[R] How to read data sequentially into R (line by line)?

[jim holtman]

Use 'readLines' instead of 'read.table'.  We want to read in the text
file and convert it into separate text files, each of which can then
be read in using 'read.table'.  My solution assumes that you have used
readLines.  Trying to do this with data frames gets messy.  Keep it
simple and do it in two phases; makes it easier to debug and to see
what is going on.



On Tue, Oct 18, 2011 at 8:57 AM, johannes rara <johannesraja at gmail.com> wrote:
> Thanks Jim,
>
> I tried to convert this solution into my situation (.txt file as an input);
>
> zz <- file("myfile.txt", "r")
>
> fileNo <- 1  # used for file name
> buffer <- NULL
> repeat{
>   input <- read.csv(zz, as.is=T, nrows=1000000, sep='!',
> row.names=NULL, na.strings="")
>   if (length(input) == 0) break  # done
>   buffer <- c(buffer, input)
>   # find separator
>   repeat{
>       indx <- which(grepl("^GG!KK!KK!", buffer))[1]
>       if (is.na(indx)) break  # not found yet; read more
>       writeLines(buffer[1:(indx - 1L)]
>           , sprintf("newFile%04d.txt", fileNo)
>           )
>       buffer <- buffer[-c(1:indx)]  # remove data
>       fileNo <- fileNo + 1
>   }
> }
>
> but it gives me an error
>
> Error in read.table(file = file, header = header, sep = sep, quote = quote,  :
>  no lines available in input
>>
>
> Do you know a reason for this?
>
> -J
>
> 2011/10/18 jim holtman <jholtman at gmail.com>:
>> Let's do it in two parts: first create all the separate files (which
>> if this what you are after, we can stop here).  You can change the
>> value on readLines to read in as many lines as you want; I set it to 2
>> just for testing.
>>
>> x <- textConnection("APE!KKU!684!
>> APE!VAL!!
>> APE!UASU!!
>> APE!PLA!1!
>> APE!E!10!
>> APE!TPVA!17122009!
>> APE!STAP!1!
>> GG!KK!KK!
>> APE!KKU!684!
>> APE!VAL!!
>> APE!UASU!!
>> APE!PLA!1!
>> APE!E!10!
>> APE!TPVA!17122009!
>> APE!STAP!1!
>> GG!KK!KK!
>> APE!KKU!684!
>> APE!VAL!!
>> APE!UASU!!
>> APE!PLA!1!
>> APE!E!10!
>> APE!TPVA!17122009!
>> APE!STAP!1!
>> GG!KK!KK!")
>>
>> fileNo <- 1  # used for file name
>> buffer <- NULL
>> repeat{
>>    input <- readLines(x, n = 100)
>>    if (length(input) == 0) break  # done
>>    buffer <- c(buffer, input)
>>    # find separator
>>    repeat{
>>        indx <- which(grepl("^GG!KK!KK!", buffer))[1]
>>        if (is.na(indx)) break  # not found yet; read more
>>        writeLines(buffer[1:(indx - 1L)]
>>            , sprintf("newFile%04d", fileNo)
>>            )
>>        buffer <- buffer[-c(1:indx)]  # remove data
>>        fileNo <- fileNo + 1
>>    }
>> }
>>
>>
>> On Tue, Oct 18, 2011 at 8:12 AM, johannes rara <johannesraja at gmail.com> wrote:
>>> I have a data set like this in one .txt file (cols separated by !):
>>>
>>> APE!KKU!684!
>>> APE!VAL!!
>>> APE!UASU!!
>>> APE!PLA!1!
>>> APE!E!10!
>>> APE!TPVA!17122009!
>>> APE!STAP!1!
>>> GG!KK!KK!
>>> APE!KKU!684!
>>> APE!VAL!!
>>> APE!UASU!!
>>> APE!PLA!1!
>>> APE!E!10!
>>> APE!TPVA!17122009!
>>> APE!STAP!1!
>>> GG!KK!KK!
>>> APE!KKU!684!
>>> APE!VAL!!
>>> APE!UASU!!
>>> APE!PLA!1!
>>> APE!E!10!
>>> APE!TPVA!17122009!
>>> APE!STAP!1!
>>> GG!KK!KK!
>>>
>>> it contains over 14 000 000 records. Now because I'm out of memory
>>> when trying to handle this data in R, I'm trying to read it
>>> sequentially and write it out in several .csv files (or .RData files)
>>> and then read these into R one-by-one. One record in this data is
>>> between lines GG!KK!KK! and GG!KK!KK!. I tried to implement Jim
>>> Holtman's approach
>>> (http://tolstoy.newcastle.edu.au/R/e6/help/09/03/8416.html) but the
>>> problem is how to avoid cutting one record from the middle? I mean
>>> that if I put nrows = 1000000, I don't know if one record (between
>>> marks GG!KK!KK! and GG!KK!KK! is ending up in two files). How to avoid
>>> that? My code so far:
>>>
>>> zz <- file("myfile.txt", "r")
>>> fileNo <- 1
>>> repeat{
>>>
>>>    gotError <- 1 # set to 2 if there is an error     # catch the
>>> error if not more data
>>>    tryCatch(input <- read.csv(zz, as.is=T, nrows=1000000, sep='!',
>>> row.names=NULL, na.strings="", header=FALSE),
>>>              error=function(x) gotError <<- 2)
>>>
>>>    if (gotError == 2) break
>>>    # save the intermediate data
>>>    save(input, file=sprintf("file%03d.RData", fileNo))
>>>    fileNo <- fileNo + 1
>>> }
>>> close(zz)
>>>
>>> ______________________________________________
>>> R-help at r-project.org mailing list
>>> 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.
>>>
>>
>>
>>
>> --
>> Jim Holtman
>> Data Munger Guru
>>
>> What is the problem that you are trying to solve?
>>
>



-- 
Jim Holtman
Data Munger Guru

What is the problem that you are trying to solve?