
}

base::read.dcf("DESCRIPTION", "Suggests") %>%
    base::gsub("\n", "", x = .) %>%
    base::strsplit(",") %>%
    base::unlist() %>%
    for (i in .) {
        if (!require(i, character.only = TRUE)) {
            BiocManager::install(i)
            require(i, character.only = TRUE)
        }
    }

Title <-
    base::dir("data") %>%
    magrittr::extract(1:2) %>%
    base::strsplit("\\.") %>%
    base::sapply(magrittr::extract, 2) %>%
    base::unique() %>%
    base::as.character()

Description <- base::c("16S rRNA sequencing data for variable regions 1–3",
                       "16S rRNA sequencing data for variable regions 3–5")

BiocVersion <-
    BiocManager::version() %>%
    base::as.character()

Genome <- base::as.character(NA)

SourceType <- base::as.character("TXT")

SourceUrl <-
    base::c(
        "http://downloads.ihmpdcc.org/data/HMQCP/otu_table_psn_v13.txt.gz,
         http://downloads.ihmpdcc.org/data/HMQCP/v13_map_uniquebyPSN.txt.bz2,
         https://www.hmpdacc.org/hmp/doc/ppAll_V13_map.txt,
         http://downloads.ihmpdcc.org/data/HMQCP/rep_set_v13.tre.gz",
        "http://downloads.ihmpdcc.org/data/HMQCP/otu_table_psn_v35.txt.gz,
         http://downloads.ihmpdcc.org/data/HMQCP/v35_map_uniquebyPSN.txt.bz2,
         https://www.hmpdacc.org/hmp/doc/ppAll_V35_map.txt,
         http://downloads.ihmpdcc.org/data/HMQCP/rep_set_v35.tre.gz"
    ) %>%
    gsub("\\s+", " ", x = .)

SourceVersion  <- base::as.character(NA)

Species <- base::as.character("Homo Sapiens")

TaxonomyId <- base::as.character("9606")

Coordinate_1_based <- base::as.logical(NA)

DataProvider <- base::as.character("NIH Common Fund Human Microbiome Project")

Maintainer <- base::as.character("Lucas Schiffer <schiffer.lucas@gmail.com>")

RDataClass <- base::as.character("SummarizedExperiment")

DispatchClass <- base::as.character("Rda")

RDataPath <-
    base::dir("data") %>%
    magrittr::extract(1:2) %>%
    base::paste("HMP16SData", ., sep = "/")

if (base::file.exists("inst/extdata/metadata.csv")) {
    old_metadata <- utils::read.csv("inst/extdata/metadata.csv")

    new_metadata <- base::data.frame(Title, Description, BiocVersion, Genome,
                                     SourceType, SourceUrl, SourceVersion,
                                     Species, TaxonomyId, Coordinate_1_based,
                                     DataProvider, Maintainer, RDataClass,
                                     DispatchClass, RDataPath)

    base::rbind(old_metadata, new_metadata) %>%
        dplyr::distinct() %>%
        utils::write.csv("inst/extdata/metadata.csv", row.names = FALSE)
} else {
    base::data.frame(Title, Description, BiocVersion, Genome, SourceType,
                     SourceUrl, SourceVersion, Species, TaxonomyId,
                     Coordinate_1_based, DataProvider, Maintainer, RDataClass,
                     DispatchClass, RDataPath) %>%
    utils::write.csv("inst/extdata/metadata.csv", row.names = FALSE)
}