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

[Ana Marija]

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 <cpolwart using 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 using 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.