[R] How to loop over two files ...

[cpoiw@rt m@iii@g oii chemo@org@uk]

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
> 
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