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
Cegiełka 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
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