R/getBridgeNames.R

In egonw/BridgeDbR: Code for using BridgeDb identifier mapping framework from within R

getBridgeNames <- function(
        code, website = "https://bridgedb.github.io/data/gene_database/", pattern) {
    if (missing(code)) code <- "\\w{2}"
    if (missing(pattern)) {
        pattern <- paste(code, "_Derby_Ensembl_\\w+.bridge", sep = "")
    }

    patternInternal <- paste(">", pattern, "<", sep = "") # require a trailing tag
    lines <- readLines(curl(website))

    i <- 1
    result <- c()
    for (line in lines) {
        expr <- gregexpr(patternInternal, line)

        matches <- expr[[1]]
        matchLengths <- attributes(matches)$match.length
        for (matchCounter in 1:length(matches)) {
            start <- matches[matchCounter] + 1
            stop <- start + matchLengths[matchCounter] - 3
            matchedString <- substr(line, start, stop)
            if (nchar(matchedString) > 0) {
                result[i] <- matchedString
                i <- i + 1
            }
        }
    }
    result
}