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

[Ana Marija]

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 <cpolwart using 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 <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.