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 at 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 at 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 at 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.
cpoiw@rt m@iii@g oii chemo@org@uk
2020-Jun-19 22:19 UTC
[R] How to loop over two files ...
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 <cpolwart at 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 at 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 at 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.
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 <cpolwart at 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 <cpolwart at 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 at 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 at 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.