[R] extracting values from txt file that follow user-supplied quote

[Gabor Grothendieck]

On Wed, Jun 6, 2012 at 12:54 PM, emorway <emorway at usgs.gov> wrote:
> useRs-
>
> I'm attempting to scan a more than 1Gb text file and read and store the
> values that follow a specific key-phrase that is repeated multiple time
> throughout the file.  A snippet of the text file I'm trying to read is
> attached.  The text file is a dumping ground for various aspects of the
> performance of the model that generates it.  Thus, the location of
> information I'm wanting to extract from the file is not in a fixed position
> (i.e. it does not always appears in a predictable location, like line 1000,
> or 2000, etc.).  Rather, the desired values always follow a specific phrase:
> "   PERCENT DISCREPANCY ="
>
> One approach I took was the following:
>
> library(R.utils)
>
> txt_con<-file(description="D:/MCR_BeoPEST - Copy/MCR.out",open="r")
> #The above will need to be altered if one desires to test code on the
> attached txt file, which will run much quicker
> system.time(num_lines<-countLines("D:/MCR_BeoPEST - Copy/MCR.out"))
> #elapsed time on full 1Gb file took about 55 seconds on a 3.6Gh Xeon
> num_lines
> #14405247
>
> system.time(
> for(i in 1:num_lines){
>  txt_line<-readLines(txt_con,n=1)
>  if (length(grep("    PERCENT DISCREPANCY =",txt_line))) {
>    pd<-c(pd,as.numeric(substr(txt_line,70,78)))
>  }
> }
> )
> #Time took about 5 minutes
>
> The inefficiencies in this approach arise due to reading the file twice
> (first to get num_lines, then to step through each line looking for the
> desired text).
>
> Is there a way to speed this process up through the use of a ?scan  ?  I
> wan't able to get anything working, but what I had in mind was scan through
> the more than 1Gb file and when the keyphrase (e.g.  "     PERCENT
> DISCREPANCY =  ") is encountered, read and store the next 13 characters
> (which will include some white spaces) as a numeric value, then resume the
> scan until the key phrase is encountered again and repeat until the
> end-of-the-file marker is encountered.  Is such an approach even possible or
> is line-by-line the best bet?
>
> http://r.789695.n4.nabble.com/file/n4632558/MCR.out MCR.out

Try this:

g <- function(url, string, from, to, ...) {
	L <- readLines(url)
	matched <- grep(string, L, value = TRUE, ...)
	as.numeric(substring(matched, from, to))
}

> url <- "http://r.789695.n4.nabble.com/file/n4632558/MCR.out"
> g(url, "PERCENT DISCREPANCY = ", 70, 78, fixed = TRUE)
[1]    NA  0.00 -0.01    NA  0.00 -0.01


-- 
Statistics & Software Consulting
GKX Group, GKX Associates Inc.
tel: 1-877-GKX-GROUP
email: ggrothendieck at gmail.com