unfortunately it complains again: > 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 rownames(f1) ) { + + for ( b in rownames(f2) ) { + + ext <- paste0( "/ld/human/pairwise/", + f1[a,1], + "/", + f2[b,1], + "?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 cat(x, file = file, sep = c(rep.int(sep, ncolumns - 1), "\n"), : argument 1 (type 'list') cannot be handled by 'cat'
> traceback() 2: cat(x, file = file, sep = c(rep.int(sep, ncolumns - 1), "\n"), append = append) 1: write(r, file = "list.txt", append = TRUE) On Fri, Jun 19, 2020 at 5:19 PM <cpolw...@chemo.org.uk> wrote: > > Sorry - its been a long week! > > there is a foreach package but I try to avoid extras > > make your for statements: > > for ( a in rownames(f1) ) { > > # a will now be a row number rather than the value, so replace ' a ' in > the paste0 with: f1[ a, 1] > > so > > ext <- paste0( "/ld/human/pairwise/", > f1[a,1], > "/", > f2[b,1], > "?population_name=1000GENOMES:phase_3:KHV") > > On 2020-06-19 22:54, Ana Marija wrote: > > 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.