On 2020-06-19 16:07 -0500, Ana Marija wrote: > HI Rasmus, > > I tried it: > > library(base) > > > r <- readRDS(paste0(population.name, ".rds")) > Error in gzfile(file, "rb") : cannot open the connection > In addition: Warning message: > In gzfile(file, "rb") : > cannot open compressed file '1000GENOMES:phase_3:KHV.rds', probable > reason 'No such file or directory'
Because I run my script again and again after
every little small change using the program
entr[1] as opposed to using Emacs Speaks
Statistics or RStudio, I find it useful to
save partial outputs in rds files, but it
also make sense to not call ensembl.org again
and again ...
Right, so you would run the commented bit
before that first, then save the output list
to the rds to not send too many requests to
the list. I have attached my rds here.
files <- c("1g.txt", "1n.txt")
files <- lapply(files, readLines)
server <- "http://rest.ensembl.org";
population.name <- "1000GENOMES:phase_3:KHV"
ext <- apply(expand.grid(files), 1, function(x) {
return(paste0(server, "/ld/human/pairwise/",
x[1], "/", x[2],
"?population_name=", population.name))
})
r <- lapply(ext, function(x) {
httr::GET(x, httr::content_type("application/json"))
})
names(r) <- ext
file <- paste0(population.name, ".rds")
saveRDS(object=r, compress="xz", file=file) # <--- Then save the list
here for another time!
# r <- readRDS(paste0(population.name, ".rds")) # Read it back like
this
r <-
sapply(r, function(x) {
x <- jsonlite::fromJSON(jsonlite::toJSON(httr::content(x)))
length(x)
})
names(r) <- NULL
r
[1] http://eradman.com/entrproject/
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