How can I read selected rows from a large file using the R “readLines” command and write them to a data frame?

Question

I am engaged in data cleaning. I have a function that identifies bad rows in a large input file (too big to read at one go, given my ram size) and returns the row numbers of the bad rows as a vector badRows . This function seems to work.

I am now trying to read just the bad rows into a data frame, so far unsuccessfully.

My current approach is to use read.table on an open connection to my file, using a vector of the number of rows to skip between each row that is read. This number is zero for consecutive bad rows.

I calculate skipVec as:

(badRowNumbers - c(0, badRowNumbers[1:(length(badRowNumbers-1]))-1

But for the moment I am just handing my function a skipVec vector of all zeros.

If my logic is correct, this should return all the rows. It does not. Instead I get an error:

"Error in read.table(con, skip = pass, nrow = 1, header = TRUE, sep = "") : no lines available in input"

My current function is loosely based on a function by Miron Kursa ("mbq"), which I found here .

My question is somewhat duplicative of that one, but I assume his function works, so I have broken it somehow. I am still trying to understand the difference between opening a file and opening a connection to a file, and I suspect that the problem is there somewhere, or in my use of lapply .

I am running R 3.0.1 under RStudio 0.97.551 on a cranky old Windows XP SP3 machine with 3gig of ram. Stone Age, I know.

Here is the code that produces the error message above:

# Make a small small test data frame, write it to a file, and read it back in 
# a row at a time.
testThis.DF <- data.frame(nnn=c(2,3,5), fff=c("aa", "bb", "cc"))  
testThis.DF 

# This function will work only if the number of bad rows is not too big for memory
write.table(testThis.DF, "testThis.DF")
con<-file("testThis.DF")
open(con)
skipVec <- c(0,0,0)
badRows.DF  <- lapply(skipVec, FUN=function(pass){
  read.table(con, skip=pass, nrow=1, header=TRUE, sep="") })
close(con)

The error occurs before the close command. If I yank the readLines command out of the lapply and the function and just stick it in by itself, I still get the same error.

Answer 1

If instead of running read.table through lapply you just run the first few iterations manually, you will see what is going on:

> read.table(con, skip=0, nrow=1, header=TRUE, sep="")
  nnn fff
1   2  aa
> read.table(con, skip=0, nrow=1, header=TRUE, sep="")
  X2 X3 bb
1  3  5 cc

Because header = TRUE it is not one line that is read at each iteration but two, so you eventually run out of lines faster than you think, here on the third iteration:

> read.table(con, skip=0, nrow=1, header=TRUE, sep="")
Error in read.table(con, skip = 0, nrow = 1, header = TRUE, sep = "") : 
  no lines available in input

Now this might still not be a very efficient way of solving your problem, but this is how you can fix your current code:

write.table(testThis.DF, "testThis.DF")
con <- file("testThis.DF")
open(con)
header <- scan(con, what = character(), nlines = 1, quiet = TRUE)
skipVec <- c(0,1,0)
badRows <- lapply(skipVec, function(pass){
  line <- read.table(con, nrow = 1, header = FALSE, sep = "",
                     row.names = 1)
  if (pass) NULL else line
  })
badRows.DF <- setNames(do.call(rbind, badRows), header)
close(con)

Some clues towards higher speeds:

1. use scan instead of read.table . Read data as character and only at the end, after you have put your data into a character matrix or data.frame, apply type.convert to each column.
2. Instead of looping over skipVec , loop over its rle if it is much shorter. So you'll be able to read or skip chunks of lines at a time.