## requires pmcfiles data.frame with
## pmcfiles <- read.delim( "ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/file_list.txt" , skip=1, header=FALSE, stringsAsFactors=FALSE)
## names(pmcfiles)<-c("dir", "citation", "pmcid")
pmcFTP <- function(id, dir=".", ...){
# check for PMC prefix
if(!grepl("^PMC[0-9]+$", id)) stop("Please include a valid PMC id like PMC3443583")
y <- subset(pmcfiles, pmcid==id)
if(nrow(y)!= 1) stop("No match to ", id)
# file names -
destfile <- paste(dir, gsub(".*/([^/]*)", "\\1", y$dir), sep="/")
ftpfile <- paste("ftp://ftp.ncbi.nlm.nih.gov/pub/pmc", y$dir, sep="/")
localfile <- paste(dir, id, sep="/")
#########################
if(file.exists( localfile ) ){
print("File exists")
}else{
download.file( ftpfile, destfile )
## untar uses Sys.getenv("TAR") -C change to dir
untar( destfile, compressed=TRUE, extras=paste("-C", dir) )
print(paste("Saved to", localfile))
z <- file.remove(destfile)
z <- file.rename( gsub(".tar.gz$", "", destfile), localfile)
}
}
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