HI Rasmus,
I tried it:
library(base)
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 <- readRDS(paste0(population.name, ".rds"))
lapply(r[1:4], function(x) {
jsonlite::fromJSON(jsonlite::toJSON(httr::content(x)))
})
and I got this error:> 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'> lapply(r[1:4], function(x) {
+ jsonlite::fromJSON(jsonlite::toJSON(httr::content(x)))
+ })
Error in lapply(r[1:4], function(x) { : object 'r' not found
Am I am doing here something wrong?
Do I need any other libraries loaded?
Thanks
Ana
On Fri, Jun 19, 2020 at 3:49 PM Rasmus Liland <jral at posteo.no>
wrote:>
> On 2020-06-19 14:34 -0500, Ana Marija wrote:
> >
> > server <- "http://rest.ensembl.org"
> > ext <-
"/ld/human/pairwise/rs6792369/rs1042779?population_name=1000GENOMES:phase_3:KHV"
> >
> > r <- GET(paste(server, ext, sep = ""),
content_type("application/json"))
> >
> > stop_for_status(r)
> > head(fromJSON(toJSON(content(r))))
> > d_prime r2 variation1 variation2 population_name
> > 1 0.975513 0.951626 rs6792369 rs1042779 1000GENOMES:phase_3:KHV
> >
> > What I would like to do is to do is to run this command for every SNP
> > in one list (1g.txt) to each SNP in another list (1n.txt). Where SNP#
> > is rs# and output every line of result in list.txt
>
> Dear Ana,
>
> I tried, but for some reason I get only a
> response for the first URL you supplied.
>
> I wrote this:
>
> 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)
>
> r <- readRDS(paste0(population.name, ".rds"))
> lapply(r[1:4], function(x) {
> jsonlite::fromJSON(jsonlite::toJSON(httr::content(x)))
> })
>
>
> Which if you are able to run it (saving the
> output in that rds file), yields this:
>
>
$`http://rest.ensembl.org/ld/human/pairwise/rs6792369/rs1042779?population_name=1000GENOMES:phase_3:KHV`
> variation2 population_name d_prime r2 variation1
> 1 rs1042779 1000GENOMES:phase_3:KHV 0.975513 0.951626 rs6792369
>
>
$`http://rest.ensembl.org/ld/human/pairwise/rs1414517/rs1042779?population_name=1000GENOMES:phase_3:KHV`
> list()
>
>
$`http://rest.ensembl.org/ld/human/pairwise/rs16857712/rs1042779?population_name=1000GENOMES:phase_3:KHV`
> list()
>
>
$`http://rest.ensembl.org/ld/human/pairwise/rs16857703/rs1042779?population_name=1000GENOMES:phase_3:KHV`
> list()
>
> For some reason, only the first url works ...
>
> I am a bit unfamiliar working with REST
> API's. Or web scraping in general. Daniel
> Cegie?ka knows something in this thread some
> days ago, where it might be similar to the
> API of borsaitaliana.it, where you can supply
> headers with curl like he quickly did [2].
>
> You might be able to supply the list of SNPs
> in a header to Ensemble in httr::GET somehow
> if you read some docs on their API?
>
> Best,
> Rasmus
>
> [1] https://marc.info/?t=159249246100002&r=1&w=2
> [2] https://marc.info/?l=r-sig-finance&m=159249894208684&w=2