R/kegg_conv.R

In utubun/keggr: KEGG API

# superfunction

kegg_conv <- function(source, target) {
    url <- sprintf('http://rest.kegg.jp/conv/%s/%s', target, source)

    resp <- httr::GET(url)

    if (.kegg_check_response(resp)) {
        return(kegg_parse_conv(resp, c(source, target)))
    }

    stop(httr::http_status(resp)$message)
}

# middleware

kegg_is_conv <- function(query) {

    if (query %in% c('ncbi-geneid', 'ncbi-proteinid', 'uniprot', 'pubmed', 'pubchem', 'chebi')) {
        return(invisible(TRUE))
    }

    return(invisible(FALSE))
}

kegg_parse_conv <- function(response, cnames = NULL) {
    txt <- httr::content(response, encoding = 'utf-8')
    res <- read.table(text = txt)
    if(length(cnames) == ncol(res)) {
        colnames(res) <- cnames
    }
    return(res)
}

#kegg_conv('pae', 'ncbi-proteinid') |> head()