I tried it: > library(httr) > library(jsonlite) > library(xml2) > library(readr) > server <- "http://rest.ensembl.org" > f1 <- read_tsv("1g", col_names=F) Parsed with column specification: cols( X1 = col_character() ) > f2 <- read_tsv("1n", col_names=F) Parsed with column specification: cols( X1 = col_character() ) > > for ( a in as.list(f1[,1]) ) { + + for ( b in as.list(f2[,1]) ) { + + ext <- paste0( "/ld/human/pairwise/", + a, + "/", + b, + "?population_name=1000GENOMES:phase_3:KHV") + + r <- GET(paste(server, ext, sep = ""), + content_type("application/json")) + + write(r,file="list.txt",append=TRUE) + + + } + + } Error in parse_url(url) : length(url) == 1 is not TRUE
> traceback() 10: stop(simpleError(msg, call = if (p <- sys.parent(1L)) sys.call(p))) 9: stopifnot(length(url) == 1) 8: parse_url(url) 7: is.url(url) 6: stopifnot(is.url(url)) 5: build_url(parse_url(url)[c("scheme", "hostname", "port")]) 4: handle_name(url) 3: handle_find(url) 2: handle_url(handle, url, ...) 1: GET(paste(server, ext, sep = ""), content_type("application/json")) On Fri, Jun 19, 2020 at 4:41 PM <cpolw...@chemo.org.uk> wrote: > > Oh - read.text isn't in base! Not sure where is came from (my head > mostly!) You may have something that adds it but better to use > something that works. So try using: > > library(readr) > f1 <- read_tsv("1g.txt", col.names=F) > > This will give you a tibble with f1$X1 with the file in it > > then loop it with (a in as.list(f1[,1]) > > Others will have much slicker code than me! > > On 2020-06-19 22:02, Ana Marija wrote: > > Hi, > > > > thanks for getting back to me, it is just for my job :) > > > > so I tried it: > > > > library(httr) > > library(jsonlite) > > library(xml2) > > library(SparkR, lib.loc = c(file.path(Sys.getenv("SPARK_HOME"), "R", > > "lib"))) > > sparkR.session(master = "local[*]", sparkConfig = > > list(spark.driver.memory = "2g")) > > > > server <- "http://rest.ensembl.org" > > > > f1 <- read.text("1g.txt") > > f2 <- read.text("1n.txt") > > > > for ( a in as.list(f1) ) { > > > > for ( b in as.list(f2) ) { > > > > ext <- paste0( "/ld/human/pairwise/", > > a, > > "/", > > b, > > "?population_name=1000GENOMES:phase_3:KHV") > > > > r <- GET(paste(server, ext, sep = ""), > > content_type("application/json")) > > > > write(r,file="list.txt",append=TRUE) > > > > > > } > > > > } > > > > and I got this error: > > Error in as.list.default(f1) : > > no method for coercing this S4 class to a vector > > > > Please advise > > > > On Fri, Jun 19, 2020 at 3:28 PM <cpolw...@chemo.org.uk> wrote: > >> > >> so (untested) if you did something like > >> > >> f1 <- read.text("1g.txt") > >> f2 <- read.text("1n.txt") > >> > >> for ( a in as.list(f1) ) { > >> > >> for ( b in as.list(f2) ) { > >> > >> ext <- paste0( "/ld/human/pairwise/", > >> a, > >> "/", > >> b, > >> "?population_name=1000GENOMES:phase_3:KHV") > >> > >> r <- GET(paste(server, ext, sep = ""), > >> content_type("application/json")) > >> > >> # You presumably need to do something with 'r' at the > >> moment its over written by the next loop.. were > >> # you appending it to list.txt? Possibly its just a > >> bit > >> of the R output you want.? > >> > >> write(r,file="list.txt",append=TRUE) > >> > >> > >> } > >> > >> } > >> > >> > >> Are we doing your PhD for you ;-) Do we get to share ;-) > >> > >> > >> On 2020-06-19 20:34, Ana Marija wrote: > >> > Hello, > >> > > >> > I have two files (each has 300 lines)like this: > >> > > >> > head 1g.txt > >> > rs6792369 > >> > rs1414517 > >> > rs16857712 > >> > rs16857703 > >> > rs12239392 > >> > ... > >> > > >> > head 1n.txt > >> > rs1042779 > >> > rs2360630 > >> > rs10753597 > >> > rs7549096 > >> > rs2343491 > >> > ... > >> > > >> > For each pair of rs# from those two files I can run this command in R > >> > > >> > library(httr) > >> > library(jsonlite) > >> > library(xml2) > >> > > >> > 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 > >> > > >> > The process is illustrated in the attachment. > >> > > >> > Please help, > >> > Ana > >> > > >> > ______________________________________________ > >> > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > >> > https://stat.ethz.ch/mailman/listinfo/r-help > >> > PLEASE do read the posting guide > >> > http://www.R-project.org/posting-guide.html > >> > and provide commented, minimal, self-contained, reproducible code. ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.